Starting phenix.real_space_refine on Sun Sep 13 15:15:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7crr_30457/09_2026/7crr_30457.cif Found real_map, /net/cci-nas-00/data/ceres_data/7crr_30457/09_2026/7crr_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7crr_30457/09_2026/7crr_30457.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7crr_30457/09_2026/7crr_30457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7crr_30457/09_2026/7crr_30457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7crr_30457/09_2026/7crr_30457.map" model { file = "/net/cci-nas-00/data/ceres_data/7crr_30457/09_2026/7crr_30457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7crr_30457/09_2026/7crr_30457.cif" } 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-2.2.1-6174/lib/python3.11/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: 2.49, per 1000 atoms: 0.17 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: 0.91 Conformation dependent library (CDL) restraints added in 335.9 milliseconds 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: 1.89 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: 2.37 Time building geometry restraints manager: 1.27 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=" C3' DC A 90 " pdb=" O3' DC A 90 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.28e+01 bond pdb=" C3' DA A 110 " pdb=" O3' DA A 110 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.10e+01 bond pdb=" C3' DG A 91 " pdb=" O3' DG A 91 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" C3' DG K 89 " pdb=" O3' DG K 89 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.95e+00 bond pdb=" C3' DG K 90 " pdb=" O3' DG K 90 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.85e+00 ... (remaining 15786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 22093 2.24 - 4.47: 641 4.47 - 6.71: 27 6.71 - 8.94: 6 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=" N3 DT A 135 " pdb=" C4 DT A 135 " pdb=" O4 DT A 135 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N3 DT K 103 " pdb=" C4 DT K 103 " pdb=" O4 DT K 103 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 ... (remaining 22764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.28: 6929 34.28 - 68.55: 1649 68.55 - 102.83: 28 102.83 - 137.11: 0 137.11 - 171.39: 1 Dihedral angle restraints: 8607 sinusoidal: 5711 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 8604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2027 0.060 - 0.120: 501 0.120 - 0.180: 40 0.180 - 0.240: 4 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.700 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.010 0.545 15801 Z= 0.653 Angle : 0.978 34.757 22781 Z= 0.731 Chirality : 0.050 0.299 2573 Planarity : 0.004 0.050 1730 Dihedral : 27.641 171.385 6741 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 are 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/Z covalent geometry : bond 0.00837 / 0.63 (15791) covalent geometry : angle 0.88572 / 0.73 (22769) hydrogen bonds : bond 0.17114 / 12.26 ( 588) hydrogen bonds : angle 6.25945 / 4.47 ( 1444) metal coordination : bond 0.21894 / 12.06 ( 10) metal coordination : angle 18.08390 / 11.21 ( 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 : 0.398 Fit side-chains revert: symmetry clash REVERT: M 79 LYS cc_start: 0.8761 (tttt) cc_final: 0.8464 (tttp) REVERT: D 110 GLU cc_start: 0.8887 (tp30) cc_final: 0.8531 (tp30) REVERT: F 25 ASN cc_start: 0.8638 (m-40) cc_final: 0.8363 (m-40) REVERT: G 75 LYS cc_start: 0.8843 (mttm) cc_final: 0.8639 (mttt) REVERT: H 28 LYS cc_start: 0.7062 (ptmm) cc_final: 0.6539 (ttmm) REVERT: H 39 TYR cc_start: 0.7972 (t80) cc_final: 0.7751 (t80) REVERT: H 65 ASP cc_start: 0.8785 (t70) cc_final: 0.8495 (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: 0.6889 (p90) REVERT: I 1222 MET cc_start: 0.7350 (mmm) cc_final: 0.6232 (mmm) outliers start: 13 outliers final: 4 residues processed: 159 average time/residue: 0.1730 time to fit residues: 36.2106 Evaluate side-chains 112 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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: 20.0000 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: 20.0000 chunk 77 optimal weight: 40.