Starting phenix.real_space_refine on Fri May 23 12:53:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7crr_30457/05_2025/7crr_30457.cif Found real_map, /net/cci-nas-00/data/ceres_data/7crr_30457/05_2025/7crr_30457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7crr_30457/05_2025/7crr_30457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7crr_30457/05_2025/7crr_30457.map" model { file = "/net/cci-nas-00/data/ceres_data/7crr_30457/05_2025/7crr_30457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7crr_30457/05_2025/7crr_30457.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'ARG:plan': 1, 'NLE:plan-1': 3} 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: {'ARG:plan': 1, 'NLE:plan-1': 2} 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: 8.48, per 1000 atoms: 0.57 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: 4.22 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 6.18 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: 5.63 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2956 1.33 - 1.45: 4947 1.45 - 1.57: 7177 1.57 - 1.69: 670 1.69 - 1.81: 41 Bond restraints: 15791 Sorted by residual: bond pdb=" C8 SAM I1501 " pdb=" N7 SAM I1501 " ideal model delta sigma weight residual 1.298 1.352 -0.054 2.00e-02 2.50e+03 7.32e+00 bond pdb=" C2 SAM I1501 " pdb=" N3 SAM I1501 " ideal model delta sigma weight residual 1.322 1.375 -0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" C2 SAM I1501 " pdb=" N1 SAM I1501 " ideal model delta sigma weight residual 1.329 1.378 -0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" CA LYS I1077 " pdb=" C LYS I1077 " ideal model delta sigma weight residual 1.522 1.552 -0.031 1.32e-02 5.74e+03 5.35e+00 bond pdb=" CA ALA H 114 " pdb=" C ALA H 114 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.38e-02 5.25e+03 5.20e+00 ... (remaining 15786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 22379 2.24 - 4.47: 357 4.47 - 6.71: 27 6.71 - 8.94: 4 8.94 - 11.18: 2 Bond angle restraints: 22769 Sorted by residual: angle pdb=" N LYS D 31 " pdb=" CA LYS D 31 " pdb=" C LYS D 31 " ideal model delta sigma weight residual 110.80 99.62 11.18 2.13e+00 2.20e-01 2.75e+01 angle pdb=" O ASP I1180 " pdb=" C ASP I1180 " pdb=" N GLU I1181 " ideal model delta sigma weight residual 122.68 117.08 5.60 1.17e+00 7.31e-01 2.29e+01 angle pdb=" N VAL G 54 " pdb=" CA VAL G 54 " pdb=" C VAL G 54 " ideal model delta sigma weight residual 113.22 107.57 5.65 1.23e+00 6.61e-01 2.11e+01 angle pdb=" C4' DA A 27 " pdb=" C3' DA A 27 " pdb=" O3' DA A 27 " ideal model delta sigma weight residual 110.00 116.64 -6.64 1.50e+00 4.44e-01 1.96e+01 angle pdb=" O3' DA A 27 " pdb=" C3' DA A 27 " pdb=" C2' DA A 27 " ideal model delta sigma weight residual 111.50 105.03 6.47 1.50e+00 4.44e-01 1.86e+01 ... (remaining 22764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.28: 6951 34.28 - 68.55: 1659 68.55 - 102.83: 28 102.83 - 137.11: 0 137.11 - 171.39: 1 Dihedral angle restraints: 8639 sinusoidal: 5743 harmonic: 2896 Sorted by residual: dihedral pdb=" CA ASP I1146 " pdb=" C ASP I1146 " pdb=" N ALA I1147 " pdb=" CA ALA I1147 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA HIS E 39 " pdb=" C HIS E 39 " pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LEU I1143 " pdb=" C LEU I1143 " pdb=" N TYR I1144 " pdb=" CA TYR I1144 " ideal model delta harmonic sigma weight residual -180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 8636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2218 0.060 - 0.120: 332 0.120 - 0.180: 19 0.180 - 0.240: 3 0.240 - 0.299: 1 Chirality restraints: 2573 Sorted by residual: chirality pdb=" C1' SAM I1501 " pdb=" C2' SAM I1501 " pdb=" N9 SAM I1501 " pdb=" O4' SAM I1501 " both_signs ideal model delta sigma weight residual False 2.30 2.60 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA LYS D 31 " pdb=" N LYS D 31 " pdb=" C LYS D 31 " pdb=" CB LYS D 31 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA SER G 113 " pdb=" N SER G 113 " pdb=" C SER G 113 " pdb=" CB SER G 113 