Starting phenix.real_space_refine on Wed Aug 27 01:47:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qku_18471/08_2025/8qku_18471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qku_18471/08_2025/8qku_18471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qku_18471/08_2025/8qku_18471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qku_18471/08_2025/8qku_18471.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qku_18471/08_2025/8qku_18471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qku_18471/08_2025/8qku_18471.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 370 5.49 5 Mg 8 5.21 5 S 122 5.16 5 Be 2 3.05 5 C 27466 2.51 5 N 8032 2.21 5 O 9387 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45395 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 651 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "F" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "G" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3608 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "J" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3649 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "M" Number of atoms: 5398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5398 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 19, 'TRANS': 668} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 5, 'TRP:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 7, 'ASP:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 167 Chain: "R" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3335 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 25, 'TRANS': 385} Chain breaks: 1 Chain: "S" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1695 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain breaks: 3 Chain: "T" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3391 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 424} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3299 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 419} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3336 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3325 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3410 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 436} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Z" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1410 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 169} Chain breaks: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 4, 'TRP:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23323 SG CYS S 244 109.455 44.663 98.315 1.00167.02 S ATOM 23343 SG CYS S 247 106.665 42.141 97.531 1.00168.61 S ATOM 23459 SG CYS S 264 107.273 43.163 101.031 1.00169.20 S ATOM 23484 SG CYS S 268 109.809 40.933 99.296 1.00177.38 S ATOM 23403 SG CYS S 256 118.847 48.759 104.246 1.00176.38 S ATOM 23424 SG CYS S 259 119.616 49.787 100.661 1.00174.05 S ATOM 23563 SG CYS S 277 121.798 47.098 102.346 1.00176.88 S Time building chain proxies: 10.65, per 1000 atoms: 0.23 Number of scatterers: 45395 At special positions: 0 Unit cell: (204.6, 166.1, 216.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 122 16.00 P 370 15.00 Mg 8 11.99 F 6 9.00 O 9387 8.00 N 8032 7.00 C 27466 6.00 Be 2 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S 501 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 264 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 247 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 244 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 268 " pdb=" ZN S 502 " pdb="ZN ZN S 502 " - pdb=" NE2 HIS S 272 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 259 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 256 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 277 " Number of angles added : 9 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9122 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 37 sheets defined 51.9% alpha, 9.7% beta 168 base pairs and 276 stacking pairs defined. Time for finding SS restraints: 6.30 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.586A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 89 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.609A pdb=" N ILE A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.833A pdb=" N LEU B 48 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 79 removed outlier: 3.877A pdb=" N ASP B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 114 Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.625A pdb=" N ILE B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 29 removed outlier: 3.950A pdb=" N ILE C 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'C' and resid 49 through 76 removed outlier: 3.891A pdb=" N GLU C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP C 68 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.798A pdb=" N ARG C 92 " --> pdb=" O TYR C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.581A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.855A pdb=" N ASP D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'E' and resid 17 through 22 removed outlier: 3.520A pdb=" N LYS E 21 " --> pdb=" O SER E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 37 Processing helix chain 'E' and resid 46 through 73 removed outlier: 3.978A pdb=" N VAL E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 91 removed outlier: 4.086A pdb=" N ASP E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 98 Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 27 through 38 Processing helix chain 'F' and resid 46 through 74 removed outlier: 4.186A pdb=" N VAL F 50 " --> pdb=" O SER F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 removed outlier: 3.539A pdb=" N LEU F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 98 removed outlier: 3.608A pdb=" N ASN F 95 " --> pdb=" O ASP F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'G' and resid 40 through 52 Processing helix chain 'G' and resid 58 through 87 removed outlier: 4.155A pdb=" N ASN G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 105 Processing helix chain 'G' and resid 106 through 128 Processing helix chain 'H' and resid 40 through 52 Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.546A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 125 Processing helix chain 'M' and resid 697 through 713 removed outlier: 3.670A pdb=" N SER M 709 " --> pdb=" O ASN M 705 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU M 710 " --> pdb=" O TRP M 706 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR M 711 " --> pdb=" O LEU M 707 " (cutoff:3.500A) Processing helix chain 'M' and resid 726 through 742 Processing helix chain 'M' and resid 753 through 755 No H-bonds generated for 'chain 'M' and resid 753 through 755' Processing helix chain 'M' and resid 756 through 767 removed outlier: 3.937A pdb=" N TRP M 760 " --> pdb=" O VAL M 756 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU M 761 " --> pdb=" O LEU M 757 " (cutoff:3.500A) Processing helix chain 'M' and resid 781 through 787 Processing helix chain 'M' and resid 803 through 814 removed outlier: 3.988A pdb=" N VAL M 807 " --> pdb=" O TYR M 803 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN M 808 " --> pdb=" O GLN M 804 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N HIS M 811 " --> pdb=" O VAL M 807 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER M 812 " --> pdb=" O GLN M 808 " (cutoff:3.500A) Processing helix chain 'M' and resid 834 through 840 removed outlier: 3.743A pdb=" N GLN M 838 " --> pdb=" O SER M 834 " (cutoff:3.500A) Processing helix chain 'M' and resid 859 through 871 removed outlier: 4.286A pdb=" N LEU M 863 " --> pdb=" O ASN M 859 " (cutoff:3.500A) Processing helix chain 'M' and resid 914 through 925 Processing helix chain 'M' and resid 954 through 971 Processing helix chain 'M' and resid 972 through 975 removed outlier: 3.772A pdb=" N ALA M 975 " --> pdb=" O ALA M 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 972 through 975' Processing helix chain 'M' and resid 978 through 995 removed outlier: 3.858A pdb=" N HIS M 995 " --> pdb=" O LYS M 991 " (cutoff:3.500A) Processing helix chain 'M' and resid 1013 through 1018 removed outlier: 3.627A pdb=" N ASP M1017 " --> pdb=" O CYS M1013 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR M1018 " --> pdb=" O VAL M1014 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1013 through 1018' Processing helix chain 'M' and resid 1018 through 1030 Processing helix chain 'M' and resid 1033 through 1037 removed outlier: 3.976A pdb=" N ARG M1037 " --> pdb=" O GLN M1034 " (cutoff:3.500A) Processing helix chain 'M' and resid 1046 through 1053 removed outlier: 4.568A pdb=" N ASP M1051 " --> pdb=" O THR M1048 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP M1053 " --> pdb=" O ASN M1050 " (cutoff:3.500A) Processing helix chain 'M' and resid 1055 through 1065 Processing helix chain 'M' and resid 1069 through 1094 removed outlier: 3.570A pdb=" N GLU M1073 " --> pdb=" O LYS M1069 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR M1081 " --> pdb=" O LYS M1077 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU M1091 " --> pdb=" O GLU M1087 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA M1092 " --> pdb=" O GLU M1088 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE M1094 " --> pdb=" O GLY M1090 " (cutoff:3.500A) Processing helix chain 'M' and resid 1095 through 1101 removed outlier: 4.500A pdb=" N ASN M1101 " --> pdb=" O PHE M1097 " (cutoff:3.500A) Processing helix chain 'M' and resid 1102 through 1133 removed outlier: 3.733A pdb=" N SER M1107 " --> pdb=" O TYR M1103 " (cutoff:3.500A) Processing helix chain 'M' and resid 1141 through 1149 removed outlier: 3.791A pdb=" N THR M1145 " --> pdb=" O ILE M1141 " (cutoff:3.500A) Processing helix chain 'M' and resid 1158 through 1164 removed outlier: 4.164A pdb=" N LYS M1164 " --> pdb=" O ASN M1160 " (cutoff:3.500A) Processing helix chain 'M' and resid 1165 through 1173 Processing helix chain 'M' and resid 1173 through 1181 Processing helix chain 'M' and resid 1191 through 1197 removed outlier: 3.620A pdb=" N LEU M1195 " --> pdb=" O ASP M1191 " (cutoff:3.500A) Processing helix chain 'M' and resid 1206 through 1220 Processing helix chain 'M' and resid 1224 through 1233 Processing helix chain 'M' and resid 1238 through 1242 Processing helix chain 'M' and resid 1245 through 1261 removed outlier: 3.560A pdb=" N LYS M1250 " --> pdb=" O GLY M1246 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA M1252 " --> pdb=" O LEU M1248 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE M1253 " --> pdb=" O GLN M1249 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU M1254 " --> pdb=" O LYS M1250 " (cutoff:3.500A) Processing helix chain 'M' and resid 1271 through 1273 No H-bonds generated for 'chain 'M' and resid 1271 through 1273' Processing helix chain 'M' and resid 1274 through 1286 Processing helix chain 'M' and resid 1297 through 1310 removed outlier: 4.143A pdb=" N GLN M1302 " --> pdb=" O ILE M1298 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE M1303 " --> pdb=" O GLU M1299 " (cutoff:3.500A) Processing helix chain 'M' and resid 1346 through 1356 removed outlier: 4.208A pdb=" N CYS M1355 " --> pdb=" O CYS M1351 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS M1356 " --> pdb=" O GLN M1352 " (cutoff:3.500A) Processing helix chain 'M' and resid 1374 through 1386 Processing helix chain 'R' and resid 68 through 81 removed outlier: 3.713A pdb=" N GLU R 72 " --> pdb=" O LEU R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 122 Processing helix chain 'R' and resid 132 through 137 removed outlier: 4.106A pdb=" N PHE R 136 " --> pdb=" O PRO R 132 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 132 through 137' Processing helix chain 'R' and resid 138 through 143 removed outlier: 4.202A pdb=" N LYS R 141 " --> pdb=" O PRO R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 