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 50.0000 chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN E 68 GLN G 38 ASN G 84 GLN G 104 GLN H 44 GLN H 106 HIS ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1137 GLN I1229 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.148560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.094068 restraints weight = 27676.659| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.88 r_work: 0.2866 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15801 Z= 0.196 Angle : 0.725 18.779 22781 Z= 0.394 Chirality : 0.049 0.268 2573 Planarity : 0.005 0.052 1730 Dihedral : 30.840 172.425 4786 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.96 % Allowed : 11.87 % 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 are not related in a simple way. whole: -3.81 (0.23), residues: 969 helix: -1.80 (0.21), residues: 524 sheet: -4.04 (0.90), residues: 16 loop : -3.42 (0.23), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.030 0.002 TYR I1261 PHE 0.010 0.002 PHE I1259 TRP 0.007 0.002 TRP I1235 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 (15791) covalent geometry : angle 0.68765 / 0.39 (22769) hydrogen bonds : bond 0.07218 / 4.75 ( 588) hydrogen bonds : angle 3.20877 / 2.20 ( 1444) metal coordination : bond 0.01004 / 0.74 ( 10) metal coordination : angle 10.02305 / 5.65 ( 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 128 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.312 Fit side-chains REVERT: M 79 LYS cc_start: 0.8903 (tttt) cc_final: 0.8568 (tttp) REVERT: M 94 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8162 (tt0) REVERT: D 110 GLU cc_start: 0.9198 (tp30) cc_final: 0.8935 (tp30) REVERT: G 75 LYS cc_start: 0.9020 (mttm) cc_final: 0.8804 (mttt) REVERT: H 28 LYS cc_start: 0.7056 (ptmm) cc_final: 0.6513 (ttmm) REVERT: H 65 ASP cc_start: 0.9079 (t70) cc_final: 0.8827 (t0) REVERT: H 105 LYS cc_start: 0.9085 (ttpt) cc_final: 0.8885 (ttmt) REVERT: I 1222 MET cc_start: 0.7657 (mmm) cc_final: 0.6326 (mmm) outliers start: 8 outliers final: 8 residues processed: 128 average time/residue: 0.1434 time to fit residues: 25.7947 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 : 0.355 ------------------------------------------------------------------------------- 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 I residue 1077 LYS Chi-restraints excluded: chain I residue 1203 THR 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: 0.9980 chunk 39 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 79 optimal weight: 30.0000 chunk 56 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS F 75 HIS ** 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 = 0.148817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094270 restraints weight = 28018.837| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.94 r_work: 0.2882 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15801 Z= 0.185 Angle : 0.662 17.222 22781 Z= 0.366 Chirality : 0.045 0.271 2573 Planarity : 0.004 0.054 1730 Dihedral : 30.899 174.029 4781 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 1.80 % Allowed : 13.07 % Favored : 85.13 % 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 are not related in a simple way. whole: -3.12 (0.24), residues: 969 helix: -1.20 (0.22), residues: 526 sheet: -3.77 (0.90), residues: 16 loop : -3.16 (0.24), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 30 TYR 0.019 0.002 TYR I1261 PHE 0.021 0.002 PHE I1170 TRP 0.008 0.002 TRP I1157 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (15791) covalent geometry : angle 0.63146 / 0.36 (22769) hydrogen bonds : bond 0.06238 / 4.09 ( 588) hydrogen bonds : angle 2.91207 / 1.96 ( 1444) metal coordination : bond 0.00877 / 0.55 ( 10) metal coordination : angle 8.67506 / 4.84 ( 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 129 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.396 Fit side-chains REVERT: M 79 LYS cc_start: 0.8873 (tttt) cc_final: 0.8533 (tttm) REVERT: D 110 GLU cc_start: 0.9194 (tp30) cc_final: 0.8903 (tp30) REVERT: G 75 LYS cc_start: 0.9051 (mttm) cc_final: 0.8839 (mttt) REVERT: H 65 ASP cc_start: 0.9122 (t70) cc_final: 0.8865 (t0) REVERT: H 105 LYS cc_start: 0.8967 (ttpt) cc_final: 0.8760 (ttmm) REVERT: I 1135 GLN cc_start: 0.8588 (mt0) cc_final: 0.8303 (mt0) REVERT: I 1222 MET cc_start: 0.7561 (mmm) cc_final: 0.6352 (mmm) outliers start: 15 outliers final: 13 residues processed: 124 average time/residue: 0.1375 time to fit residues: 23.7127 Evaluate side-chains 124 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 D residue 119 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 113 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 126 optimal weight: 20.0000 chunk 114 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 76 optimal weight: 50.0000 