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2570 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE I1076 " -0.013 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ILE I1076 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE I1076 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS I1077 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR I1261 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C TYR I1261 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR I1261 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN I1262 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I1180 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C ASP I1180 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP I1180 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU I1181 " 0.013 2.00e-02 2.50e+03 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 208 2.61 - 3.18: 11844 3.18 - 3.75: 24033 3.75 - 4.33: 33881 4.33 - 4.90: 48996 Nonbonded interactions: 118962 Sorted by model distance: nonbonded pdb=" N2 DG A 26 " pdb=" N3 DT K 163 " model vdw 2.037 3.200 nonbonded pdb=" NZ LYS G 119 " pdb=" OE2 GLU I1111 " model vdw 2.114 3.120 nonbonded pdb=" C2 DA A 27 " pdb=" O2 DC K 162 " model vdw 2.151 3.340 nonbonded pdb=" N1 DA A 27 " pdb=" O2 DC K 162 " model vdw 2.186 3.120 nonbonded pdb=" OP1 DC K 165 " pdb=" NZ LYS I1074 " model vdw 2.188 3.120 ... (remaining 118957 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and ((resid 20 and (name N or name CA or name C or name O or name CB \ )) or resid 21 through 101)) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 27 through 121) } ncs_group { reference = chain 'E' selection = (chain 'M' and resid 37 through 134) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.93 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 42.260 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.545 15801 Z= 0.383 Angle : 0.859 34.757 22781 Z= 0.462 Chirality : 0.042 0.299 2573 Planarity : 0.004 0.050 1730 Dihedral : 27.668 171.385 6773 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 1.56 % Allowed : 4.80 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP I1157 HIS 0.006 0.001 HIS C 31 PHE 0.011 0.002 PHE H 67 TYR 0.015 0.002 TYR H 118 ARG 0.005 0.001 ARG I1220 Details of bonding type rmsd hydrogen bonds : bond 0.17114 ( 588) hydrogen bonds : angle 6.25945 ( 1444) metal coordination : bond 0.21894 ( 10) metal coordination : angle 18.08390 ( 12) covalent geometry : bond 0.00743 (15791) covalent geometry : angle 0.75187 (22769) *********************** 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 : 1.138 Fit side-chains revert: symmetry clash REVERT: M 79 LYS cc_start: 0.8761 (tttt) cc_final: 0.8464 (tttp) REVERT: B 35 ARG cc_start: 0.8748 (mtp85) cc_final: 0.8417 (mtt-85) 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: 0.6537 (ttmm) REVERT: H 39 TYR cc_start: 0.7972 (t80) cc_final: 0.7746 (t80) REVERT: H 65 ASP cc_start: 0.8785 (t70) cc_final: 0.8493 (t0) REVERT: H 105 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8718 (ttmt) REVERT: I 1073 TYR cc_start: 0.7178 (p90) cc_final: 0.6888 (p90) REVERT: I 1222 MET cc_start: 0.7350 (mmm) cc_final: 0.6233 (mmm) outliers start: 13 outliers final: 4 residues processed: 159 average time/residue: 0.3907 time to fit residues: 80.8775 Evaluate side-chains 114 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 108 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 116 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN B 25 ASN C 112 GLN E 68 GLN G 38 ASN G 104 GLN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1137 GLN I1217 ASN I1229 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.150332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095791 restraints weight = 27699.381| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.91 r_work: 0.2922 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- 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 = 0.93 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 