213 Processing helix chain 'R' and resid 219 through 235 Processing helix chain 'R' and resid 242 through 253 removed outlier: 3.610A pdb=" N LEU R 253 " --> pdb=" O LYS R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 266 Processing helix chain 'R' and resid 308 through 313 removed outlier: 4.024A pdb=" N ILE R 313 " --> pdb=" O GLU R 309 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 318 Processing helix chain 'R' and resid 319 through 324 Processing helix chain 'R' and resid 329 through 341 Processing helix chain 'R' and resid 345 through 352 removed outlier: 3.708A pdb=" N VAL R 350 " --> pdb=" O ARG R 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY R 351 " --> pdb=" O PRO R 347 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN R 352 " --> pdb=" O LEU R 348 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 362 removed outlier: 3.728A pdb=" N LEU R 362 " --> pdb=" O ASN R 359 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 377 removed outlier: 3.586A pdb=" N GLN R 376 " --> pdb=" O GLU R 372 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 406 Processing helix chain 'R' and resid 406 through 413 removed outlier: 4.044A pdb=" N ARG R 410 " --> pdb=" O THR R 406 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS R 411 " --> pdb=" O ASP R 407 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 423 through 431 removed outlier: 3.952A pdb=" N CYS R 427 " --> pdb=" O GLY R 423 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR R 428 " --> pdb=" O PRO R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 433 through 438 removed outlier: 3.865A pdb=" N TRP R 437 " --> pdb=" O GLY R 433 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 62 Processing helix chain 'S' and resid 91 through 107 Processing helix chain 'S' and resid 115 through 125 removed outlier: 3.600A pdb=" N LEU S 119 " --> pdb=" O ASN S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 135 Processing helix chain 'S' and resid 168 through 180 Processing helix chain 'S' and resid 192 through 203 Processing helix chain 'S' and resid 207 through 213 Processing helix chain 'S' and resid 218 through 227 Processing helix chain 'S' and resid 265 through 276 removed outlier: 3.891A pdb=" N GLU S 274 " --> pdb=" O LYS S 270 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR S 275 " --> pdb=" O LEU S 271 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.800A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 removed outlier: 3.849A pdb=" N SER T 93 " --> pdb=" O ALA T 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 111 removed outlier: 3.544A pdb=" N TYR T 111 " --> pdb=" O SER T 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 108 through 111' Processing helix chain 'T' and resid 116 through 129 removed outlier: 3.889A pdb=" N ILE T 129 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 182 through 192 Processing helix chain 'T' and resid 217 through 222 removed outlier: 4.813A pdb=" N THR T 220 " --> pdb=" O ALA T 217 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE T 222 " --> pdb=" O ALA T 219 " (cutoff:3.500A) Processing helix chain 'T' and resid 248 through 258 removed outlier: 3.559A pdb=" N LEU T 252 " --> pdb=" O THR T 248 " (cutoff:3.500A) Processing helix chain 'T' and resid 264 through 273 Processing helix chain 'T' and resid 281 through 298 removed outlier: 3.521A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 316 Processing helix chain 'T' and resid 317 through 329 removed outlier: 3.601A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU T 329 " --> pdb=" O ASN T 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 360 through 367 Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 Processing helix chain 'T' and resid 411 through 429 removed outlier: 3.553A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix removed outlier: 3.716A pdb=" N ILE T 424 " --> pdb=" O ALA T 420 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 446 Processing helix chain 'T' and resid 448 through 458 removed outlier: 3.896A pdb=" N THR T 458 " --> pdb=" O LYS T 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 64 Processing helix chain 'U' and resid 81 through 93 removed outlier: 3.565A pdb=" N ALA U 85 " --> pdb=" O LYS U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 107 Processing helix chain 'U' and resid 112 through 124 removed outlier: 3.630A pdb=" N SER U 124 " --> pdb=" O ALA U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 182 removed outlier: 3.980A pdb=" N GLU U 182 " --> pdb=" O GLY U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 249 Processing helix chain 'U' and resid 252 through 254 No H-bonds generated for 'chain 'U' and resid 252 through 254' Processing helix chain 'U' and resid 255 through 260 Processing helix chain 'U' and resid 266 through 283 removed outlier: 3.530A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 301 Processing helix chain 'U' and resid 302 through 313 removed outlier: 3.600A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 343 Processing helix chain 'U' and resid 344 through 350 Processing helix chain 'U' and resid 360 through 376 removed outlier: 3.524A pdb=" N THR U 366 " --> pdb=" O GLN U 362 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 3.792A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 Processing helix chain 'U' and resid 432 through 443 Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.540A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 97 removed outlier: 3.666A pdb=" N SER V 93 " --> pdb=" O ALA V 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 108 through 111 Processing helix chain 'V' and resid 116 through 129 removed outlier: 3.797A pdb=" N ILE V 129 " --> pdb=" O PHE V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 182 through 192 Processing helix chain 'V' and resid 217 through 219 No H-bonds generated for 'chain 'V' and resid 217 through 219' Processing helix chain 'V' and resid 248 through 258 removed outlier: 3.507A pdb=" N LEU V 252 " --> pdb=" O THR V 248 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 274 removed outlier: 4.042A pdb=" N LYS V 274 " --> pdb=" O GLY V 270 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.604A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN V 298 " --> pdb=" O LYS V 294 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 316 Processing helix chain 'V' and resid 317 through 329 removed outlier: 3.771A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU V 329 " --> pdb=" O ASN V 325 " (cutoff:3.500A) Processing helix chain 'V' and resid 360 through 365 removed outlier: 3.670A pdb=" N ASP V 365 " --> pdb=" O PRO V 361 " (cutoff:3.500A) Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 429 removed outlier: 4.102A pdb=" N ALA V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU V 416 " --> pdb=" O LEU V 412 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA V 420 " --> pdb=" O LEU V 416 " (cutoff:3.500A) Proline residue: V 421 - end of helix Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 458 Processing helix chain 'W' and resid 47 through 64 Processing helix chain 'W' and resid 80 through 93 removed outlier: 3.532A pdb=" N GLY W 93 " --> pdb=" O SER W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 104 through 107 Processing helix chain 'W' and resid 112 through 124 removed outlier: 3.711A pdb=" N SER W 124 " --> pdb=" O ALA W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 172 through 182 removed outlier: 3.587A pdb=" N ASP W 177 " --> pdb=" O ASN W 173 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU W 182 " --> pdb=" O GLY W 178 " (cutoff:3.500A) Processing helix chain 'W' and resid 241 through 250 removed outlier: 4.128A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 260 removed outlier: 4.195A pdb=" N ALA W 256 " --> pdb=" O GLN W 252 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU W 257 " --> pdb=" O GLY W 253 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.552A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 removed outlier: 3.598A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 343 Processing helix chain 'W' and resid 344 through 350 removed outlier: 3.697A pdb=" N LEU W 348 " --> pdb=" O PRO W 344 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 413 removed outlier: 3.807A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS W 412 " --> pdb=" O GLN W 408 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG W 413 " --> pdb=" O ILE W 409 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 Processing helix chain 'W' and resid 432 through 443 Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.714A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 97 removed outlier: 3.634A pdb=" N ALA X 89 " --> pdb=" O LYS X 85 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY X 97 " --> pdb=" O SER X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 108 through 110 No H-bonds generated for 'chain 'X' and resid 108 through 110' Processing helix chain 'X' and resid 116 through 129 removed outlier: 3.671A pdb=" N ILE X 129 " --> pdb=" O PHE X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 184 No H-bonds generated for 'chain 'X' and resid 182 through 184' Processing helix chain 'X' and resid 185 through 192 Processing helix chain 'X' and resid 217 through 222 removed outlier: 4.494A pdb=" N THR X 220 " --> pdb=" O ALA X 217 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE X 222 " --> pdb=" O ALA X 219 " (cutoff:3.500A) Processing helix chain 'X' and resid 248 through 258 Processing helix chain 'X' and resid 264 through 271 removed outlier: 3.773A pdb=" N MET X 268 " --> pdb=" O ASP X 264 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN X 271 " --> pdb=" O SER X 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 297 removed outlier: 3.578A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 316 Processing helix chain 'X' and resid 317 through 328 Processing helix chain 'X' and resid 360 through 366 Processing helix chain 'X' and resid 376 through 391 Processing helix chain 'X' and resid 396 through 410 Processing helix chain 'X' and resid 411 through 429 removed outlier: 3.540A pdb=" N ALA X 415 " --> pdb=" O SER X 411 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU X 419 " --> pdb=" O ALA X 415 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA X 420 " --> pdb=" O LEU X 416 " (cutoff:3.500A) Proline residue: X 421 - end of helix Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 459 Processing helix chain 'Y' and resid 47 through 64 removed outlier: 3.502A pdb=" N GLY Y 64 " --> pdb=" O MET Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 80 through 93 Processing helix chain 'Y' and resid 104 through 107 removed outlier: 3.519A pdb=" N PHE Y 107 " --> pdb=" O SER Y 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 104 through 107' Processing helix chain 'Y' and resid 112 through 124 Processing helix chain 'Y' and resid 172 through 181 removed outlier: 3.737A pdb=" N LYS Y 181 " --> pdb=" O ASP Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 209 Processing helix chain 'Y' and resid 240 through 250 removed outlier: 3.549A pdb=" N ILE Y 244 " --> pdb=" O SER Y 240 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG Y 250 " --> pdb=" O VAL Y 246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 253 through 260 removed outlier: 3.567A pdb=" N LEU Y 257 " --> pdb=" O GLY Y 253 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE Y 258 " --> pdb=" O PHE Y 254 " (cutoff:3.500A) Processing helix chain 'Y' and resid 266 through 284 removed outlier: 3.586A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 302 through 313 Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 344 through 350 Processing helix chain 'Y' and resid 360 through 375 Processing helix chain 'Y' and resid 380 through 394 removed outlier: 3.537A pdb=" N GLU Y 393 " --> pdb=" O