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.0970 chunk 61 optimal weight: 0.0980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN I1066 ASN I1217 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.151870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.097736 restraints weight = 28121.274| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.94 r_work: 0.2951 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 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 = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15801 Z= 0.127 Angle : 0.582 14.178 22781 Z= 0.333 Chirality : 0.040 0.271 2573 Planarity : 0.004 0.056 1730 Dihedral : 30.630 176.538 4781 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.08 % Allowed : 14.27 % Favored : 84.65 % 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 are not related in a simple way. whole: -2.28 (0.25), residues: 969 helix: -0.53 (0.23), residues: 533 sheet: -3.20 (0.90), residues: 16 loop : -2.78 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I1190 TYR 0.020 0.001 TYR I1200 PHE 0.013 0.001 PHE I1283 TRP 0.009 0.001 TRP I1157 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.13 (15791) covalent geometry : angle 0.56115 / 0.33 (22769) hydrogen bonds : bond 0.04951 / 3.21 ( 588) hydrogen bonds : angle 2.43397 / 1.62 ( 1444) metal coordination : bond 0.00710 / 0.43 ( 10) metal coordination : angle 6.81226 / 3.61 ( 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 135 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.373 Fit side-chains REVERT: M 79 LYS cc_start: 0.8850 (tttt) cc_final: 0.8570 (tttm) REVERT: M 123 ASP cc_start: 0.8239 (m-30) cc_final: 0.8000 (m-30) REVERT: D 110 GLU cc_start: 0.9197 (tp30) cc_final: 0.8905 (tp30) REVERT: H 43 LYS cc_start: 0.9195 (mmtm) cc_final: 0.8981 (mmtm) REVERT: H 65 ASP cc_start: 0.9069 (t70) cc_final: 0.8774 (t0) REVERT: I 1068 ARG cc_start: 0.4399 (mtm-85) cc_final: 0.4150 (mtm-85) REVERT: I 1169 GLU cc_start: 0.6442 (mm-30) cc_final: 0.6212 (mm-30) REVERT: I 1193 GLU cc_start: 0.5509 (OUTLIER) cc_final: 0.5173 (mm-30) REVERT: I 1219 SER cc_start: 0.7258 (OUTLIER) cc_final: 0.6508 (m) REVERT: I 1221 PHE cc_start: 0.7558 (m-80) cc_final: 0.7319 (m-10) REVERT: I 1222 MET cc_start: 0.7623 (mmm) cc_final: 0.6481 (mmm) outliers start: 9 outliers final: 4 residues processed: 134 average time/residue: 0.1579 time to fit residues: 28.8799 Evaluate side-chains 118 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1219 SER 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: 20.0000 chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 75 optimal weight: 50.0000 chunk 85 optimal weight: 20.0000 chunk 37 optimal weight: 0.0770 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1075 HIS ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.149627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.095041 restraints weight = 28127.150| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.94 r_work: 0.2896 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15801 Z= 0.179 Angle : 0.609 13.637 22781 Z= 0.340 Chirality : 0.043 0.276 2573 Planarity : 0.004 0.053 1730 Dihedral : 30.829 179.932 4779 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.04 % Allowed : 15.83 % Favored : 82.13 % 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 are not related in a simple way. whole: -2.15 (0.26), residues: 969 helix: -0.40 (0.23), residues: 528 sheet: -2.86 (0.84), residues: 18 loop : -2.74 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I1190 TYR 0.011 0.001 TYR I1261 PHE 0.009 0.001 PHE H 67 TRP 0.006 0.002 TRP I1157 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (15791) covalent geometry : angle 0.58839 / 0.34 (22769) hydrogen bonds : bond 0.05711 / 3.73 ( 588) hydrogen bonds : angle 2.62534 / 1.75 ( 1444) metal coordination : bond 0.00815 / 0.54 ( 10) metal coordination : angle 6.82394 / 3.84 ( 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 128 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.374 Fit side-chains REVERT: M 79 LYS cc_start: 0.8859 (tttt) cc_final: 0.8550 (tttm) REVERT: D 110 GLU cc_start: 0.9214 (tp30) cc_final: 0.8898 (tp30) REVERT: H 43 LYS cc_start: 0.9217 (mmtm) cc_final: 0.8994 (mmtm) REVERT: H 65 ASP cc_start: 0.9109 (t70) cc_final: 0.8806 (t0) REVERT: I 1068 ARG cc_start: 0.4143 (mtm-85) cc_final: 0.3931 (mtm-85) REVERT: I 1169 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6336 (mm-30) REVERT: I 1193 GLU cc_start: 0.5507 (OUTLIER) cc_final: 0.5220 (mm-30) REVERT: I 1219 