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15801 Z= 0.153 Angle : 0.606 20.050 22781 Z= 0.336 Chirality : 0.035 0.168 2573 Planarity : 0.004 0.053 1730 Dihedral : 30.419 172.013 4818 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.60 % Allowed : 11.15 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.23), residues: 969 helix: -1.56 (0.21), residues: 531 sheet: -4.15 (0.86), residues: 16 loop : -3.29 (0.24), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I1157 HIS 0.003 0.001 HIS C 31 PHE 0.008 0.001 PHE I1170 TYR 0.016 0.001 TYR I1218 ARG 0.005 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.05201 ( 588) hydrogen bonds : angle 2.78959 ( 1444) metal coordination : bond 0.01636 ( 10) metal coordination : angle 9.06248 ( 12) covalent geometry : bond 0.00325 (15791) covalent geometry : angle 0.56901 (22769) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 1.172 Fit side-chains REVERT: M 79 LYS cc_start: 0.8877 (tttt) cc_final: 0.8571 (tttm) REVERT: B 35 ARG cc_start: 0.8883 (mtp85) cc_final: 0.8664 (mtt-85) REVERT: D 31 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8270 (mmtp) REVERT: D 110 GLU cc_start: 0.9166 (tp30) cc_final: 0.8868 (tp30) REVERT: G 75 LYS cc_start: 0.9035 (mttm) cc_final: 0.8816 (mttt) REVERT: H 39 TYR cc_start: 0.8620 (t80) cc_final: 0.8388 (t80) REVERT: H 65 ASP cc_start: 0.9072 (t70) cc_final: 0.8805 (t0) REVERT: H 105 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8798 (ttmm) REVERT: I 1169 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6667 (mm-30) REVERT: I 1190 ARG cc_start: 0.6998 (tmm160) cc_final: 0.6792 (ttp80) REVERT: I 1222 MET cc_start: 0.7577 (mmm) cc_final: 0.6358 (mmm) outliers start: 5 outliers final: 3 residues processed: 131 average time/residue: 0.3670 time to fit residues: 65.8822 Evaluate side-chains 117 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain I residue 1077 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4037 r_free = 0.4037 target = 0.148716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.093987 restraints weight = 27910.835| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.95 r_work: 0.2871 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 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 = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15801 Z= 0.207 Angle : 0.603 15.845 22781 Z= 0.336 Chirality : 0.036 0.147 2573 Planarity : 0.004 0.056 1730 Dihedral : 30.553 174.138 4811 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.44 % Allowed : 12.59 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.24), residues: 969 helix: -1.05 (0.22), residues: 528 sheet: -3.66 (0.81), residues: 18 loop : -3.06 (0.25), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP I1157 HIS 0.004 0.001 HIS C 31 PHE 0.020 0.002 PHE I1170 TYR 0.015 0.001 TYR I1261 ARG 0.007 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.05582 ( 588) hydrogen bonds : angle 2.79712 ( 1444) metal coordination : bond 0.00865 ( 10) metal coordination : angle 8.01853 ( 12) covalent geometry : bond 0.00475 (15791) covalent geometry : angle 0.57459 (22769) *********************** 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 126 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 1.296 Fit side-chains REVERT: M 79 LYS cc_start: 0.8893 (tttt) cc_final: 0.8570 (tttm) REVERT: B 35 ARG cc_start: 0.8957 (mtp85) cc_final: 0.8741 (mtt-85) REVERT: D 110 GLU cc_start: 0.9206 (tp30) cc_final: 0.8911 (tp30) REVERT: G 75 LYS cc_start: 0.9047 (mttm) cc_final: 0.8836 (mttt) REVERT: H 39 TYR cc_start: 0.8697 (t80) cc_final: 0.8457 (t80) REVERT: H 65 ASP cc_start: 0.9136 (t70) cc_final: 0.8867 (t0) REVERT: I 1169 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6605 (mm-30) REVERT: I 1193 GLU cc_start: 0.5462 (OUTLIER) cc_final: 0.5063 (mm-30) REVERT: I 1218 TYR cc_start: 0.6630 (m-10) cc_final: 0.6292 (m-80) REVERT: I 1222 MET cc_start: 0.7505 (mmm) cc_final: 0.6254 (mmm) outliers start: 12 outliers final: 9 residues processed: 123 average time/residue: 0.3601 time