Starting phenix.real_space_refine on Mon Aug 25 00:59:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7crr_30457/08_2025/7crr_30457.cif Found real_map, /net/cci-nas-00/data/ceres_data/7crr_30457/08_2025/7crr_30457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7crr_30457/08_2025/7crr_30457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7crr_30457/08_2025/7crr_30457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7crr_30457/08_2025/7crr_30457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7crr_30457/08_2025/7crr_30457.map" } resolution = 3.48 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12070 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 336 5.49 5 S 29 5.16 5 C 8248 2.51 5 N 2788 2.21 5 O 3435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s 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: 14839 Number of models: 1 Model: "" Number of chains: 12 Chain: "M" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 833 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'NLE:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 803 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'NLE:plan-1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 676 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "A" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3420 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "K" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3468 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "I" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1757 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14351 SG CYS I1226 38.218 63.873 58.261 1.00113.15 S ATOM 14727 SG CYS I1275 38.079 65.107 53.684 1.00119.40 S ATOM 13313 SG CYS I1098 59.658 91.848 72.527 1.00 91.57 S ATOM 13327 SG CYS I1100 61.798 91.590 69.925 1.00 96.58 S ATOM 13386 SG CYS I1108 58.780 92.971 68.769 1.00 94.35 S ATOM 13428 SG CYS I1114 57.707 89.812 70.185 1.00 82.06 S ATOM 13386 SG CYS I1108 58.780 92.971 68.769 1.00 94.35 S ATOM 13507 SG CYS I1123 55.139 94.831 69.726 1.00 83.93 S ATOM 13546 SG CYS I1128 58.262 96.686 69.941 1.00 98.17 S ATOM 13587 SG CYS I1134 55.714 95.818 66.274 1.00102.54 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N SAM I1501 " occ=0.93 ... (25 atoms not shown) pdb=" O4' SAM I1501 " occ=0.93 Time building chain proxies: 3.72, per 1000 atoms: 0.25 Number of scatterers: 14839 At special positions: 0 Unit cell: (133.92, 145.8, 171.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 29 16.00 P 336 15.00 O 3435 8.00 N 2788 7.00 C 8248 6.00 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=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 568.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I1502 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1275 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1226 " pdb=" ZN I1503 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1108 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1114 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1100 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1098 " pdb=" ZN I1504 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1123 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1108 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1134 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1128 " Number of angles added : 12 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 59.2% alpha, 0.0% beta 122 base pairs and 272 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'M' and resid 44 through 57 removed outlier: 3.942A pdb=" N LEU M 48 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU M 50 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER M 57 " --> pdb=" O ARG M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 77 removed outlier: 3.518A pdb=" N LEU M 70 " --> pdb=" O PRO M 66 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.613A pdb=" N NLE M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA M 91 " --> pdb=" O SER M 87 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU M 92 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN M 93 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU M 94 " --> pdb=" O NLE M 90 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU M 105 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN M 108 " --> pdb=" O PHE M 104 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS M 110 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 132 removed outlier: 3.959A pdb=" N ILE M 124 " --> pdb=" O NLE M 120 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN M 125 " --> pdb=" O PRO M 121 