SER cc_start: 0.7243 (OUTLIER) cc_final: 0.6567 (m) REVERT: I 1221 PHE cc_start: 0.7556 (m-80) cc_final: 0.7308 (m-10) REVERT: I 1222 MET cc_start: 0.7663 (mmm) cc_final: 0.6534 (mmm) outliers start: 17 outliers final: 13 residues processed: 123 average time/residue: 0.1522 time to fit residues: 25.8962 Evaluate side-chains 124 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 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 G residue 107 VAL Chi-restraints excluded: chain G residue 119 LYS 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 Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 77 optimal weight: 50.0000 chunk 62 optimal weight: 0.0040 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4041 r_free = 0.4041 target = 0.149026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.093733 restraints weight = 27738.482| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.02 r_work: 0.2871 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 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 = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15801 Z= 0.185 Angle : 0.619 12.738 22781 Z= 0.342 Chirality : 0.043 0.277 2573 Planarity : 0.004 0.052 1730 Dihedral : 30.896 178.884 4779 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.64 % Allowed : 15.95 % Favored : 81.41 % 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 are not related in a simple way. whole: -2.00 (0.26), residues: 969 helix: -0.29 (0.23), residues: 528 sheet: -2.53 (0.94), residues: 16 loop : -2.67 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I1190 TYR 0.012 0.001 TYR H 118 PHE 0.009 0.001 PHE H 67 TRP 0.005 0.001 TRP I1157 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (15791) covalent geometry : angle 0.59909 / 0.34 (22769) hydrogen bonds : bond 0.05866 / 3.81 ( 588) hydrogen bonds : angle 2.69857 / 1.80 ( 1444) metal coordination : bond 0.00871 / 0.59 ( 10) metal coordination : angle 6.74037 / 4.00 ( 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 132 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.388 Fit side-chains REVERT: M 79 LYS cc_start: 0.8886 (tttt) cc_final: 0.8560 (tttm) REVERT: D 110 GLU cc_start: 0.9218 (tp30) cc_final: 0.8925 (tp30) REVERT: H 65 ASP cc_start: 0.9123 (t70) cc_final: 0.8862 (t0) REVERT: I 1193 GLU cc_start: 0.5518 (OUTLIER) cc_final: 0.5228 (mm-30) REVERT: I 1219 SER cc_start: 0.7187 (OUTLIER) cc_final: 0.6486 (m) REVERT: I 1221 PHE cc_start: 0.8016 (m-80) cc_final: 0.7766 (m-10) REVERT: I 1222 MET cc_start: 0.7683 (mmm) cc_final: 0.6591 (mmm) outliers start: 22 outliers final: 18 residues processed: 128 average time/residue: 0.1309 time to fit residues: 23.3066 Evaluate side-chains 125 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 73 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 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 1232 THR 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: 20.0000 chunk 89 optimal weight: 50.0000 chunk 34 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 1 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 30.0000 chunk 101 optimal weight: 30.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4062 r_free = 0.4062 target = 0.150756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.096420 restraints weight = 27864.118| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.97 r_work: 0.2919 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 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 = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15801 Z= 0.131 Angle : 0.569 12.050 22781 Z= 0.322 Chirality : 0.040 0.274 2573 Planarity : 0.004 0.050 1730 Dihedral : 30.717 178.046 4775 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.68 % Allowed : 16.79 % Favored : 81.53 % 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 are not related in a simple way. whole: -1.56 (0.26), residues: 969 helix: 0.06 (0.23), residues: 532 sheet: -2.33 (1.00), residues: 16 loop : -2.48 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I1190 TYR 0.011 0.001 TYR I1200 PHE 0.016 0.001 PHE I1259 TRP 0.005 0.001 TRP I1157 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (15791) covalent geometry : angle 0.55272 / 0.32 (22769) hydrogen bonds : bond 0.05099 / 3.32 ( 588) hydrogen bonds : angle 2.45695 / 1.63 ( 1444) metal coordination : bond 0.00713 / 0.40 ( 10) metal coordination : angle 5.88751 / 3.32 ( 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 120 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.503 