to fit residues: 60.1496 Evaluate side-chains 118 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1165 ILE Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 50.0000 chunk 111 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.0170 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN 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 = 0.4044 r_free = 0.4044 target = 0.149243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.094521 restraints weight = 27696.555| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.96 r_work: 0.2886 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 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 = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15801 Z= 0.179 Angle : 0.578 14.686 22781 Z= 0.325 Chirality : 0.035 0.143 2573 Planarity : 0.004 0.053 1730 Dihedral : 30.509 174.516 4811 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.80 % Allowed : 12.95 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.25), residues: 969 helix: -0.73 (0.22), residues: 529 sheet: -3.43 (0.80), residues: 18 loop : -2.91 (0.26), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I1157 HIS 0.004 0.001 HIS C 31 PHE 0.018 0.001 PHE I1283 TYR 0.018 0.001 TYR I1200 ARG 0.007 0.000 ARG I1190 Details of bonding type rmsd hydrogen bonds : bond 0.05158 ( 588) hydrogen bonds : angle 2.67713 ( 1444) metal coordination : bond 0.00794 ( 10) metal coordination : angle 7.34001 ( 12) covalent geometry : bond 0.00404 (15791) covalent geometry : angle 0.55267 (22769) *********************** 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 128 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 1.172 Fit side-chains REVERT: M 79 LYS cc_start: 0.8900 (tttt) cc_final: 0.8589 (tttm) REVERT: B 35 ARG cc_start: 0.8949 (mtp85) cc_final: 0.8739 (mtt-85) REVERT: D 110 GLU cc_start: 0.9200 (tp30) cc_final: 0.8895 (tp30) REVERT: G 75 LYS cc_start: 0.9046 (mttm) cc_final: 0.8835 (mttt) REVERT: H 39 TYR cc_start: 0.8705 (t80) cc_final: 0.8450 (t80) REVERT: H 65 ASP cc_start: 0.9137 (t70) cc_final: 0.8870 (t0) REVERT: I 1169 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6663 (mm-30) REVERT: I 1193 GLU cc_start: 0.5478 (OUTLIER) cc_final: 0.5171 (mm-30) REVERT: I 1219 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6458 (m) REVERT: I 1222 MET cc_start: 0.7505 (mmm) cc_final: 0.6285 (mmm) outliers start: 15 outliers final: 12 residues processed: 127 average time/residue: 0.3461 time to fit residues: 59.7149 Evaluate side-chains 122 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 56 GLU 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 1165 ILE Chi-restraints excluded: chain I residue 1193 GLU Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1219 SER Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 5 optimal weight: 0.0070 chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 42 optimal weight: 0.0980 chunk 27 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.150946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095977 restraints weight = 28016.681| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.03 r_work: 0.2918 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 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 = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15801 Z= 0.141 Angle : 0.537 12.467 22781 Z= 0.307 Chirality : 0.033 0.134 2573 Planarity : 0.004 0.052 1730 Dihedral : 30.305 176.873 4811 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.32 % Allowed : 15.35 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.26), residues: 969 helix: -0.23 (0.23), residues: 530 sheet: -2.92 (0.83), residues: 18 loop : -2.60 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I1157 HIS 0.005 0.001 HIS I1075 PHE 0.013 0.001 PHE I1221 TYR 0.016 0.001 TYR I1073 ARG 0.008 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04488 ( 588) hydrogen bonds : angle 2.39663 ( 1444) metal coordination : bond 0.00710 ( 10) metal coordination : angle 6.13594 ( 12) covalent geometry : bond 