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 42 removed outlier: 4.882A pdb=" N GLY B 28 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N THR B 30 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS B 31 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 3.658A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.648A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.029A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.626A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 21' Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.783A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 5.057A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 61 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 66 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 97 removed outlier: 3.659A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLU C 92 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.373A pdb=" N LEU C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.743A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 4.194A pdb=" N SER D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 120 removed outlier: 3.694A pdb=" N VAL D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Proline residue: D 100 - end of helix removed outlier: 5.918A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.909A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.732A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.242A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N NLE E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU E 94 " --> pdb=" O NLE E 90 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.071A pdb=" N ILE E 124 " --> pdb=" O NLE E 120 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 41 removed outlier: 5.724A pdb=" N GLY F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N THR F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS F 31 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Proline residue: F 32 - end of helix removed outlier: 3.833A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.726A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.925A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.701A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 16 through 21' Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.610A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.909A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU G 58 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 97 removed outlier: 3.787A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU G 91 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLU G 92 " --> pdb=" O ARG G 88 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU G 93 " --> pdb=" O ASN G 89 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 4.069A pdb=" N LEU G 116 " --> pdb=" O GLN G 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 112 through 116' Processing helix chain 'H' and resid 34 through 46 removed outlier: 4.218A pdb=" N TYR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.607A pdb=" N SER H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 121 removed outlier: 3.720A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR H 93 " --> pdb=" O ARG H 89 " (cutoff:3.500A) Proline residue: H 100 - end of helix removed outlier: 6.154A pdb=" N LEU H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 1091 through 1095 removed outlier: 4.647A pdb=" N ILE I1095 " --> pdb=" O ASP I1091 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1091 through 1095' Processing helix chain 'I' and resid 1114 through 1119 Processing helix chain 'I' and resid 1137 through 1142 removed outlier: 4.443A pdb=" N LYS I1141 " --> pdb=" O GLN I1137 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG I1142 " --> pdb=" O CYS I1138 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1137 through 1142' Processing helix chain 'I' and resid 1180 through 1194 removed outlier: 4.308A pdb=" N ASN I1194 " --> pdb=" O ARG I1190 " (cutoff:3.500A) Processing helix chain 'I' and resid 1217 through 1222 removed outlier: 5.078A pdb=" N PHE I1221 " --> pdb=" O ASN I1217 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N MET I1222 " --> pdb=" O TYR I1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1217 through 1222' 272 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 316 hydrogen bonds 628 hydrogen bond angles 0 basepair planarities 122 basepair parallelities 272 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 1.64 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: 2956 1.33 - 1.45: 4947 1.45 - 1.57: 7177 1.57 - 1.69: 670 1.69 - 1.81: 41 Bond restraints: 