LYS Y 389 " (cutoff:3.500A) Processing helix chain 'Y' and resid 396 through 414 removed outlier: 3.863A pdb=" N SER Y 400 " --> pdb=" O LEU Y 396 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN Y 401 " --> pdb=" O ARG Y 397 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU Y 402 " --> pdb=" O TYR Y 398 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 Processing helix chain 'Y' and resid 432 through 443 Processing helix chain 'Z' and resid 196 through 231 removed outlier: 3.911A pdb=" N THR Z 203 " --> pdb=" O VAL Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 243 through 265 removed outlier: 4.313A pdb=" N PHE Z 259 " --> pdb=" O SER Z 255 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS Z 260 " --> pdb=" O LEU Z 256 " (cutoff:3.500A) Processing helix chain 'Z' and resid 265 through 275 removed outlier: 4.023A pdb=" N LYS Z 275 " --> pdb=" O LEU Z 271 " (cutoff:3.500A) Processing helix chain 'Z' and resid 301 through 318 Processing helix chain 'Z' and resid 605 through 617 removed outlier: 4.014A pdb=" N PHE Z 616 " --> pdb=" O ASN Z 612 " (cutoff:3.500A) Processing helix chain 'Z' and resid 617 through 623 Processing sheet with id=AA1, first strand: chain 'E' and resid 43 through 44 removed outlier: 7.200A pdb=" N ARG E 43 " --> pdb=" O ILE G 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 78 through 79 Processing sheet with id=AA3, first strand: chain 'F' and resid 43 through 44 removed outlier: 7.206A pdb=" N ARG F 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'M' and resid 718 through 719 removed outlier: 6.438A pdb=" N MET M 821 " --> pdb=" O LEU M 849 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LEU M 851 " --> pdb=" O MET M 821 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU M 823 " --> pdb=" O LEU M 851 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE M 750 " --> pdb=" O VAL M 801 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU M 774 " --> pdb=" O ILE M 800 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER M 802 " --> pdb=" O LEU M 774 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 944 through 951 removed outlier: 6.275A pdb=" N VAL M1336 " --> pdb=" O TYR M1367 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE M1369 " --> pdb=" O VAL M1336 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE M1338 " --> pdb=" O PHE M1369 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N SER M1371 " --> pdb=" O PHE M1338 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU M1266 " --> pdb=" O ILE M1337 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N MET M1290 " --> pdb=" O ILE M1318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 26 through 29 Processing sheet with id=AA7, first strand: chain 'R' and resid 40 through 41 Processing sheet with id=AA8, first strand: chain 'R' and resid 147 through 151 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 147 through 151 current: chain 'R' and resid 198 through 204 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 207 through 208 current: chain 'R' and resid 384 through 388 Processing sheet with id=AA9, first strand: chain 'R' and resid 286 through 288 Processing sheet with id=AB1, first strand: chain 'S' and resid 5 through 8 removed outlier: 4.040A pdb=" N THR V 178 " --> pdb=" O ILE S 8 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL V 166 " --> pdb=" O LEU V 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 18 through 21 removed outlier: 6.501A pdb=" N THR U 159 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE U 143 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS U 157 " --> pdb=" O ILE U 143 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU U 158 " --> pdb=" O TYR U 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 171 current: chain 'U' and resid 198 through 204 Processing sheet with id=AB3, first strand: chain 'S' and resid 254 through 255 Processing sheet with id=AB4, first strand: chain 'T' and resid 44 through 45 Processing sheet with id=AB5, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.351A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU T 308 " --> pdb=" O VAL T 337 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ALA T 339 " --> pdb=" O LEU T 308 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE T 310 " --> pdb=" O ALA T 339 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER T 340 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY T 79 " --> pdb=" O SER T 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 130 through 133 Processing sheet with id=AB7, first strand: chain 'T' and resid 135 through 151 removed outlier: 6.653A pdb=" N GLY T 169 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU T 147 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE T 167 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS T 165 " --> pdb=" O PRO T 149 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP T 151 " --> pdb=" O ILE T 163 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE T 163 " --> pdb=" O ASP T 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 176 through 181 current: chain 'T' and resid 209 through 215 removed outlier: 6.523A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ARG T 214 " --> pdb=" O VAL T 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'T' and resid 344 through 346 Processing sheet with id=AB9, first strand: chain 'T' and resid 394 through 395 removed outlier: 7.877A pdb=" N GLN T 394 " --> pdb=" O ILE T 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'U' and resid 40 through 41 Processing sheet with id=AC2, first strand: chain 'U' and resid 98 through 102 removed outlier: 5.953A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 330 through 331 Processing sheet with id=AC4, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.395A pdb=" N CYS V 103 " --> pdb=" O PHE V 309 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ASP V 311 " --> pdb=" O CYS V 103 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU V 105 " --> pdb=" O ASP V 311 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU V 308 " --> pdb=" O VAL V 337 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA V 339 " --> pdb=" O LEU V 308 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE V 310 " --> pdb=" O ALA V 339 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER V 340 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 130 through 133 removed outlier: 3.714A pdb=" N ILE V 304 " --> pdb=" O GLY V 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 229 through 230 removed outlier: 6.322A pdb=" N VAL V 230 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG V 214 " --> pdb=" O VAL V 230 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL V 199 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS V 241 " --> pdb=" O LYS V 137 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 344 through 346 removed outlier: 3.560A pdb=" N THR V 345 " --> pdb=" O SER V 355 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AC9, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.127A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU W 293 " --> pdb=" O MET W 322 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ALA W 324 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE W 295 " --> pdb=" O ALA W 324 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 126 through 147 removed outlier: 5.223A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU W 142 " --> pdb=" O THR W 159 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 166 through 170 current: chain 'W' and resid 199 through 204 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 199 through 204 current: chain 'X' and resid 162 through 172 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 175 through 181 current: chain 'X' and resid 207 through 215 removed outlier: 5.935A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 229 through 230 current: chain 'Z' and resid 592 through 596 Processing sheet with id=AD2, first strand: chain 'W' and resid 330 through 331 Processing sheet with id=AD3, first strand: chain 'X' and resid 44 through 45 Processing sheet with id=AD4, first strand: chain 'X' and resid 102 through 106 removed outlier: 6.436A pdb=" N CYS X 103 " --> pdb=" O PHE X 309 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ASP X 311 " --> pdb=" O CYS X 103 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU X 105 " --> pdb=" O ASP X 311 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU X 308 " --> pdb=" O VAL X 337 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ALA X 339 " --> pdb=" O LEU X 308 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE X 310 " --> pdb=" O ALA X 339 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 344 through 346 removed outlier: 3.535A pdb=" N THR X 345 " --> pdb=" O SER X 355 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 394 through 395 removed outlier: 7.807A pdb=" N GLN X 394 " --> pdb=" O ILE X 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'Y' and resid 40 through 41 Processing sheet with id=AD8, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.048A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASP Y 296 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE Y 101 " --> pdb=" O ASP Y 296 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 126 through 144 removed outlier: 6.605A pdb=" N THR Y 159 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE Y 143 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS Y 157 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU Y 158 " --> pdb=" O TYR Y 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 166 through 170 current: chain 'Y' and resid 199 through 204 Processing sheet with id=AE1, first strand: chain 'Y' and resid 330 through 331 1746 hydrogen bonds defined for protein. 5049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 426 hydrogen bonds 832 hydrogen bond angles 0 basepair planarities 168 basepair parallelities 276 stacking parallelities Total time for adding SS restraints: 14.81 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10959 1.33 - 1.45: 10296 1.45 - 1.58: 24640 1.58 - 1.70: 730 1.70 - 1.82: 202 Bond restraints: 46827 Sorted by residual: bond pdb=" CA ASP D 24 " pdb=" CB ASP D 24 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.50e-02 4.44e+03 2.16e+00 bond pdb=" C3' DG J 77 " pdb=" O3' DG J 77 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.09e+00 bond pdb=" CB GLN E 114 " pdb=" CG GLN E 114 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" CB GLN H 59 " pdb=" CG GLN H 59 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" CG GLU A 105 " pdb=" CD GLU A 105 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.58e+00 ... (remaining 46822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.34: 64728 5.34 - 10.68: 103 10.68 - 16.01: 6 16.01 - 21.35: 0 21.35 - 26.69: 4 Bond angle restraints: 64841 Sorted by residual: angle pdb=" O3' DC I -77 " pdb=" P DG I -76 " pdb=" OP1 DG I -76 " ideal model delta sigma weight residual 108.00 81.31 26.69 3.00e+00 1.11e-01 7.91e+01 angle pdb=" O3' DA J -77 " pdb=" P DT J -76 " pdb=" OP2 DT J -76 " ideal model delta sigma weight residual 108.00 82.84 25.16 3.00e+00 1.11e-01 7.03e+01 angle pdb=" O3' DA J -77 " pdb=" P DT J -76 " pdb=" OP1 DT J -76 " ideal model delta sigma weight residual 108.00 83.36 24.64 3.00e+00 1.11e-01 6.74e+01 angle pdb=" O3' DC I -77 " pdb=" P DG I -76 " pdb=" OP2 DG I -76 " ideal model delta sigma weight residual 108.00 84.75 23.25 3.00e+00 1.11e-01 6.01e+01 angle pdb=" C PRO Z 587 " pdb=" N GLU Z 588 " pdb=" CA GLU Z 588 " ideal model delta sigma weight residual 121.70 134.05 -12.35 1.80e+00 3.09e-01 4.71e+01 ... (remaining 64836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.45: 25232 33.45 - 66.90: 2323 66.90 - 100.36: 67 100.36 - 133.81: 2 133.81 - 167.26: 4 Dihedral angle restraints: 27628 sinusoidal: 