0.00306 (15791) covalent geometry : angle 0.51804 (22769) *********************** 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 121 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 1.113 Fit side-chains REVERT: M 79 LYS cc_start: 0.8866 (tttt) cc_final: 0.8575 (tttm) REVERT: B 35 ARG cc_start: 0.8918 (mtp85) cc_final: 0.8711 (mtt-85) REVERT: C 91 GLU cc_start: 0.7973 (tp30) cc_final: 0.7743 (mm-30) REVERT: D 110 GLU cc_start: 0.9183 (tp30) cc_final: 0.8870 (tp30) REVERT: G 75 LYS cc_start: 0.9067 (mttm) cc_final: 0.8851 (mttt) REVERT: H 39 TYR cc_start: 0.8673 (t80) cc_final: 0.8420 (t80) REVERT: H 65 ASP cc_start: 0.9128 (t70) cc_final: 0.8845 (t0) REVERT: H 96 ARG cc_start: 0.8769 (mtm-85) cc_final: 0.8475 (mtm-85) REVERT: I 1169 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6660 (mm-30) REVERT: I 1219 SER cc_start: 0.7026 (OUTLIER) cc_final: 0.6381 (m) REVERT: I 1222 MET cc_start: 0.7576 (mmm) cc_final: 0.6362 (mmm) outliers start: 11 outliers final: 7 residues processed: 120 average time/residue: 0.3472 time to fit residues: 56.7491 Evaluate side-chains 117 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1188 ILE Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1219 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 105 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.147864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.092554 restraints weight = 27921.568| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.04 r_work: 0.2855 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15801 Z= 0.276 Angle : 0.617 11.876 22781 Z= 0.345 Chirality : 0.038 0.150 2573 Planarity : 0.004 0.052 1730 Dihedral : 30.638 177.194 4807 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.52 % Allowed : 14.99 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.25), residues: 969 helix: -0.47 (0.22), residues: 529 sheet: -2.60 (0.97), residues: 16 loop : -2.67 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP I1235 HIS 0.005 0.001 HIS C 31 PHE 0.010 0.002 PHE D 62 TYR 0.018 0.002 TYR I1073 ARG 0.008 0.001 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.05975 ( 588) hydrogen bonds : angle 2.84146 ( 1444) metal coordination : bond 0.00969 ( 10) metal coordination : angle 6.72572 ( 12) covalent geometry : bond 0.00646 (15791) covalent geometry : angle 0.59782 (22769) *********************** 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 133 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.159 Fit side-chains REVERT: M 79 LYS cc_start: 0.8914 (tttt) cc_final: 0.8569 (tttm) REVERT: B 35 ARG cc_start: 0.9011 (mtp85) cc_final: 0.8794 (mtt-85) REVERT: D 110 GLU cc_start: 0.9221 (tp30) cc_final: 0.8958 (tp30) REVERT: G 75 LYS cc_start: 0.9067 (mttm) cc_final: 0.8863 (mttt) REVERT: H 39 TYR cc_start: 0.8800 (t80) cc_final: 0.8533 (t80) REVERT: H 65 ASP cc_start: 0.9181 (t70) cc_final: 0.8911 (t0) REVERT: H 96 ARG cc_start: 0.8806 (mtm-85) cc_final: 0.8559 (mtm-85) REVERT: I 1169 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6665 (mm-30) REVERT: I 1174 TYR cc_start: 0.8608 (t80) cc_final: 0.7949 (t80) REVERT: I 1219 SER cc_start: 0.6911 (OUTLIER) cc_final: 0.6230 (m) REVERT: I 1222 MET cc_start: 0.7732 (mmm) cc_final: 0.6667 (mmm) outliers start: 21 outliers final: 17 residues processed: 131 average time/residue: 0.3269 time to fit residues: 59.0925 Evaluate side-chains 128 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 60 VAL 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 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1165 ILE 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 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 107 optimal weight: 30.0000 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 0.0770 chunk 80 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.151779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097234 restraints weight = 28088.840| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.00 r_work: 0.2946 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15801 