15791 Sorted by residual: bond pdb=" C8 SAM I1501 " pdb=" N7 SAM I1501 " ideal model delta sigma weight residual 1.298 1.352 -0.054 2.00e-02 2.50e+03 7.32e+00 bond pdb=" C2 SAM I1501 " pdb=" N3 SAM I1501 " ideal model delta sigma weight residual 1.322 1.375 -0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" C2 SAM I1501 " pdb=" N1 SAM I1501 " ideal model delta sigma weight residual 1.329 1.378 -0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" CA LYS I1077 " pdb=" C LYS I1077 " ideal model delta sigma weight residual 1.522 1.552 -0.031 1.32e-02 5.74e+03 5.35e+00 bond pdb=" CA ALA H 114 " pdb=" C ALA H 114 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.38e-02 5.25e+03 5.20e+00 ... (remaining 15786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 22379 2.24 - 4.47: 357 4.47 - 6.71: 27 6.71 - 8.94: 4 8.94 - 11.18: 2 Bond angle restraints: 22769 Sorted by residual: angle pdb=" N LYS D 31 " pdb=" CA LYS D 31 " pdb=" C LYS D 31 " ideal model delta sigma weight residual 110.80 99.62 11.18 2.13e+00 2.20e-01 2.75e+01 angle pdb=" O ASP I1180 " pdb=" C ASP I1180 " pdb=" N GLU I1181 " ideal model delta sigma weight residual 122.68 117.08 5.60 1.17e+00 7.31e-01 2.29e+01 angle pdb=" N VAL G 54 " pdb=" CA VAL G 54 " pdb=" C VAL G 54 " ideal model delta sigma weight residual 113.22 107.57 5.65 1.23e+00 6.61e-01 2.11e+01 angle pdb=" C4' DA A 27 " pdb=" C3' DA A 27 " pdb=" O3' DA A 27 " ideal model delta sigma weight residual 110.00 116.64 -6.64 1.50e+00 4.44e-01 1.96e+01 angle pdb=" O3' DA A 27 " pdb=" C3' DA A 27 " pdb=" C2' DA A 27 " ideal model delta sigma weight residual 111.50 105.03 6.47 1.50e+00 4.44e-01 1.86e+01 ... (remaining 22764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.28: 6951 34.28 - 68.55: 1659 68.55 - 102.83: 28 102.83 - 137.11: 0 137.11 - 171.39: 1 Dihedral angle restraints: 8639 sinusoidal: 5743 harmonic: 2896 Sorted by residual: dihedral pdb=" CA ASP I1146 " pdb=" C ASP I1146 " pdb=" N ALA I1147 " pdb=" CA ALA I1147 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA HIS E 39 " pdb=" C HIS E 39 " pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LEU I1143 " pdb=" C LEU I1143 " pdb=" N TYR I1144 " pdb=" CA TYR I1144 " ideal model delta harmonic sigma weight residual -180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 8636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2218 0.060 - 0.120: 332 0.120 - 0.180: 19 0.180 - 0.240: 3 0.240 - 0.299: 1 Chirality restraints: 2573 Sorted by residual: chirality pdb=" C1' SAM I1501 " pdb=" C2' SAM I1501 " pdb=" N9 SAM I1501 " pdb=" O4' SAM I1501 " both_signs ideal model delta sigma weight residual False 2.30 2.60 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA LYS D 31 " pdb=" N LYS D 31 " pdb=" C LYS D 31 " pdb=" CB LYS D 31 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA SER G 113 " pdb=" N SER G 113 " pdb=" C SER G 113 " pdb=" CB SER G 113 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2570 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE I1076 " -0.013 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ILE I1076 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE I1076 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS I1077 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR I1261 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C TYR I1261 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR I1261 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN I1262 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I1180 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C ASP I1180 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP I1180 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU I1181 " 0.013 2.00e-02 2.50e+03 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 208 2.61 - 3.18: 11844 3.18 - 3.75: 24033 3.75 - 4.33: 33881 4.33 - 4.90: 48996 Nonbonded interactions: 118962 Sorted by model distance: nonbonded pdb=" N2 DG A 26 " pdb=" N3 DT K 163 " model vdw 2.037 3.200 nonbonded pdb=" NZ LYS G 119 " pdb=" OE2 GLU I1111 " model vdw 2.114 3.120 nonbonded pdb=" C2 DA A 27 " pdb=" O2 DC K 162 " model vdw 2.151 3.340 nonbonded pdb=" N1 DA A 27 " pdb=" O2 DC K 162 " model vdw 2.186 3.120 nonbonded pdb=" OP1 DC K 165 " pdb=" NZ LYS I1074 " model vdw 2.188 3.120 ... (remaining 118957 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 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and ((resid 20 and (name N or name CA or name C or name O or name CB \ )) or resid 21 through 101)) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 27 through 121) } ncs_group { reference = chain 'E' selection = (chain 'M' and resid 37 