13532 harmonic: 14096 Sorted by residual: dihedral pdb=" CA LEU M 998 " pdb=" C LEU M 998 " pdb=" N PHE M 999 " pdb=" CA PHE M 999 " ideal model delta harmonic sigma weight residual 180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA PHE M 999 " pdb=" C PHE M 999 " pdb=" N GLU M1000 " pdb=" CA GLU M1000 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" C5' ADP W 501 " pdb=" O5' ADP W 501 " pdb=" PA ADP W 501 " pdb=" O2A ADP W 501 " ideal model delta sinusoidal sigma weight residual -60.00 -150.36 90.36 1 2.00e+01 2.50e-03 2.42e+01 ... (remaining 27625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.400: 7553 0.400 - 0.799: 0 0.799 - 1.199: 0 1.199 - 1.599: 0 1.599 - 1.998: 2 Chirality restraints: 7555 Sorted by residual: chirality pdb=" P DT J -76 " pdb=" OP1 DT J -76 " pdb=" OP2 DT J -76 " pdb=" O5' DT J -76 " both_signs ideal model delta sigma weight residual True 2.35 0.35 2.00 2.00e-01 2.50e+01 9.98e+01 chirality pdb=" P DG I -76 " pdb=" OP1 DG I -76 " pdb=" OP2 DG I -76 " pdb=" O5' DG I -76 " both_signs ideal model delta sigma weight residual True 2.35 0.37 1.97 2.00e-01 2.50e+01 9.74e+01 chirality pdb=" CG LEU F 59 " pdb=" CB LEU F 59 " pdb=" CD1 LEU F 59 " pdb=" CD2 LEU F 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 7552 not shown) Planarity restraints: 7001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU M 998 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C LEU M 998 " -0.055 2.00e-02 2.50e+03 pdb=" O LEU M 998 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE M 999 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR Z 298 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO Z 299 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO Z 299 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO Z 299 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 80 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO F 81 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO F 81 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 81 " -0.026 5.00e-02 4.00e+02 ... (remaining 6998 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 496 2.54 - 3.13: 35055 3.13 - 3.72: 78384 3.72 - 4.31: 100429 4.31 - 4.90: 159437 Nonbonded interactions: 373801 Sorted by model distance: nonbonded pdb=" O2B ADP Y 501 " pdb="MG MG Y 502 " model vdw 1.949 2.170 nonbonded pdb=" O2B ADP U 502 " pdb="MG MG U 503 " model vdw 1.959 2.170 nonbonded pdb=" O3B ADP W 501 " pdb="MG MG W 502 " model vdw 1.964 2.170 nonbonded pdb=" F3 BEF R 502 " pdb="MG MG R 503 " model vdw 1.981 2.120 nonbonded pdb=" F3 BEF M1602 " pdb="MG MG M1603 " model vdw 1.984 2.120 ... (remaining 373796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 23 through 102) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 17 through 117) selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 35 through 125) selection = (chain 'H' and (resid 35 through 111 or (resid 112 through 113 and (name N or na \ me CA or name C or name O or name CB )) or resid 114 through 125)) } ncs_group { reference = (chain 'T' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 501)) selection = (chain 'V' and (resid 22 through 161 or (resid 162 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 501)) selection = (chain 'X' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 161 through 163 and (name N or name CA or \ name C or name O or name CB )) or resid 164 through 501)) } ncs_group { reference = (chain 'U' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 222 or (resid 223 and (name N or name C \ A or name C or name O or name CB )) or resid 224 through 459)) selection = (chain 'W' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 200 or (resid 201 and (name N or name C \ A or name C or name O or name CB )) or resid 202 through 205 or resid 222 throug \ h 459)) selection = (chain 'Y' and (resid 15 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 205 or resid 222 or (resid 223 \ and (name N or name CA or name C or name O or name CB )) or resid 224 through 45 \ 9)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 55.910 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 46836 Z= 0.126 Angle : 0.641 26.689 64850 Z= 0.318 Chirality : 0.050 1.998 7555 Planarity : 0.003 0.058 7001 Dihedral : 21.077 167.261 18506 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 0.31 % Allowed : 24.77 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.13), residues: 4809 helix: 1.58 (0.11), residues: 2308 sheet: 0.90 (0.20), residues: 681 loop : -0.68 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 191 TYR 0.022 0.001 TYR H 86 PHE 0.028 0.001 PHE H 68 TRP 0.032 0.001 TRP Z 309 HIS 0.004 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00272 (46827) covalent geometry : angle 0.64097 (64841) hydrogen bonds : bond 0.14435 ( 2172) hydrogen bonds : angle 5.04284 ( 5881) metal coordination : bond 0.00571 ( 8) metal coordination : angle 1.91906 ( 9) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 271 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 97 LEU cc_start: 0.8027 (mt) cc_final: 0.7468 (mt) REVERT: F 57 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7936 (mm-30) REVERT: G 60 LYS cc_start: 0.9704 (mmmm) cc_final: 0.9384 (mmmt) REVERT: H 62 MET cc_start: 0.8594 (tpt) cc_final: 0.8310 (mmm) REVERT: V 58 CYS cc_start: 0.9115 (m) cc_final: 0.8546 (t) REVERT: Y 175 MET cc_start: 0.8701 (tpp) cc_final: 0.8161 (mtm) outliers start: 13 outliers final: 9 residues processed: 277 average time/residue: 0.2794 time to fit residues: 131.4394 Evaluate side-chains 269 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 260 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 409 ILE Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain Z residue 603 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 0.9980 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN F 42 GLN ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 22 ASN U 63 ASN V 124 ASN ** V 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 260 GLN Y 47 GLN ** Z 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 603 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.059206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.040789 restraints weight = 283485.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.041813 restraints weight = 153075.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.042534 restraints weight = 100285.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.042924 restraints weight = 74237.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.043293 restraints weight = 61317.671| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 46836 Z= 0.158 Angle : 0.621 26.396 64850 Z= 0.314 Chirality : 0.051 2.001 7555 Planarity : 0.004 0.059 7001 Dihedral : 22.820 163.427 9206 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.10 % Favored : 95.84 % Rotamer: Outliers : 2.27 % Allowed : 22.28 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.12), residues: 4809 helix: 1.54 (0.11), residues: 2344 sheet: 0.74 (0.20), residues: 705 loop : -0.68 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M1133 TYR 0.020 0.001 TYR S 179 PHE 0.025 0.001 PHE H 68 TRP 0.018 0.001 TRP Z 309 HIS 0.004 0.001 HIS T 27 Details of bonding type rmsd covalent geometry : bond 0.00346 (46827) covalent geometry : angle 0.62028 (64841) hydrogen bonds : bond 0.04611 ( 2172) hydrogen bonds : angle 4.15376 ( 5881) metal coordination : bond 0.00904 ( 8) metal coordination : angle 2.85316 ( 9) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 283 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ASP cc_start: 0.8322 (t70) cc_final: 0.8116 (t70) REVERT: B 94 GLU cc_start: 0.8178 (tt0) cc_final: 0.7789 (tt0) REVERT: B 97 GLU cc_start: 0.8496 (pp20) cc_final: 0.8276 (pp20) REVERT: C 52 GLU cc_start: 0.8176 (pm20) cc_final: 0.7933 (pm20) REVERT: C 53 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8442 (mm-30) REVERT: D 26 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8487 (mp) REVERT: D 97 LEU cc_start: 0.7918 (mt) cc_final: 0.7506 (mt) REVERT: G 60 LYS cc_start: 0.9712 (mmmm) cc_final: 0.9396 (mmmt) REVERT: G 74 GLU cc_start: 0.9000 (pp20) cc_final: 0.8539 (pp20) REVERT: M 987 MET cc_start: 0.9468 (tpp) cc_final: 0.9101 (tpp) REVERT: M 1154 LYS cc_start: 0.5659 (OUTLIER) cc_final: 0.5047 (pptt) REVERT: T 344 MET cc_start: 0.9630 (mmm) cc_final: 0.9384 (mmp) REVERT: U 20 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8643 (mm) REVERT: V 58 CYS cc_start: 0.9075 (m) cc_final: 0.8496 (t) REVERT: V 268 MET cc_start: 0.9190 (tpp) cc_final: 0.8940 (tpp) REVERT: X 350 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8725 (p) REVERT: Z 229 GLU cc_start: 0.7314 (tp30) cc_final: 0.7004 (mp0) outliers start: 94 outliers final: 40 residues processed: 363 average time/residue: 0.2743 time to fit residues: 167.3175 Evaluate side-chains 298 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain M residue 800 ILE Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1135 ILE Chi-restraints excluded: chain M residue 1154 LYS Chi-restraints excluded: chain M residue 1335 THR Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 122 ASP Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain V residue 307 VAL Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 221 PHE Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 458 ILE Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 350 THR Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 341 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 215 optimal weight: 9.9990 chunk 384 optimal weight: 8.9990 chunk 372 optimal weight: 0.9980 chunk 449 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 492 optimal weight: 3.9990 chunk 452 optimal weight: 0.8980 chunk 218 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 508 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 16 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1012 HIS ** M1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 256 ASN ** X 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 624 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.058596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.040153 restraints weight = 281373.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041163 restraints weight = 152786.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.041872 restraints weight = 100415.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.042325 restraints weight = 74517.