Z= 0.130 Angle : 0.525 10.750 22781 Z= 0.302 Chirality : 0.032 0.129 2573 Planarity : 0.004 0.050 1730 Dihedral : 30.183 177.959 4807 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.08 % Allowed : 17.15 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.26), residues: 969 helix: 0.22 (0.23), residues: 529 sheet: -2.35 (0.89), residues: 18 loop : -2.37 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I1157 HIS 0.004 0.001 HIS C 31 PHE 0.016 0.001 PHE I1259 TYR 0.009 0.001 TYR I1261 ARG 0.008 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 588) hydrogen bonds : angle 2.31517 ( 1444) metal coordination : bond 0.00644 ( 10) metal coordination : angle 5.08419 ( 12) covalent geometry : bond 0.00276 (15791) covalent geometry : angle 0.51154 (22769) *********************** 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 127 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.240 Fit side-chains REVERT: M 79 LYS cc_start: 0.8827 (tttt) cc_final: 0.8532 (tttm) REVERT: C 91 GLU cc_start: 0.7884 (tp30) cc_final: 0.7555 (mm-30) REVERT: D 110 GLU cc_start: 0.9191 (tp30) cc_final: 0.8957 (tp30) REVERT: E 129 ARG cc_start: 0.8199 (ttt-90) cc_final: 0.7753 (tpt90) REVERT: G 75 LYS cc_start: 0.9076 (mttm) cc_final: 0.8866 (mttt) REVERT: H 39 TYR cc_start: 0.8642 (t80) cc_final: 0.8430 (t80) REVERT: H 65 ASP cc_start: 0.9094 (t70) cc_final: 0.8816 (t0) REVERT: H 96 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.8478 (mtm-85) REVERT: I 1219 SER cc_start: 0.6924 (OUTLIER) cc_final: 0.6242 (m) REVERT: I 1222 MET cc_start: 0.7597 (mmm) cc_final: 0.6497 (mmm) outliers start: 9 outliers final: 8 residues processed: 125 average time/residue: 0.3451 time to fit residues: 59.2696 Evaluate side-chains 119 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 106 optimal weight: 0.0070 chunk 1 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 62 optimal weight: 0.0670 chunk 96 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.152654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.098450 restraints weight = 28157.331| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.98 r_work: 0.2961 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15801 Z= 0.125 Angle : 0.512 8.693 22781 Z= 0.297 Chirality : 0.032 0.132 2573 Planarity : 0.004 0.049 1730 Dihedral : 30.109 179.502 4807 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.84 % Allowed : 17.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.27), residues: 969 helix: 0.80 (0.24), residues: 531 sheet: -2.13 (0.93), residues: 18 loop : -2.19 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I1157 HIS 0.003 0.000 HIS C 31 PHE 0.023 0.002 PHE I1221 TYR 0.010 0.001 TYR B 51 ARG 0.007 0.000 ARG I1190 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 588) hydrogen bonds : angle 2.20114 ( 1444) metal coordination : bond 0.00574 ( 10) metal coordination : angle 4.39200 ( 12) covalent geometry : bond 0.00264 (15791) covalent geometry : angle 0.50238 (22769) *********************** 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 118 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 1.118 Fit side-chains REVERT: M 79 LYS cc_start: 0.8815 (tttt) cc_final: 0.8563 (tttm) REVERT: C 91 GLU cc_start: 0.7842 (tp30) cc_final: 0.7520 (mm-30) REVERT: D 110 GLU cc_start: 0.9187 (tp30) cc_final: 0.8918 (tp30) REVERT: E 129 ARG cc_start: 0.8186 (ttt-90) cc_final: 0.7756 (tpt90) REVERT: G 75 LYS cc_start: 0.9072 (mttm) cc_final: 0.8870 (mttt) REVERT: H 39 TYR cc_start: 0.8629 (t80) cc_final: 0.8424 (t80) REVERT: H 65 ASP cc_start: 0.9063 (t70) cc_final: 0.8734 (t0) REVERT: H 96 ARG cc_start: 0.8743 (mtm-85) cc_final: 0.8460 (mtm-85) REVERT: I 1169 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6570 (mm-30) REVERT: I 1219 SER cc_start: 0.6803 (OUTLIER) cc_final: 0.5950 (m) REVERT: I 1221 PHE cc_start: 0.8581 (m-10) cc_final: 0.8285 (m-80) REVERT: I 1222 MET cc_start: 0.7613 (mmm) cc_final: 0.6524 (mmm) outliers start: 7 outliers final: 4 residues processed: 117 average