through 134) } 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=0.93 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.620 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 : 0.009 0.545 15801 Z= 0.383 Angle : 0.859 34.757 22781 Z= 0.462 Chirality : 0.042 0.299 2573 Planarity : 0.004 0.050 1730 Dihedral : 27.668 171.385 6773 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 1.56 % Allowed : 4.80 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -5.14 (0.19), residues: 969 helix: -3.06 (0.16), residues: 522 sheet: -4.28 (0.88), residues: 16 loop : -3.80 (0.21), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I1220 TYR 0.015 0.002 TYR H 118 PHE 0.011 0.002 PHE H 67 TRP 0.004 0.001 TRP I1157 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00743 (15791) covalent geometry : angle 0.75187 (22769) hydrogen bonds : bond 0.17114 ( 588) hydrogen bonds : angle 6.25945 ( 1444) metal coordination : bond 0.21894 ( 10) metal coordination : angle 18.08390 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.388 Fit side-chains REVERT: M 79 LYS cc_start: 0.8761 (tttt) cc_final: 0.8463 (tttp) REVERT: B 35 ARG cc_start: 0.8748 (mtp85) cc_final: 0.8416 (mtt-85) REVERT: D 110 GLU cc_start: 0.8887 (tp30) cc_final: 0.8532 (tp30) REVERT: F 25 ASN cc_start: 0.8638 (m-40) cc_final: 0.8365 (m-40) REVERT: G 75 LYS cc_start: 0.8843 (mttm) cc_final: 0.8640 (mttt) REVERT: H 28 LYS cc_start: 0.7062 (ptmm) cc_final: 0.6534 (ttmm) REVERT: H 39 TYR cc_start: 0.7972 (t80) cc_final: 0.7747 (t80) REVERT: H 65 ASP cc_start: 0.8785 (t70) cc_final: 0.8494 (t0) REVERT: H 105 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8719 (ttmt) REVERT: I 1073 TYR cc_start: 0.7178 (p90) cc_final: 0.6888 (p90) REVERT: I 1222 MET cc_start: 0.7350 (mmm) cc_final: 0.6233 (mmm) outliers start: 13 outliers final: 4 residues processed: 159 average time/residue: 0.2025 time to fit residues: 42.0212 Evaluate side-chains 114 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain I residue 1200 TYR Chi-restraints excluded: chain I residue 1201 MET Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN E 68 GLN F 75 HIS G 38 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 106 HIS ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1137 GLN I1217 ASN I1229 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.148589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094274 restraints weight = 27786.469| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.91 r_work: 0.2875 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15801 Z= 0.209 Angle : 0.644 18.481 22781 Z= 0.355 Chirality : 0.037 0.174 2573 Planarity : 0.004 0.052 1730 Dihedral : 30.615 171.540 4818 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.08 % Allowed : 11.75 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.70 (0.23), residues: 969 helix: -1.72 (0.20), residues: 528 sheet: -4.11 (0.88), residues: 16 loop : -3.36 (0.23), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.022 0.002 TYR I1261 PHE 0.010 0.001 PHE E 78 TRP 0.007 0.002 TRP I1157 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00479 (15791) covalent geometry : angle 0.60858 (22769) hydrogen bonds : bond 0.05801 ( 588) hydrogen bonds : angle 3.01013 ( 1444) metal coordination : bond 0.00987 ( 10) metal coordination : angle 9.14674 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.410 Fit side-chains REVERT: M 79 LYS cc_start: 0.8900 (tttt) cc_final: 0.8574 (tttm) REVERT: B 35 ARG cc_start: 0.8947 (mtp85) cc_final: 0.8732 (mtt-85) REVERT: D 110 GLU cc_start: 0.9197 (tp30) cc_final: 0.8882 (tp30) REVERT: G 75 LYS cc_start: 0.9040 (mttm) cc_final: 0.8825 (mttt) REVERT: H 39 TYR cc_start: 0.8647 (t80) cc_final: 0.8425 (t80) REVERT: H 65 ASP cc_start: 0.9147 (t70) cc_final: 0.8877 (t0) REVERT: I 1169 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6637 (mm-30) REVERT: I 1174 TYR cc_start: 0.8499 (t80) cc_final: 0.8271 (t80) REVERT: I 1222 MET cc_start: 0.7633 (mmm) cc_final: 0.6328 (mmm) outliers start: 9 outliers final: 8 residues processed: 131 average time/residue: 0.1758 time to fit residues: 31.3044 Evaluate side-chains 122 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 79 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS I1135 GLN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.148839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.094027 restraints weight = 27980.969| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.02 r_work: 0.2881 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15801 Z= 0.186 Angle : 0.596 15.306 22781 Z= 0.334 Chirality : 0.036 0.140 2573 Planarity : 0.004 0.054 1730 Dihedral : 30.572 