Fit side-chains REVERT: M 79 LYS cc_start: 0.8867 (tttt) cc_final: 0.8575 (tttm) REVERT: D 110 GLU cc_start: 0.9206 (tp30) cc_final: 0.8930 (tp30) REVERT: G 84 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8102 (tp-100) REVERT: H 65 ASP cc_start: 0.9091 (t70) cc_final: 0.8823 (t0) REVERT: I 1219 SER cc_start: 0.7016 (OUTLIER) cc_final: 0.6357 (m) REVERT: I 1221 PHE cc_start: 0.7968 (m-80) cc_final: 0.7767 (m-80) REVERT: I 1222 MET cc_start: 0.7676 (mmm) cc_final: 0.6630 (mmm) outliers start: 14 outliers final: 9 residues processed: 117 average time/residue: 0.1642 time to fit residues: 26.6516 Evaluate side-chains 117 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1112 SER Chi-restraints excluded: chain I residue 1175 VAL 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: 3.9990 chunk 15 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4060 r_free = 0.4060 target = 0.150543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.096196 restraints weight = 27970.927| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.91 r_work: 0.2921 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15801 Z= 0.138 Angle : 0.570 11.460 22781 Z= 0.322 Chirality : 0.040 0.274 2573 Planarity : 0.004 0.052 1730 Dihedral : 30.711 176.585 4775 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % 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 are not related in a simple way. whole: -1.38 (0.27), residues: 969 helix: 0.23 (0.23), residues: 529 sheet: -2.23 (1.04), residues: 16 loop : -2.41 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I1190 TYR 0.015 0.001 TYR G 57 PHE 0.013 0.001 PHE I1259 TRP 0.006 0.001 TRP I1157 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (15791) covalent geometry : angle 0.55518 / 0.32 (22769) hydrogen bonds : bond 0.05178 / 3.37 ( 588) hydrogen bonds : angle 2.49533 / 1.66 ( 1444) metal coordination : bond 0.00730 / 0.43 ( 10) metal coordination : angle 5.69389 / 3.28 ( 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 125 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.402 Fit side-chains REVERT: M 79 LYS cc_start: 0.8865 (tttt) cc_final: 0.8557 (tttm) REVERT: D 110 GLU cc_start: 0.9221 (tp30) cc_final: 0.8925 (tp30) REVERT: G 84 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: H 65 ASP cc_start: 0.9111 (t70) cc_final: 0.8833 (t0) REVERT: I 1094 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6174 (tm-30) REVERT: I 1219 SER cc_start: 0.6978 (OUTLIER) cc_final: 0.6292 (m) REVERT: I 1222 MET cc_start: 0.7670 (mmm) cc_final: 0.6677 (mmm) outliers start: 15 outliers final: 12 residues processed: 121 average time/residue: 0.1580 time to fit residues: 26.6871 Evaluate side-chains 122 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 45 VAL 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 G residue 84 GLN Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1094 GLU Chi-restraints excluded: chain I residue 1112 SER Chi-restraints excluded: chain I residue 1175 VAL 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: 5.9990 chunk 75 optimal weight: 50.0000 chunk 114 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 74 optimal weight: 40.0000 chunk 60 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4058 r_free = 0.4058 target = 0.150386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.095902 restraints weight = 28147.381| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.00 r_work: 0.2903 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15801 Z= 0.149 Angle : 0.578 11.538 22781 Z= 0.325 Chirality : 0.041 0.277 2573 Planarity : 0.004 0.051 1730 Dihedral : 30.716 176.039 4775 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.16 % Allowed : 17.63 % Favored : 80.22 % 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 are not related in a simple way. whole: -1.32 (0.27), residues: 969 helix: 0.30 (0.23), residues: 531 sheet: -2.15 (1.08), residues: 16 loop : -2.42 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.015 0.001 TYR I1073 PHE 0.009 0.001 PHE I1283 TRP 0.005 0.001 TRP I1157 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (15791) covalent geometry : angle 0.56393 / 0.32 (22769) hydrogen bonds : bond 0.05262 / 3.43 ( 588) hydrogen bonds : angle 2.52420 / 1.68 ( 1444) metal coordination : bond 0.00747 / 0.44 ( 10) metal coordination : angle 5.59042 / 3.26 ( 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 125 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.397 Fit side-chains REVERT: M 79 LYS cc_start: 0.8850 (tttt) cc_final: 