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.042639 restraints weight = 60765.996| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 46836 Z= 0.176 Angle : 0.624 26.775 64850 Z= 0.314 Chirality : 0.051 2.002 7555 Planarity : 0.004 0.058 7001 Dihedral : 22.879 160.208 9193 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 3.36 % Allowed : 21.70 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.12), residues: 4809 helix: 1.55 (0.11), residues: 2337 sheet: 0.61 (0.20), residues: 707 loop : -0.73 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M1133 TYR 0.031 0.001 TYR G 86 PHE 0.022 0.001 PHE M 999 TRP 0.020 0.001 TRP Z 309 HIS 0.005 0.001 HIS T 238 Details of bonding type rmsd covalent geometry : bond 0.00388 (46827) covalent geometry : angle 0.62291 (64841) hydrogen bonds : bond 0.04451 ( 2172) hydrogen bonds : angle 4.07482 ( 5881) metal coordination : bond 0.01013 ( 8) metal coordination : angle 3.25650 ( 9) Misc. bond : bond 0.00078 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 270 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 GLU cc_start: 0.8233 (tt0) cc_final: 0.7801 (tt0) REVERT: B 97 GLU cc_start: 0.8564 (pp20) cc_final: 0.8270 (pp20) REVERT: C 53 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8387 (mm-30) REVERT: D 97 LEU cc_start: 0.7978 (mt) cc_final: 0.7395 (mt) REVERT: G 34 LYS cc_start: 0.5911 (OUTLIER) cc_final: 0.5379 (tmmt) REVERT: G 60 LYS cc_start: 0.9683 (mmmm) cc_final: 0.9416 (mmmt) REVERT: G 74 GLU cc_start: 0.8958 (pp20) cc_final: 0.8516 (pp20) REVERT: G 88 LYS cc_start: 0.9295 (tppt) cc_final: 0.9075 (tptp) REVERT: H 52 HIS cc_start: 0.8413 (m-70) cc_final: 0.8184 (m-70) REVERT: H 79 GLU cc_start: 0.9673 (tp30) cc_final: 0.9471 (tp30) REVERT: M 762 MET cc_start: 0.9201 (mmp) cc_final: 0.8776 (mmm) REVERT: M 871 MET cc_start: 0.7457 (pmm) cc_final: 0.7184 (pmm) REVERT: M 921 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8874 (mm) REVERT: M 987 MET cc_start: 0.9512 (tpp) cc_final: 0.9143 (tpp) REVERT: M 1118 MET cc_start: 0.8355 (mmm) cc_final: 0.8155 (mmm) REVERT: M 1242 GLN cc_start: 0.9447 (OUTLIER) cc_final: 0.9066 (tm-30) REVERT: M 1347 MET cc_start: 0.8414 (pmm) cc_final: 0.7952 (pmm) REVERT: T 344 MET cc_start: 0.9615 (mmm) cc_final: 0.9330 (mmp) REVERT: U 20 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8692 (mm) REVERT: V 268 MET cc_start: 0.9234 (tpp) cc_final: 0.9012 (tpp) REVERT: W 165 MET cc_start: 0.8412 (ppp) cc_final: 0.8110 (ppp) REVERT: W 386 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9239 (pp) REVERT: X 138 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: Z 229 GLU cc_start: 0.7360 (tp30) cc_final: 0.7003 (mp0) outliers start: 139 outliers final: 62 residues processed: 386 average time/residue: 0.2582 time to fit residues: 167.4774 Evaluate side-chains 321 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 253 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 800 ILE Chi-restraints excluded: chain M residue 921 LEU Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1135 ILE Chi-restraints excluded: chain M residue 1154 LYS Chi-restraints excluded: chain M residue 1242 GLN Chi-restraints excluded: chain M residue 1335 THR Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 122 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 307 VAL Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 177 ASP Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 458 ILE Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 138 GLU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 322 MET Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Z residue 325 ARG Chi-restraints excluded: chain Z residue 598 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 370 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 213 optimal weight: 0.3980 chunk 42 optimal weight: 8.9990 chunk 480 optimal weight: 0.8980 chunk 366 optimal weight: 8.9990 chunk 243 optimal weight: 0.7980 chunk 246 optimal weight: 0.8980 chunk 315 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 16 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN G 52 HIS ** M 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1110 GLN ** X 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 234 HIS Z 262 GLN Z 624 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.059578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.041130 restraints weight = 278595.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.042159 restraints weight = 150034.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042889 restraints weight = 97307.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.043360 restraints weight = 71769.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043650 restraints weight = 58262.295| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 46836 Z= 0.120 Angle : 0.606 26.681 64850 Z= 0.302 Chirality : 0.051 2.005 7555 Planarity : 0.003 0.058 7001 Dihedral : 22.847 158.411 9193 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.10 % Favored : 95.82 % Rotamer: Outliers : 2.71 % Allowed : 22.40 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.12), residues: 4809 helix: 1.58 (0.11), residues: 2338 sheet: 0.59 (0.20), residues: 690 loop : -0.71 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 78 TYR 0.023 0.001 TYR C 88 PHE 0.023 0.001 PHE H 68 TRP 0.015 0.001 TRP Z 309 HIS 0.003 0.001 HIS T 238 Details of bonding type rmsd covalent geometry : bond 0.00256 (46827) covalent geometry : angle 0.60551 (64841) hydrogen bonds : bond 0.03880 ( 2172) hydrogen bonds : angle 3.87081 ( 5881) metal coordination : bond 0.00349 ( 8) metal coordination : angle 2.83587 ( 9) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 296 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 GLN cc_start: 0.8470 (mt0) cc_final: 0.8207 (mt0) REVERT: B 94 GLU cc_start: 0.8193 (tt0) cc_final: 0.7484 (tt0) REVERT: B 97 GLU cc_start: 0.8548 (pp20) cc_final: 0.8213 (pp20) REVERT: B 120 GLN cc_start: 0.8524 (tt0) cc_final: 0.8140 (tt0) REVERT: C 52 GLU cc_start: 0.8195 (pm20) cc_final: 0.7806 (pm20) REVERT: C 53 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8707 (mm-30) REVERT: D 97 LEU cc_start: 0.7735 (mt) cc_final: 0.7327 (mt) REVERT: G 34 LYS cc_start: 0.5787 (OUTLIER) cc_final: 0.5506 (tmmt) REVERT: G 60 LYS cc_start: 0.9666 (mmmm) cc_final: 0.9395 (mmmt) REVERT: G 74 GLU cc_start: 0.8901 (pp20) cc_final: 0.8459 (pp20) REVERT: G 88 LYS cc_start: 0.9242 (tppt) cc_final: 0.9014 (tptp) REVERT: H 45 TYR cc_start: 0.9272 (OUTLIER) cc_final: 0.8989 (m-80) REVERT: H 62 MET cc_start: 0.8568 (mmm) cc_final: 0.7727 (mmm) REVERT: H 79 GLU cc_start: 0.9673 (tp30) cc_final: 0.9437 (tp30) REVERT: M 760 TRP cc_start: 0.8773 (m100) cc_final: 0.8489 (m100) REVERT: M 762 MET cc_start: 0.9185 (mmp) cc_final: 0.8773 (mmm) REVERT: M 871 MET cc_start: 0.7353 (pmm) cc_final: 0.7067 (pmm) REVERT: M 921 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8853 (mm) REVERT: M 987 MET cc_start: 0.9496 (tpp) cc_final: 0.9120 (tpp) REVERT: M 1118 MET cc_start: 0.8418 (mmm) cc_final: 0.8162 (mmm) REVERT: M 1148 ARG cc_start: 0.8423 (mmm160) cc_final: 0.8162 (mmp80) REVERT: M 1154 LYS cc_start: 0.5722 (OUTLIER) cc_final: 0.4861 (pptt) REVERT: M 1242 GLN cc_start: 0.9427 (OUTLIER) cc_final: 0.9047 (tm-30) REVERT: M 1347 MET cc_start: 0.8342 (pmm) cc_final: 0.7749 (pmm) REVERT: R 188 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.8896 (tp-100) REVERT: T 344 MET cc_start: 0.9624 (mmm) cc_final: 0.9273 (mmp) REVERT: U 20 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8644 (mm) REVERT: U 300 MET cc_start: 0.8592 (ppp) cc_final: 0.8110 (ppp) REVERT: V 268 MET cc_start: 0.9284 (tpp) cc_final: 0.9057 (tpp) REVERT: W 17 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9155 (mm) REVERT: W 245 ASP cc_start: 0.9038 (m-30) cc_final: 0.8825 (m-30) REVERT: X 350 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8760 (p) REVERT: Y 175 MET cc_start: 0.8793 (tpp) cc_final: 0.7957 (mtm) REVERT: Y 257 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9447 (mm) REVERT: Z 229 GLU cc_start: 0.7339 (tp30) cc_final: 0.6998 (mp0) outliers start: 112 outliers final: 55 residues processed: 389 average time/residue: 0.2761 time to fit residues: 180.8363 Evaluate side-chains 330 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 265 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 800 ILE Chi-restraints excluded: chain M residue 921 LEU Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1154 LYS Chi-restraints excluded: chain M residue 1242 GLN Chi-restraints excluded: chain M residue 1305 THR Chi-restraints excluded: chain M residue 1335 THR Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 90 TYR Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 122 ASP Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 409 ILE Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 177 ASP Chi-restraints excluded: chain W residue 221 PHE Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 458 ILE Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 263 GLN Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 350 THR Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Z residue 200 MET Chi-restraints excluded: chain Z residue 325 ARG Chi-restraints excluded: chain Z residue 598 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 253 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 445 optimal weight: 0.9990 chunk 236 optimal weight: 9.9990 chunk 338 optimal weight: 4.9990 chunk 435 optimal weight: 0.9980 chunk 451 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 305 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 378 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 16 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1012 HIS ** M1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 289 ASN U 36 GLN X 190 GLN Y 223 GLN Y 453 ASN Z 624 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.057371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.038943 restraints weight = 283839.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.039928 restraints weight = 154139.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040608 restraints weight = 101393.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.041057 restraints weight = 75691.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.041313 restraints weight = 61857.483| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 46836 Z= 0.241 Angle : 0.672 26.894 64850 Z= 0.339 Chirality : 0.052 1.997 7555 Planarity : 0.004 0.058 7001 Dihedral : 22.949 156.209 9191 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 3.51 % Allowed : 22.52 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.12), residues: 4809 helix: 1.54 (0.11), residues: 2340 sheet: 0.40 (0.20), residues: 705 loop : -0.80 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M1133 TYR 0.025 0.002 TYR G 86 PHE 0.026 0.002 PHE M 999 TRP 0.021 0.001 TRP Z 309 HIS 0.006 0.001 HIS T 238 Details of bonding type rmsd covalent geometry : bond 0.00530 (46827) covalent geometry : angle 0.67113 (64841) hydrogen bonds : bond 0.04878 ( 2172) hydrogen bonds : angle 4.10643 ( 5881) metal coordination : bond 0.01644 ( 8) metal coordination : angle 3.13354 ( 9) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 258 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 GLU cc_start: 0.8219 (tt0) cc_final: 0.7900 (tt0) REVERT: B 97 GLU cc_start: 0.8511 (pp20) cc_final: 0.8188 (pp20) REVERT: D 97 LEU cc_start: 0.7795 (mt) cc_final: 0.7415 (mt) REVERT: G 74 GLU cc_start: 0.8910 (pp20) cc_final: 0.8464 (pp20) REVERT: H 45 TYR cc_start: 0.9303 (OUTLIER) cc_final: 0.9058 (m-80) REVERT: H 102 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8949 (ttp80) REVERT: M 921 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8903 (mm) REVERT: M 987 MET cc_start: 0.9512 (tpp) cc_final: 0.9154 (tpp) REVERT: M 1005 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9024 (mm) REVERT: M 1118 MET cc_start: 0.8520 (mmm) cc_final: 0.8256 (mmm) REVERT: M 1242 GLN cc_start: 0.9443 (OUTLIER) cc_final: 0.9063 (tm-30) REVERT: M 1347 MET cc_start: 0.8301 (pmm) cc_final: 0.7697 (pmm) REVERT: R 70 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8687 (pm20) REVERT: T 344 MET cc_start: 0.9586 (mmm) cc_final: 0.9105 (mmt) REVERT: U 20 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8733 (mm) REVERT: V 245 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.7667 (pp30) REVERT: V 268 MET cc_start: 0.9253 (tpp) cc_final: 0.8835 (tpp) REVERT: W 386 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9271 (pp) REVERT: X 190 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8327 (tp-100) REVERT: Y 175 MET cc_start: 0.8913 (tpp) cc_final: 0.8081 (mtm) REVERT: Y 322 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8379 (ptm) REVERT: Z 229 GLU cc_start: 0.7233 (tp30) cc_final: 0.6820 (mp0) outliers start: 145 outliers final: 93 residues processed: 383 average time/residue: 0.2750 time to fit residues: 177.8651 Evaluate side-chains 349 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 245 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 715 THR Chi-restraints excluded: chain M residue 764 PHE Chi-restraints excluded: chain M residue 800 ILE Chi-restraints excluded: chain M residue 921 LEU Chi-restraints excluded: chain M residue 948 ILE Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1005 LEU Chi-restraints excluded: chain M residue 1013 CYS Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1049 LEU Chi-restraints excluded: chain M residue 1135 ILE Chi-restraints excluded: chain M residue 1141 ILE Chi-restraints excluded: chain M residue 1154 LYS Chi-restraints excluded: chain M residue 1242 GLN Chi-restraints excluded: chain M residue 1254 LEU Chi-restraints excluded: chain M residue 1271 MET Chi-restraints excluded: chain M residue 1305 THR Chi-restraints excluded: chain M residue 1335 THR Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 44 ARG Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 122 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 265 VAL Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 387 LEU Chi-restraints excluded: chain U residue 409 ILE Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 200 ILE Chi-restraints excluded: chain V residue 212 VAL Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 307 VAL Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 177 ASP Chi-restraints excluded: chain W residue 221 PHE Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 300 MET Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 335 THR Chi-restraints excluded: chain W residue 347 LEU Chi-restraints excluded: chain W residue 379 LEU Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 458 ILE Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 190 GLN Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 322 MET Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Z residue 200 MET Chi-restraints excluded: chain Z residue 325 ARG Chi-restraints excluded: chain Z residue 598 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 103 optimal weight: 8.9990 chunk 371 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 506 optimal weight: 8.9990 chunk 232 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 262 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 431 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 844 ASN M1012 HIS ** M1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 144 GLN Y 223 GLN Y 248 ASN Z 624 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.057481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.039028 restraints weight = 283035.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.040021 restraints weight = 153211.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.040709 restraints weight = 100595.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041168 restraints weight = 74924.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.041424 restraints weight = 61112.972| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 46836 Z= 0.196 Angle : 0.651 26.918 64850 Z= 0.327 Chirality : 0.052 2.002 7555 Planarity : 0.004 0.060 7001 Dihedral : 23.007 154.716 9191 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.64 % Favored : 95.26 % Rotamer: Outliers : 3.48 % Allowed : 22.79 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.12), residues: 4809 helix: 1.54 (0.11), residues: 2332 sheet: 0.34 (0.20), residues: 705 loop : -0.83 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M1133 TYR 0.019 0.001 TYR V 462 PHE 0.026 0.001 PHE M 999 TRP 0.017 0.001 TRP Z 309 HIS 0.005 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00431 (46827) covalent geometry : angle 0.65020 (64841) hydrogen bonds : bond 0.04381 ( 2172) hydrogen bonds : angle 4.04881 ( 5881) metal coordination : bond 0.01248 ( 8) metal coordination : angle 3.24653 ( 9) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 265 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8186 (p) REVERT: B 94 GLU cc_start: 0.8193 (tt0) cc_final: 0.7837 (tt0) REVERT: B 97 GLU cc_start: 0.8554 (pp20) cc_final: 0.8244 (pp20) REVERT: D 97 LEU cc_start: 0.7875 (mt) cc_final: 0.7520 (mt) REVERT: G 34 LYS cc_start: 0.5896 (OUTLIER) cc_final: 0.5676 (tmmt) REVERT: G 60 LYS cc_start: 0.9671 (mmmm) cc_final: 0.9356 (mmmt) REVERT: G 71 ASP cc_start: 0.9190 (OUTLIER) cc_final: 0.8511 (t0) REVERT: G 74 GLU cc_start: 0.8883 (pp20) cc_final: 0.8442 (pp20) REVERT: H 102 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8953 (ttp80) REVERT: M 790 TRP cc_start: 0.8836 (OUTLIER) cc_final: 0.8142 (t60) REVERT: M 820 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.8749 (m-80) REVERT: M 921 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8911 (mm) REVERT: M 987 MET cc_start: 0.9512 (tpp) cc_final: 0.9154 (tpp) REVERT: M 1005 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9032 (mm) REVERT: M 1118 MET cc_start: 0.8603 (mmm) cc_final: 0.8301 (mmm) REVERT: M 1148 ARG cc_start: 0.8255 (mmp80) cc_final: 0.7894 (mmp80) REVERT: M 1242 GLN cc_start: 0.9442 (OUTLIER) cc_final: 0.9028 (tm-30) REVERT: M 1347 MET cc_start: 0.8204 (pmm) cc_final: 0.7668 (pmm) REVERT: R 70 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8634 (pm20) REVERT: R 418 GLU cc_start: 0.9154 (tt0) cc_final: 0.8823 (pt0) REVERT: T 344 MET cc_start: 0.9581 (mmm) cc_final: 0.9197 (mmt) REVERT: U 20 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8744 (mm) REVERT: V 245 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.7637 (pp30) REVERT: V 268 MET cc_start: 0.9259 (tpp) cc_final: 0.8857 (tpp) REVERT: W 179 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9344 (mm) REVERT: W 386 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9278 (pp) REVERT: Y 165 MET cc_start: 0.8178 (ppp) cc_final: 0.7976 (ppp) REVERT: Y 322 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8352 (ptm) REVERT: Z 229 GLU cc_start: 0.7207 (tp30) cc_final: 0.6802 (mp0) outliers start: 144 outliers final: 90 residues processed: 388 average time/residue: 0.2669 time to fit residues: 175.1486 Evaluate side-chains 352 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 247 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 715 THR Chi-restraints excluded: chain M residue 764 PHE Chi-restraints excluded: chain M residue 790 TRP Chi-restraints excluded: chain M residue 800 ILE Chi-restraints excluded: chain M residue 820 TYR Chi-restraints excluded: chain M residue 921 LEU Chi-restraints excluded: chain M residue 948 ILE Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1005 LEU Chi-restraints excluded: chain M residue 1013 CYS Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1049 LEU Chi-restraints excluded: chain M residue 1141 ILE Chi-restraints excluded: chain M residue 1154 LYS Chi-restraints excluded: chain M residue 1242 GLN Chi-restraints excluded: chain M residue 1254 LEU Chi-restraints excluded: chain M residue 1305 THR Chi-restraints excluded: chain M residue 1335 THR Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 239 MET Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 44 ARG Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 90 TYR Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 122 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 265 VAL Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 387 LEU Chi-restraints excluded: chain U residue 409 ILE Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain V residue 212 VAL Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 307 VAL Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 177 ASP Chi-restraints excluded: chain W residue 179 LEU Chi-restraints excluded: chain W residue 221 PHE Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 305 CYS Chi-restraints excluded: chain W residue 335 THR Chi-restraints excluded: chain W residue 379 LEU Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 458 ILE Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 383 ILE Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 322 MET Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Z residue 237 THR Chi-restraints excluded: chain Z residue 325 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 405 optimal weight: 2.9990 chunk 114 optimal weight: 0.3980 chunk 483 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 325 optimal weight: 8.9990 chunk 501 optimal weight: 4.9990 chunk 264 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 224 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN E 16 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** M 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1012 HIS M1110 GLN ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 260 GLN Z 624 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.058558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.040084 restraints weight = 278895.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041086 restraints weight = 151144.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.041786 restraints weight = 98490.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.042263 restraints weight = 73233.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.042582 restraints weight = 59488.464| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 46836 Z= 0.124 Angle : 0.632 26.839 64850 Z= 0.313 Chirality : 0.051 2.003 7555 Planarity : 0.003 0.056 7001 Dihedral : 22.933 153.289 9189 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.51 % Rotamer: Outliers : 2.81 % Allowed : 23.66 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.12), residues: 4809 helix: 1.62 (0.11), residues: 2330 sheet: 0.44 (0.20), residues: 695 loop : -0.82 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M1133 TYR 0.041 0.001 TYR G 86 PHE 0.025 0.001 PHE M 999 TRP 0.029 0.001 TRP Z 309 HIS 0.004 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00274 (46827) covalent geometry : angle 0.63097 (64841) hydrogen bonds : bond 0.03840 ( 2172) hydrogen bonds : angle 3.82578 ( 5881) metal coordination : bond 0.00450 ( 8) metal coordination : angle 2.98710 ( 9) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 282 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8663 (m-30) cc_final: 0.8329 (m-30) REVERT: B 76 GLN cc_start: 0.8513 (mt0) cc_final: 0.8220 (mt0) REVERT: B 94 GLU cc_start: 0.8179 (tt0) cc_final: 0.7665 (tt0) REVERT: B 97 GLU cc_start: 0.8580 (pp20) cc_final: 0.8277 (pp20) REVERT: C 53 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8515 (mm-30) REVERT: D 97 LEU cc_start: 0.7653 (mt) cc_final: 0.7314 (mt) REVERT: F 57 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8188 (mm-30) REVERT: G 34 LYS cc_start: 0.6090 (OUTLIER) cc_final: 0.5835 (tmmt) REVERT: G 60 LYS cc_start: 0.9648 (mmmm) cc_final: 0.9443 (mmmt) REVERT: G 71 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8441 (t0) REVERT: G 74 GLU cc_start: 0.8875 (pp20) cc_final: 0.8436 (pp20) REVERT: M 760 TRP cc_start: 0.8777 (m100) cc_final: 0.8478 (m100) REVERT: M 762 MET cc_start: 0.9223 (mmm) cc_final: 0.8724 (mmm) REVERT: M 776 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: M 790 TRP cc_start: 0.8791 (OUTLIER) cc_final: 0.8181 (t60) REVERT: M 921 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8862 (mm) REVERT: M 980 MET cc_start: 0.8250 (mmp) cc_final: 0.7434 (mmp) REVERT: M 987 MET cc_start: 0.9502 (tpp) cc_final: 0.9154 (tpp) REVERT: M 1005 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9009 (mm) REVERT: M 1118 MET cc_start: 0.8571 (mmm) cc_final: 0.8226 (mmm) REVERT: M 1148 ARG cc_start: 0.8180 (mmp80) cc_final: 0.7635 (mmp80) REVERT: M 1242 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.9003 (tm-30) REVERT: M 1279 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8503 (mt-10) REVERT: M 1290 MET cc_start: 0.8359 (ptm) cc_final: 0.7966 (ptm) REVERT: M 1347 MET cc_start: 0.8210 (pmm) cc_final: 0.7680 (pmm) REVERT: R 148 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8683 (ptm-80) REVERT: R 188 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.8823 (tp-100) REVERT: R 418 GLU cc_start: 0.9163 (tt0) cc_final: 0.8817 (pt0) REVERT: T 344 MET cc_start: 0.9617 (mmm) cc_final: 0.9211 (mmt) REVERT: U 20 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8707 (mm) REVERT: V 245 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8288 (pp30) REVERT: V 268 MET cc_start: 0.9313 (tpp) cc_final: 0.9020 (tpp) REVERT: W 179 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9296 (mm) REVERT: W 245 ASP cc_start: 0.9091 (m-30) cc_final: 0.8837 (m-30) REVERT: Y 175 MET cc_start: 0.8733 (tpp) cc_final: 0.7993 (mpp) REVERT: Z 229 GLU cc_start: 0.7233 (tp30) cc_final: 0.6877 (mp0) outliers start: 116 outliers final: 76 residues processed: 383 average time/residue: 0.2296 time to fit residues: 148.3490 Evaluate side-chains 347 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 259 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 764 PHE Chi-restraints excluded: chain M residue 776 TYR Chi-restraints excluded: chain M residue 790 TRP Chi-restraints excluded: chain M residue 800 ILE Chi-restraints excluded: chain M residue 921 LEU Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1005 LEU Chi-restraints excluded: chain M residue 1013 CYS Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1049 LEU Chi-restraints excluded: chain M residue 1154 LYS Chi-restraints excluded: chain M residue 1242 GLN Chi-restraints excluded: chain M residue 1271 MET Chi-restraints excluded: chain M residue 1335 THR Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 44 ARG Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 90 TYR Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 122 ASP Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 409 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 179 LEU Chi-restraints excluded: chain W residue 221 PHE Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 305 CYS Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 458 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 263 GLN Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 322 MET Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Z residue 200 MET Chi-restraints excluded: chain Z residue 237 THR Chi-restraints excluded: chain Z residue 325 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 399 optimal weight: 2.9990 chunk 326 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 252 optimal weight: 0.4980 chunk 436 optimal weight: 2.9990 chunk 294 optimal weight: 0.0570 chunk 268 optimal weight: 1.9990 chunk 311 optimal weight: 5.9990 chunk 360 optimal weight: 3.9990 chunk 306 optimal weight: 0.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN F 42 GLN ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1012 HIS ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 624 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.058926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.040467 restraints weight = 280166.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.041501 restraints weight = 151675.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.042213 restraints weight = 98770.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.042683 restraints weight = 73226.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.042993 restraints weight = 59449.657| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 46836 Z= 0.120 Angle : 0.636 26.790 64850 Z= 0.314 Chirality : 0.051 2.002 7555 Planarity : 0.003 0.057 7001 Dihedral : 22.870 153.171 9189 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 2.66 % Allowed : 24.12 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.12), residues: 4809 helix: 1.60 (0.11), residues: 2335 sheet: 0.47 (0.20), residues: 704 loop : -0.83 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 43 TYR 0.053 0.001 TYR G 86 PHE 0.024 0.001 PHE M 999 TRP 0.030 0.001 TRP Z 309 HIS 0.005 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00264 (46827) covalent geometry : angle 0.63464 (64841) hydrogen bonds : bond 0.03785 ( 2172) hydrogen bonds : angle 3.78351 ( 5881) metal coordination : bond 0.00336 ( 8) metal coordination : angle 2.89681 ( 9) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 279 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8657 (m-30) cc_final: 0.8318 (m-30) REVERT: B 76 GLN cc_start: 0.8533 (mt0) cc_final: 0.8271 (mt0) REVERT: B 94 GLU cc_start: 0.8158 (tt0) cc_final: 0.7552 (tt0) REVERT: B 97 GLU cc_start: 0.8574 (pp20) cc_final: 0.8244 (pp20) REVERT: C 53 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8566 (mm-30) REVERT: D 97 LEU cc_start: 0.7672 (mt) cc_final: 0.7379 (mt) REVERT: F 39 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7755 (t0) REVERT: F 57 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8186 (mm-30) REVERT: G 71 ASP cc_start: 0.9147 (OUTLIER) cc_final: 0.8428 (t0) REVERT: G 74 GLU cc_start: 0.8886 (pp20) cc_final: 0.8451 (pp20) REVERT: H 59 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8384 (pp30) REVERT: H 102 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8917 (ttp80) REVERT: M 723 MET cc_start: 0.7310 (ppp) cc_final: 0.6986 (tmm) REVERT: M 760 TRP cc_start: 0.8749 (m100) cc_final: 0.8457 (m100) REVERT: M 762 MET cc_start: 0.9236 (mmm) cc_final: 0.8750 (mmm) REVERT: M 776 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7215 (m-80) REVERT: M 874 THR cc_start: 0.7610 (OUTLIER) cc_final: 0.7187 (p) REVERT: M 921 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8847 (mm) REVERT: M 987 MET cc_start: 0.9495 (tpp) cc_final: 0.9191 (tpp) REVERT: M 1005 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8996 (mm) REVERT: M 1118 MET cc_start: 0.8591 (mmm) cc_final: 0.8271 (mmm) REVERT: M 1148 ARG cc_start: 0.8213 (mmp80) cc_final: 0.7650 (mmp80) REVERT: M 1154 LYS cc_start: 0.5528 (OUTLIER) cc_final: 0.4605 (pptt) REVERT: M 1242 GLN cc_start: 0.9401 (OUTLIER) cc_final: 0.8986 (tm-30) REVERT: M 1279 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8480 (mt-10) REVERT: M 1290 MET cc_start: 0.8331 (ptm) cc_final: 0.7963 (ptm) REVERT: M 1347 MET cc_start: 0.8204 (pmm) cc_final: 0.7694 (pmm) REVERT: R 148 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8658 (ptm-80) REVERT: R 188 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8839 (tp-100) REVERT: R 418 GLU cc_start: 0.9163 (tt0) cc_final: 0.8819 (pt0) REVERT: T 344 MET cc_start: 0.9638 (mmm) cc_final: 0.9210 (mmt) REVERT: U 20 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8658 (mm) REVERT: V 58 CYS cc_start: 0.8990 (m) cc_final: 0.8453 (t) REVERT: V 245 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8238 (pp30) REVERT: V 268 MET cc_start: 0.9248 (tpp) cc_final: 0.8911 (tpp) REVERT: W 179 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9270 (mm) REVERT: W 245 ASP cc_start: 0.9062 (m-30) cc_final: 0.8845 (m-30) REVERT: Y 175 MET cc_start: 0.8781 (tpp) cc_final: 0.7969 (mpp) REVERT: Z 229 GLU cc_start: 0.7171 (tp30) cc_final: 0.6741 (mp0) outliers start: 110 outliers final: 78 residues processed: 377 average time/residue: 0.2279 time to fit residues: 145.3085 Evaluate side-chains 357 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 265 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 764 PHE Chi-restraints excluded: chain M residue 776 TYR Chi-restraints excluded: chain M residue 800 ILE Chi-restraints excluded: chain M residue 874 THR Chi-restraints excluded: chain M residue 921 LEU Chi-restraints excluded: chain M residue 948 ILE Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1005 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1040 LEU Chi-restraints excluded: chain M residue 1049 LEU Chi-restraints excluded: chain M residue 1112 LEU Chi-restraints excluded: chain M residue 1154 LYS Chi-restraints excluded: chain M residue 1242 GLN Chi-restraints excluded: chain M residue 1269 THR Chi-restraints excluded: chain M residue 1305 THR Chi-restraints excluded: chain M residue 1335 THR Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 44 ARG Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 122 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 238 HIS Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 409 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 212 VAL Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 179 LEU Chi-restraints excluded: chain W residue 221 PHE Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 305 CYS Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 458 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 263 GLN Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 322 MET Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Z residue 200 MET Chi-restraints excluded: chain Z residue 237 THR Chi-restraints excluded: chain Z residue 325 ARG Chi-restraints excluded: chain Z residue 590 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 275 optimal weight: 0.7980 chunk 290 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 359 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 432 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN E 16 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1012 HIS ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 HIS ** X 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.058582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.040193 restraints weight = 279181.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.041186 restraints weight = 151312.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.041897 restraints weight = 99154.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.042367 restraints weight = 73485.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042682 restraints weight = 59814.375| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 46836 Z= 0.133 Angle : 0.639 26.831 64850 Z= 0.315 Chirality : 0.051 1.999 7555 Planarity : 0.003 0.056 7001 Dihedral : 22.857 153.239 9189 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.41 % Favored : 95.47 % Rotamer: Outliers : 2.59 % Allowed : 24.14 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.12), residues: 4809 helix: 1.62 (0.11), residues: 2336 sheet: 0.42 (0.20), residues: 688 loop : -0.84 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 132 TYR 0.028 0.001 TYR F 40 PHE 0.024 0.001 PHE M 999 TRP 0.026 0.001 TRP Z 309 HIS 0.004 0.001 HIS T 238 Details of bonding type rmsd covalent geometry : bond 0.00295 (46827) covalent geometry : angle 0.63832 (64841) hydrogen bonds : bond 0.03827 ( 2172) hydrogen bonds : angle 3.77949 ( 5881) metal coordination : bond 0.00521 ( 8) metal coordination : angle 2.88501 ( 9) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 274 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8676 (m-30) cc_final: 0.8341 (m-30) REVERT: B 76 GLN cc_start: 0.8548 (mt0) cc_final: 0.8274 (mt0) REVERT: B 94 GLU cc_start: 0.8193 (tt0) cc_final: 0.7763 (tt0) REVERT: B 97 GLU cc_start: 0.8565 (pp20) cc_final: 0.8244 (pp20) REVERT: D 97 LEU cc_start: 0.7707 (mt) cc_final: 0.7380 (mt) REVERT: G 60 LYS cc_start: 0.9438 (mmmt) cc_final: 0.9167 (mmmt) REVERT: G 71 ASP cc_start: 0.9155 (OUTLIER) cc_final: 0.8436 (t0) REVERT: G 74 GLU cc_start: 0.8893 (pp20) cc_final: 0.8451 (pp20) REVERT: H 102 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8918 (ttp80) REVERT: M 723 MET cc_start: 0.7318 (ppp) cc_final: 0.6986 (tmm) REVERT: M 760 TRP cc_start: 0.8774 (m100) cc_final: 0.8455 (m100) REVERT: M 762 MET cc_start: 0.9255 (mmm) cc_final: 0.8778 (mmm) REVERT: M 776 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: M 790 TRP cc_start: 0.8807 (OUTLIER) cc_final: 0.8243 (t60) REVERT: M 921 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8849 (mm) REVERT: M 980 MET cc_start: 0.8263 (mmp) cc_final: 0.7464 (mmp) REVERT: M 987 MET cc_start: 0.9586 (tpp) cc_final: 0.9238 (tpp) REVERT: M 1005 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8998 (mm) REVERT: M 1118 MET cc_start: 0.8604 (mmm) cc_final: 0.8281 (mmm) REVERT: M 1148 ARG cc_start: 0.8312 (mmp80) cc_final: 0.7735 (mmp80) REVERT: M 1154 LYS cc_start: 0.5543 (OUTLIER) cc_final: 0.4672 (pptt) REVERT: M 1242 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.9002 (tm-30) REVERT: M 1279 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8550 (mt-10) REVERT: M 1290 MET cc_start: 0.8340 (ptm) cc_final: 0.8011 (ptm) REVERT: M 1343 TRP cc_start: 0.7619 (t60) cc_final: 0.7020 (t60) REVERT: M 1347 MET cc_start: 0.8211 (pmm) cc_final: 0.7918 (pmm) REVERT: R 148 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8654 (ptm-80) REVERT: R 188 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.8861 (tp-100) REVERT: R 418 GLU cc_start: 0.9169 (tt0) cc_final: 0.8823 (pt0) REVERT: T 344 MET cc_start: 0.9606 (mmm) cc_final: 0.9223 (mmt) REVERT: U 20 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8664 (mm) REVERT: V 58 CYS cc_start: 0.8975 (m) cc_final: 0.8421 (t) REVERT: V 245 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8188 (pp30) REVERT: V 268 MET cc_start: 0.9200 (tpp) cc_final: 0.8721 (tpp) REVERT: W 179 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9286 (mm) REVERT: W 245 ASP cc_start: 0.9076 (m-30) cc_final: 0.8856 (m-30) REVERT: W 386 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9255 (pp) REVERT: X 191 ARG cc_start: 0.8793 (mtp-110) cc_final: 0.8499 (mtm110) REVERT: Y 175 MET cc_start: 0.8805 (tpp) cc_final: 0.8000 (mpp) REVERT: Z 229 GLU cc_start: 0.7179 (tp30) cc_final: 0.6737 (mp0) outliers start: 107 outliers final: 80 residues processed: 369 average time/residue: 0.2254 time to fit residues: 140.0468 Evaluate side-chains 366 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 272 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 764 PHE Chi-restraints excluded: chain M residue 776 TYR Chi-restraints excluded: chain M residue 790 TRP Chi-restraints excluded: chain M residue 800 ILE Chi-restraints excluded: chain M residue 921 LEU Chi-restraints excluded: chain M residue 948 ILE Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1005 LEU Chi-restraints excluded: chain M residue 1013 CYS Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1049 LEU Chi-restraints excluded: chain M residue 1112 LEU Chi-restraints excluded: chain M residue 1154 LYS Chi-restraints excluded: chain M residue 1242 GLN Chi-restraints excluded: chain M residue 1254 LEU Chi-restraints excluded: chain M residue 1269 THR Chi-restraints excluded: chain M residue 1305 THR Chi-restraints excluded: chain M residue 1335 THR Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 122 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 409 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 212 VAL Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 179 LEU Chi-restraints excluded: chain W residue 221 PHE Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 458 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 263 GLN Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 143 ILE Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 322 MET Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Z residue 206 VAL Chi-restraints excluded: chain Z residue 237 THR Chi-restraints excluded: chain Z residue 325 ARG Chi-restraints excluded: chain Z residue 590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 511 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 378 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 495 optimal weight: 5.9990 chunk 324 optimal weight: 6.9990 chunk 204 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 344 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1012 HIS ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 624 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.057762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.039342 restraints weight = 283572.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.040353 restraints weight = 153586.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.041046 restraints weight = 100414.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.041515 restraints weight = 74740.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.041807 restraints weight = 60784.039| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 46836 Z= 0.178 Angle : 0.668 26.915 64850 Z= 0.330 Chirality : 0.052 2.000 7555 Planarity : 0.004 0.057 7001 Dihedral : 22.901 153.297 9189 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 2.52 % Allowed : 24.12 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.13), residues: 4809 helix: 1.64 (0.11), residues: 2330 sheet: 0.34 (0.20), residues: 681 loop : -0.86 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M1148 TYR 0.038 0.001 TYR G 86 PHE 0.025 0.001 PHE M 999 TRP 0.025 0.001 TRP Z 309 HIS 0.005 0.001 HIS T 238 Details of bonding type rmsd covalent geometry : bond 0.00394 (46827) covalent geometry : angle 0.66723 (64841) hydrogen bonds : bond 0.04190 ( 2172) hydrogen bonds : angle 3.88879 ( 5881) metal coordination : bond 0.01036 ( 8) metal coordination : angle 3.09355 ( 9) Misc. bond : bond 0.00035 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 273 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8689 (m-30) cc_final: 0.8349 (m-30) REVERT: B 76 GLN cc_start: 0.8550 (mt0) cc_final: 0.8093 (mt0) REVERT: B 94 GLU cc_start: 0.8210 (tt0) cc_final: 0.7784 (tt0) REVERT: B 97 GLU cc_start: 0.8587 (pp20) cc_final: 0.8264 (pp20) REVERT: C 53 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8508 (mm-30) REVERT: D 97 LEU cc_start: 0.7844 (mt) cc_final: 0.7508 (mt) REVERT: F 57 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8206 (mm-30) REVERT: G 71 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8435 (t0) REVERT: G 74 GLU cc_start: 0.8906 (pp20) cc_final: 0.8497 (pp20) REVERT: H 59 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8634 (pm20) REVERT: H 62 MET cc_start: 0.8604 (mmm) cc_final: 0.8396 (mmm) REVERT: H 102 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8924 (ttp80) REVERT: M 762 MET cc_start: 0.9272 (mmm) cc_final: 0.8803 (mmm) REVERT: M 776 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: M 790 TRP cc_start: 0.8857 (OUTLIER) cc_final: 0.8294 (t60) REVERT: M 921 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8852 (mm) REVERT: M 980 MET cc_start: 0.8304 (mmp) cc_final: 0.7508 (mmp) REVERT: M 987 MET cc_start: 0.9595 (tpp) cc_final: 0.9255 (tpp) REVERT: M 1005 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.9018 (mm) REVERT: M 1118 MET cc_start: 0.8614 (mmm) cc_final: 0.8340 (mmm) REVERT: M 1148 ARG cc_start: 0.8412 (mmp80) cc_final: 0.7878 (mmp80) REVERT: M 1242 GLN cc_start: 0.9422 (OUTLIER) cc_final: 0.9040 (tm-30) REVERT: M 1279 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8565 (mt-10) REVERT: M 1290 MET cc_start: 0.8401 (ptm) cc_final: 0.8127 (ptm) REVERT: M 1347 MET cc_start: 0.8180 (pmm) cc_final: 0.7661 (pmm) REVERT: R 70 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8692 (pm20) REVERT: R 106 MET cc_start: 0.6813 (tpt) cc_final: 0.5385 (tmm) REVERT: R 148 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8613 (ptm-80) REVERT: R 418 GLU cc_start: 0.9174 (tt0) cc_final: 0.8822 (pt0) REVERT: T 236 GLU cc_start: 0.7861 (pm20) cc_final: 0.7265 (pm20) REVERT: T 344 MET cc_start: 0.9598 (mmm) cc_final: 0.9212 (mmt) REVERT: T 406 MET cc_start: 0.9200 (ppp) cc_final: 0.8877 (ppp) REVERT: U 20 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8724 (mm) REVERT: V 245 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.7617 (pp30) REVERT: V 268 MET cc_start: 0.9169 (tpp) cc_final: 0.8613 (tpp) REVERT: W 179 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9318 (mm) REVERT: W 245 ASP cc_start: 0.9124 (m-30) cc_final: 0.8862 (m-30) REVERT: W 386 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9266 (pp) REVERT: X 191 ARG cc_start: 0.8764 (mtp-110) cc_final: 0.8492 (mtm110) REVERT: Y 175 MET cc_start: 0.8857 (tpp) cc_final: 0.8083 (mpp) REVERT: Z 229 GLU cc_start: 0.7167 (tp30) cc_final: 0.6713 (mp0) outliers start: 104 outliers final: 81 residues processed: 365 average time/residue: 0.2295 time to fit residues: 141.3117 Evaluate side-chains 355 residues out of total 4240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 261 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 102 ARG Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 764 PHE Chi-restraints excluded: chain M residue 776 TYR Chi-restraints excluded: chain M residue 790 TRP Chi-restraints excluded: chain M residue 800 ILE Chi-restraints excluded: chain M residue 921 LEU Chi-restraints excluded: chain M residue 948 ILE Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1005 LEU Chi-restraints excluded: chain M residue 1013 CYS Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1049 LEU Chi-restraints excluded: chain M residue 1112 LEU Chi-restraints excluded: chain M residue 1154 LYS Chi-restraints excluded: chain M residue 1242 GLN Chi-restraints excluded: chain M residue 1254 LEU Chi-restraints excluded: chain M residue 1269 THR Chi-restraints excluded: chain M residue 1305 THR Chi-restraints excluded: chain M residue 1335 THR Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain R residue 239 MET Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 122 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 409 ILE Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 202 ILE Chi-restraints excluded: chain V residue 212 VAL Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 179 LEU Chi-restraints excluded: chain W residue 221 PHE Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 379 LEU Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 458 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 143 ILE Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 322 MET Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Z residue 206 VAL Chi-restraints excluded: chain Z residue 237 THR Chi-restraints excluded: chain Z residue 325 ARG Chi-restraints excluded: chain Z residue 590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 514 random chunks: chunk 294 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 306 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 493 optimal weight: 3.9990 chunk 366 optimal weight: 7.9990 chunk 428 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 451 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 509 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN E 16 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1012 HIS M1033 ASN ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 299 HIS ** X 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 248 ASN Z 614 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.057245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.038849 restraints weight = 284111.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.039845 restraints weight = 153103.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.040533 restraints weight = 100155.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.040996 restraints weight = 74764.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.041280 restraints weight = 60839.839| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 46836 Z= 0.189 Angle : 0.679 26.957 64850 Z= 0.337 Chirality : 0.052 2.009 7555 Planarity : 0.004 0.056 7001 Dihedral : 23.006 153.098 9189 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 2.52 % Allowed : 24.36 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.12), residues: 4809 helix: 1.53 (0.11), residues: 2344 sheet: 0.25 (0.20), residues: 699 loop : -0.87 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M1133 TYR 0.024 0.001 TYR G 86 PHE 0.026 0.001 PHE M 999 TRP 0.022 0.001 TRP Z 309 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00418 (46827) covalent geometry : angle 0.67783 (64841) hydrogen bonds : bond 0.04281 ( 2172) hydrogen bonds : angle 3.95539 ( 5881) metal coordination : bond 0.01129 ( 8) metal coordination : angle 3.39636 ( 9) Misc. bond : bond 0.00018 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9153.26 seconds wall clock time: 158 minutes 24.54 seconds (9504.54 seconds total)