173.211 4813 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.16 % Allowed : 12.83 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.94 (0.24), residues: 969 helix: -1.06 (0.22), residues: 527 sheet: -3.91 (0.86), residues: 16 loop : -3.05 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I1190 TYR 0.017 0.001 TYR I1261 PHE 0.021 0.002 PHE I1170 TRP 0.008 0.002 TRP I1157 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00425 (15791) covalent geometry : angle 0.56755 (22769) hydrogen bonds : bond 0.05432 ( 588) hydrogen bonds : angle 2.79111 ( 1444) metal coordination : bond 0.00856 ( 10) metal coordination : angle 7.97093 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.425 Fit side-chains REVERT: M 79 LYS cc_start: 0.8878 (tttt) cc_final: 0.8546 (tttm) REVERT: B 35 ARG cc_start: 0.8947 (mtp85) cc_final: 0.8744 (mtt-85) REVERT: D 110 GLU cc_start: 0.9211 (tp30) cc_final: 0.8914 (tp30) REVERT: G 75 LYS cc_start: 0.9061 (mttm) cc_final: 0.8854 (mttt) REVERT: H 39 TYR cc_start: 0.8712 (t80) cc_final: 0.8453 (t80) REVERT: H 65 ASP cc_start: 0.9142 (t70) cc_final: 0.8876 (t0) REVERT: I 1169 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6606 (mm-30) REVERT: I 1193 GLU cc_start: 0.5485 (OUTLIER) cc_final: 0.5070 (mm-30) REVERT: I 1219 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6404 (m) REVERT: I 1222 MET cc_start: 0.7524 (mmm) cc_final: 0.6232 (mmm) outliers start: 18 outliers final: 13 residues processed: 131 average time/residue: 0.1743 time to fit residues: 31.0459 Evaluate side-chains 126 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1112 SER Chi-restraints excluded: chain I residue 1188 ILE Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1219 SER Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 0.0470 chunk 57 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 126 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 44 optimal weight: 0.4980 chunk 46 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN I1066 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.152419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098408 restraints weight = 28270.778| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.99 r_work: 0.2960 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15801 Z= 0.130 Angle : 0.531 12.352 22781 Z= 0.305 Chirality : 0.033 0.132 2573 Planarity : 0.004 0.060 1730 Dihedral : 30.158 177.231 4813 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.84 % Allowed : 15.11 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.98 (0.26), residues: 969 helix: -0.28 (0.23), residues: 530 sheet: -3.23 (0.86), residues: 16 loop : -2.63 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 30 TYR 0.012 0.001 TYR I1218 PHE 0.011 0.001 PHE I1170 TRP 0.009 0.001 TRP I1157 HIS 0.005 0.001 HIS I1075 Details of bonding type rmsd covalent geometry : bond 0.00271 (15791) covalent geometry : angle 0.51402 (22769) hydrogen bonds : bond 0.04172 ( 588) hydrogen bonds : angle 2.26063 ( 1444) metal coordination : bond 0.00655 ( 10) metal coordination : angle 5.89721 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.429 Fit side-chains REVERT: M 79 LYS cc_start: 0.8803 (tttt) cc_final: 0.8558 (tttm) REVERT: C 91 GLU cc_start: 0.7856 (tp30) cc_final: 0.7635 (mm-30) REVERT: D 110 GLU cc_start: 0.9187 (tp30) cc_final: 0.8893 (tp30) REVERT: E 129 ARG cc_start: 0.8180 (ttt-90) cc_final: 0.7753 (tpt90) REVERT: G 75 LYS cc_start: 0.9042 (mttm) cc_final: 0.8833 (mttt) REVERT: H 39 TYR cc_start: 0.8616 (t80) cc_final: 0.8374 (t80) REVERT: H 65 ASP cc_start: 0.9048 (t70) cc_final: 0.8716 (t0) REVERT: I 1193 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.5163 (mm-30) REVERT: I 1222 MET cc_start: 0.7569 (mmm) cc_final: 0.6441 (mmm) outliers start: 7 outliers final: 4 residues processed: 127 average time/residue: 0.1786 time to fit residues: 30.5997 Evaluate side-chains 116 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1112 SER Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 45 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.148353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.093201 restraints weight = 28097.106| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.00 r_work: 0.2867 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15801 Z= 0.236 Angle : 0.599 11.411 22781 Z= 0.337 Chirality : 0.037 0.148 2573 Planarity : 0.004 0.055 1730 Dihedral : 30.593 177.852 4807 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.40 % Allowed : 15.23 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.11 (0.26), residues: 969 helix: -0.42 (0.23), residues: 529 sheet: -2.78 (0.96), residues: 16 loop : -2.65 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 39 TYR 0.014 0.002 TYR H 118 PHE 0.010 0.002 PHE D 62 TRP 0.005 0.001 TRP I1157 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00547 (15791) covalent geometry : angle 0.58019 (22769) hydrogen bonds : bond 0.05825 ( 588) hydrogen bonds : angle 2.75691 ( 1444) metal coordination : bond 0.00917 ( 10) metal coordination : angle 6.46913 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.412 Fit side-chains REVERT: M 79 LYS cc_start: 0.8899 (tttt) cc_final: 0.8578 (tttm) REVERT: C 91 GLU cc_start: 0.8072 (tp30) cc_final: 0.7869 (mm-30) REVERT: D 110 GLU cc_start: 0.9198 (tp30) cc_final: 0.8926 (tp30) REVERT: H 39 TYR cc_start: 0.8798 (t80) cc_final: 0.8524 (t80) REVERT: H 65 ASP cc_start: 0.9147 (t70) cc_final: 0.8878 (t0) REVERT: I 1193 GLU cc_start: 0.5519 (OUTLIER) cc_final: 0.5223 (mm-30) REVERT: I 1219 SER cc_start: 0.6929 (OUTLIER) cc_final: 0.6354 (m) REVERT: I 1222 MET cc_start: 0.7554 (mmm) cc_final: 0.6459 (mmm) outliers start: 20 outliers final: 15 residues processed: 126 average time/residue: 0.1650 time to fit residues: 28.5198 Evaluate side-chains 121 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1175 VAL Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1219 SER Chi-restraints excluded: chain I residue 1232 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.149990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.095128 restraints weight = 27759.009| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.93 r_work: 0.2898 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15801 Z= 0.160 Angle : 0.546 11.168 22781 Z= 0.311 Chirality : 0.034 0.137 2573 Planarity : 0.004 0.054 1730 Dihedral : 30.388 177.451 4807 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.68 % Allowed : 17.39 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.71 (0.26), residues: 969 helix: -0.09 (0.23), residues: 533 sheet: -2.50 (0.98), residues: 16 loop : -2.51 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I1190 TYR 0.013 0.001 TYR I1218 PHE 0.013 0.001 PHE I1221 TRP 0.005 0.001 TRP I1157 HIS 0.005 0.001 HIS I1075 Details of bonding type rmsd covalent geometry : bond 0.00359 (15791) covalent geometry : angle 0.53020 (22769) hydrogen bonds : bond 0.04836 ( 588) hydrogen bonds : angle 2.50327 ( 1444) metal coordination : bond 0.00747 ( 10) metal coordination : angle 5.69867 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.444 Fit side-chains REVERT: M 79 LYS cc_start: 0.8852 (tttt) cc_final: 0.8537 (tttm) REVERT: C 91 GLU cc_start: 0.7988 (tp30) cc_final: 0.7737 (mm-30) REVERT: D 110 GLU cc_start: 0.9192 (tp30) cc_final: 0.8916 (tp30) REVERT: H 39 TYR cc_start: 0.8717 (t80) cc_final: 0.8461 (t80) REVERT: H 65 ASP cc_start: 0.9122 (t70) cc_final: 0.8844 (t0) REVERT: I 1193 GLU cc_start: 0.5508 (OUTLIER) cc_final: 0.5230 (mm-30) REVERT: I 1219 SER cc_start: 0.6993 (OUTLIER) cc_final: 0.6299 (m) REVERT: I 1222 MET cc_start: 0.7670 (mmm) cc_final: 0.6544 (mmm) outliers start: 14 outliers final: 11 residues processed: 121 average time/residue: 0.1681 time to fit residues: 27.8546 Evaluate side-chains 121 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1175 VAL Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1219 SER Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 99 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.151362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096980 restraints weight = 27917.385| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.94 r_work: 0.2933 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15801 Z= 0.134 Angle : 0.524 10.011 22781 Z= 0.302 Chirality : 0.033 0.131 2573 Planarity : 0.004 0.051 1730 Dihedral : 30.205 178.860 4807 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.80 % Allowed : 17.27 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.16 (0.27), residues: 969 helix: 0.39 (0.23), residues: 529 sheet: -2.30 (0.92), residues: 18 loop : -2.28 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I1190 TYR 0.009 0.001 TYR I1261 PHE 0.016 0.001 PHE I1283 TRP 0.007 0.001 TRP I1157 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00289 (15791) covalent geometry : angle 0.51184 (22769) hydrogen bonds : bond 0.04386 ( 588) hydrogen bonds : angle 2.32344 ( 1444) metal coordination : bond 0.00648 ( 10) metal coordination : angle 4.97317 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.427 Fit side-chains REVERT: M 79 LYS cc_start: 0.8829 (tttt) cc_final: 0.8537 (tttm) REVERT: C 91 GLU cc_start: 0.7934 (tp30) cc_final: 0.7607 (mm-30) REVERT: D 57 SER cc_start: 0.9338 (t) cc_final: 0.9128 (m) REVERT: D 110 GLU cc_start: 