0.8552 (tttm) REVERT: D 110 GLU cc_start: 0.9220 (tp30) cc_final: 0.8936 (tp30) REVERT: G 84 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: H 65 ASP cc_start: 0.9123 (t70) cc_final: 0.8846 (t0) REVERT: I 1094 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6377 (tm-30) REVERT: I 1219 SER cc_start: 0.7010 (OUTLIER) cc_final: 0.6292 (m) REVERT: I 1222 MET cc_start: 0.7754 (mmm) cc_final: 0.6645 (mmm) outliers start: 18 outliers final: 15 residues processed: 122 average time/residue: 0.1592 time to fit residues: 27.0338 Evaluate side-chains 125 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 45 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 G residue 84 GLN Chi-restraints excluded: chain H residue 39 TYR 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 1175 VAL 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: 20.0000 chunk 82 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 chunk 3 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 79 optimal weight: 30.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4067 r_free = 0.4067 target = 0.151087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096602 restraints weight = 28028.822| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.93 r_work: 0.2929 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15801 Z= 0.124 Angle : 0.559 10.973 22781 Z= 0.317 Chirality : 0.040 0.274 2573 Planarity : 0.004 0.051 1730 Dihedral : 30.671 175.795 4775 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.92 % Allowed : 17.63 % Favored : 80.46 % 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 are not related in a simple way. whole: -1.17 (0.27), residues: 969 helix: 0.43 (0.23), residues: 531 sheet: -2.05 (1.08), residues: 16 loop : -2.38 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 30 TYR 0.011 0.001 TYR G 57 PHE 0.019 0.001 PHE I1283 TRP 0.007 0.001 TRP I1157 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.12 (15791) covalent geometry : angle 0.54548 / 0.32 (22769) hydrogen bonds : bond 0.05048 / 3.30 ( 588) hydrogen bonds : angle 2.44437 / 1.62 ( 1444) metal coordination : bond 0.00670 / 0.38 ( 10) metal coordination : angle 5.39804 / 3.13 ( 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: 16 poor density : 111 time to evaluate : 0.417 Fit side-chains REVERT: M 79 LYS cc_start: 0.8834 (tttt) cc_final: 0.8543 (tttm) REVERT: D 110 GLU cc_start: 0.9211 (tp30) cc_final: 0.8932 (tp30) REVERT: G 84 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8134 (tp-100) REVERT: H 65 ASP cc_start: 0.9091 (t70) cc_final: 0.8778 (t0) REVERT: I 1094 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6209 (tm-30) REVERT: I 1219 SER cc_start: 0.6995 (OUTLIER) cc_final: 0.6237 (m) REVERT: I 1222 MET cc_start: 0.7715 (mmm) cc_final: 0.6631 (mmm) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 0.1584 time to fit residues: 27.4444 Evaluate side-chains 125 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 45 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 G residue 84 GLN Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1094 GLU Chi-restraints excluded: chain I residue 1175 VAL 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: 50.0000 chunk 103 optimal weight: 30.0000 chunk 123 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.151531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096999 restraints weight = 28061.438| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.96 r_work: 0.2929 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15801 Z= 0.123 Angle : 0.550 10.308 22781 Z= 0.314 Chirality : 0.039 0.276 2573 Planarity : 0.004 0.050 1730 Dihedral : 30.608 175.256 4775 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.80 % Allowed : 17.99 % Favored : 80.22 % 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 are not related in a simple way. whole: -0.91 (0.27), residues: 969 helix: 0.66 (0.23), residues: 530 sheet: -2.07 (0.99), residues: 18 loop : -2.27 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.011 0.001 TYR G 57 PHE 0.009 0.001 PHE I1221 TRP 0.006 0.001 TRP I1157 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.12 (15791) covalent geometry : angle 0.53821 / 0.31 (22769) hydrogen bonds : bond 0.04891 / 3.19 ( 588) hydrogen bonds : angle 2.38929 / 1.58 ( 1444) metal coordination : bond 0.00659 / 0.37 ( 10) metal coordination : angle 5.03138 / 2.91 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3775.95 seconds wall clock time: 64 minutes 58.31 seconds (3898.31 seconds total)