0.9189 (tp30) cc_final: 0.8919 (tp30) REVERT: H 39 TYR cc_start: 0.8668 (t80) cc_final: 0.8448 (t80) REVERT: H 65 ASP cc_start: 0.9105 (t70) cc_final: 0.8833 (t0) REVERT: I 1193 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.5018 (mm-30) REVERT: I 1219 SER cc_start: 0.6782 (OUTLIER) cc_final: 0.5950 (m) REVERT: I 1221 PHE cc_start: 0.7726 (m-80) cc_final: 0.7427 (m-10) REVERT: I 1222 MET cc_start: 0.7721 (mmm) cc_final: 0.6555 (mmm) outliers start: 15 outliers final: 12 residues processed: 126 average time/residue: 0.1638 time to fit residues: 28.0835 Evaluate side-chains 123 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1175 VAL Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1219 SER Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 125 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 117 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 0.0050 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 113 HIS F 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.153172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.098976 restraints weight = 28209.882| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.01 r_work: 0.2970 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15801 Z= 0.126 Angle : 0.512 9.175 22781 Z= 0.296 Chirality : 0.032 0.129 2573 Planarity : 0.004 0.052 1730 Dihedral : 29.994 179.476 4807 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.68 % Allowed : 17.75 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.55 (0.27), residues: 969 helix: 0.91 (0.24), residues: 531 sheet: -1.99 (0.97), residues: 18 loop : -2.04 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I1190 TYR 0.009 0.001 TYR I1261 PHE 0.032 0.001 PHE I1170 TRP 0.007 0.001 TRP I1157 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00268 (15791) covalent geometry : angle 0.50398 (22769) hydrogen bonds : bond 0.04055 ( 588) hydrogen bonds : angle 2.15893 ( 1444) metal coordination : bond 0.00562 ( 10) metal coordination : angle 3.96592 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.415 Fit side-chains REVERT: M 79 LYS cc_start: 0.8795 (tttt) cc_final: 0.8574 (tttm) REVERT: C 91 GLU cc_start: 0.7906 (tp30) cc_final: 0.7541 (mm-30) REVERT: D 56 MET cc_start: 0.8500 (tpp) cc_final: 0.8195 (tpp) REVERT: D 110 GLU cc_start: 0.9183 (tp30) cc_final: 0.8903 (tp30) REVERT: E 129 ARG cc_start: 0.8177 (ttt-90) cc_final: 0.7752 (tpt90) REVERT: H 39 TYR cc_start: 0.8598 (t80) cc_final: 0.8374 (t80) REVERT: H 65 ASP cc_start: 0.9033 (t70) cc_final: 0.8798 (t0) REVERT: H 68 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8259 (mt-10) REVERT: I 1193 GLU cc_start: 0.5394 (OUTLIER) cc_final: 0.5061 (mm-30) REVERT: I 1219 SER cc_start: 0.7015 (OUTLIER) cc_final: 0.6219 (m) REVERT: I 1221 PHE cc_start: 0.7585 (m-80) cc_final: 0.7325 (m-10) REVERT: I 1222 MET cc_start: 0.7621 (mmm) cc_final: 0.6656 (mmm) outliers start: 14 outliers final: 10 residues processed: 122 average time/residue: 0.1650 time to fit residues: 27.7817 Evaluate side-chains 122 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1175 VAL Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1219 SER Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 59 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 74 optimal weight: 30.0000 chunk 60 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 HIS I1135 GLN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.152108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097588 restraints weight = 28440.398| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.00 r_work: 0.2940 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15801 Z= 0.143 Angle : 0.517 9.526 22781 Z= 0.297 Chirality : 0.032 0.136 2573 Planarity : 0.004 0.052 1730 Dihedral : 30.046 179.150 4807 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.04 % Allowed : 17.03 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.45 (0.27), residues: 969 helix: 1.00 (0.24), residues: 531 sheet: -1.91 (1.03), residues: 18 loop : -2.00 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I1190 TYR 0.007 0.001 TYR I1261 PHE 0.018 0.001 PHE I1170 TRP 0.005 0.001 TRP I1157 HIS 0.003 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00317 (15791) covalent geometry : angle 0.50835 (22769) hydrogen bonds : bond 0.04382 ( 588) hydrogen bonds : angle 2.22815 ( 1444) metal coordination : bond 0.00616 ( 10) metal coordination : angle 4.05104 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.423 Fit side-chains REVERT: M 79 LYS cc_start: 0.8802 (tttt) cc_final: 0.8551 (tttm) REVERT: C 91 GLU cc_start: 0.7959 (tp30) cc_final: 0.7596 (mm-30) REVERT: D 28 LYS cc_start: 0.4600 (OUTLIER) cc_final: 0.4163 (pttm) REVERT: D 56 MET cc_start: 0.8590 (tpp) cc_final: 0.8286 (tpp) REVERT: D 110 GLU cc_start: 0.9200 (tp30) cc_final: 0.8899 (tp30) REVERT: E 129 ARG cc_start: 0.8208 (ttt-90) cc_final: 0.7770 (tpt90) REVERT: F 18 HIS cc_start: 0.6654 (OUTLIER) cc_final: 0.6274 (t-90) REVERT: H 39 TYR cc_start: 0.8642 (t80) cc_final: 0.8412 (t80) REVERT: H 65 ASP cc_start: 0.9090 (t70) cc_final: 0.8761 (t0) REVERT: I 1193 GLU cc_start: 0.5398 (OUTLIER) cc_final: 0.5037 (mm-30) REVERT: I 1219 SER cc_start: 0.7038 (OUTLIER) cc_final: 0.6330 (m) REVERT: I 1221 PHE cc_start: 0.7620 (m-80) cc_final: 0.7342 (m-10) REVERT: I 1222 MET cc_start: 0.7630 (mmm) cc_final: 0.6627 (mmm) outliers start: 17 outliers final: 12 residues processed: 124 average time/residue: 0.1672 time to fit residues: 28.4369 Evaluate side-chains 124 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1175 VAL Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1219 SER Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 117 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.151983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097387 restraints weight = 28251.822| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.99 r_work: 0.2938 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15801 Z= 0.144 Angle : 0.524 9.300 22781 Z= 0.300 Chirality : 0.033 0.136 2573 Planarity : 0.004 0.053 1730 Dihedral : 30.055 179.299 4807 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.04 % Allowed : 17.03 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.38 (0.27), residues: 969 helix: 1.09 (0.23), residues: 530 sheet: -1.97 (1.04), residues: 18 loop : -2.00 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I1190 TYR 0.008 0.001 TYR I1200 PHE 0.016 0.001 PHE I1170 TRP 0.005 0.001 TRP I1157 HIS 0.005 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00321 (15791) covalent geometry : angle 0.51542 (22769) hydrogen bonds : bond 0.04445 ( 588) hydrogen bonds : angle 2.25989 ( 1444) metal coordination : bond 0.00618 ( 10) metal coordination : angle 4.07900 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.424 Fit side-chains REVERT: M 79 LYS cc_start: 0.8807 (tttt) cc_final: 0.8545 (tttm) REVERT: C 91 GLU cc_start: 0.7937 (tp30) cc_final: 0.7602 (mm-30) REVERT: D 28 LYS cc_start: 0.4684 (OUTLIER) cc_final: 0.4280 (pttm) REVERT: D 56 MET cc_start: 0.8647 (tpp) cc_final: 0.8359 (tpp) REVERT: D 110 GLU cc_start: 0.9192 (tp30) cc_final: 0.8896 (tp30) REVERT: E 129 ARG cc_start: 0.8205 (ttt-90) cc_final: 0.7785 (tpt90) REVERT: F 18 HIS cc_start: 0.6324 (OUTLIER) cc_final: 0.6073 (t-90) REVERT: H 39 TYR cc_start: 0.8644 (t80) cc_final: 0.8402 (t80) REVERT: H 65 ASP cc_start: 0.9088 (t70) cc_final: 0.8753 (t0) REVERT: I 1094 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6496 (tm-30) REVERT: I 1193 GLU cc_start: 0.5548 (OUTLIER) cc_final: 0.5205 (mm-30) REVERT: I 1219 SER cc_start: 0.7042 (OUTLIER) cc_final: 0.6335 (m) REVERT: I 1221 PHE cc_start: 0.7620 (m-80) cc_final: 0.7328 (m-10) REVERT: I 1222 MET cc_start: 0.7642 (mmm) cc_final: 0.6627 (mmm) outliers start: 17 outliers final: 12 residues processed: 123 average time/residue: 0.1683 time to fit residues: 28.1342 Evaluate side-chains 126 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1094 GLU Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1175 VAL Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1219 SER Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 88 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.152149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097590 restraints weight = 28173.609| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.98 r_work: 0.2945 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15801 Z= 0.137 Angle : 0.513 8.991 22781 Z= 0.296 Chirality : 0.032 0.135 2573 Planarity : 0.004 0.052 1730 Dihedral : 30.039 179.254 4807 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.80 % Allowed : 17.15 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.28 (0.27), residues: 969 helix: 1.19 (0.24), residues: 529 sheet: -2.00 (1.05), residues: 18 loop : -1.98 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 30 TYR 0.008 0.001 TYR I1261 PHE 0.014 0.001 PHE I1170 TRP 0.005 0.001 TRP I1157 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00301 (15791) covalent geometry : angle 0.50524 (22769) hydrogen bonds : bond 0.04392 ( 588) hydrogen bonds : angle 2.23404 ( 1444) metal coordination : bond 0.00600 ( 10) metal coordination : angle 3.98644 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4191.76 seconds wall clock time: 72 minutes 6.66 seconds (4326.66 seconds total)