time/residue: 0.3387 time to fit residues: 54.3632 Evaluate side-chains 112 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1219 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 63 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 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 = 0.4031 r_free = 0.4031 target = 0.148241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.093216 restraints weight = 27897.302| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.94 r_work: 0.2867 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 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 = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15801 Z= 0.265 Angle : 0.612 9.867 22781 Z= 0.343 Chirality : 0.038 0.149 2573 Planarity : 0.005 0.053 1730 Dihedral : 30.516 178.632 4807 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 1.44 % Allowed : 17.27 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.26), residues: 969 helix: 0.16 (0.23), residues: 529 sheet: -2.20 (1.05), residues: 16 loop : -2.38 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I1235 HIS 0.004 0.001 HIS C 31 PHE 0.020 0.002 PHE I1170 TYR 0.018 0.002 TYR G 57 ARG 0.007 0.001 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.06011 ( 588) hydrogen bonds : angle 2.80173 ( 1444) metal coordination : bond 0.00956 ( 10) metal coordination : angle 5.85535 ( 12) covalent geometry : bond 0.00618 (15791) covalent geometry : angle 0.59728 (22769) *********************** 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 121 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.088 Fit side-chains REVERT: M 79 LYS cc_start: 0.8897 (tttt) cc_final: 0.8571 (tttm) REVERT: C 91 GLU cc_start: 0.8032 (tp30) cc_final: 0.7717 (mm-30) REVERT: D 110 GLU cc_start: 0.9201 (tp30) cc_final: 0.8953 (tp30) REVERT: H 39 TYR cc_start: 0.8748 (t80) cc_final: 0.8507 (t80) REVERT: H 65 ASP cc_start: 0.9133 (t70) cc_final: 0.8844 (t0) REVERT: H 96 ARG cc_start: 0.8824 (mtm-85) cc_final: 0.8556 (mtm-85) REVERT: I 1219 SER cc_start: 0.6931 (OUTLIER) cc_final: 0.6289 (m) REVERT: I 1222 MET cc_start: 0.7795 (mmm) cc_final: 0.6821 (mmm) outliers start: 12 outliers final: 9 residues processed: 119 average time/residue: 0.3228 time to fit residues: 52.7611 Evaluate side-chains 117 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1175 VAL Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1219 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 12 optimal weight: 0.0050 chunk 95 optimal weight: 10.0000 chunk 113 optimal weight: 0.0670 chunk 96 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.151418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096648 restraints weight = 28003.129| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.99 r_work: 0.2931 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- 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 = 0.89 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 = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15801 Z= 0.132 Angle : 0.529 9.680 22781 Z= 0.305 Chirality : 0.033 0.130 2573 Planarity : 0.004 0.049 1730 Dihedral : 30.181 178.594 4807 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.72 % Allowed : 17.99 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.27), residues: 969 helix: 0.74 (0.23), residues: 527 sheet: -2.06 (0.98), residues: 18 loop : -2.24 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I1157 HIS 0.018 0.001 HIS F 18 PHE 0.026 0.001 PHE I1170 TYR 0.013 0.001 TYR G 57 ARG 0.008 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 588) hydrogen bonds : angle 2.33711 ( 1444) metal coordination : bond 0.00623 ( 10) metal coordination : angle 4.73109 ( 12) covalent geometry : bond 0.00280 (15791) covalent geometry : angle 0.51833 (22769) ********************** 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 121 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 1.230 Fit side-chains REVERT: M 79 LYS cc_start: 0.8849 (tttt) cc_final: 0.8548 (tttm) REVERT: C 91 GLU cc_start: 0.7908 (tp30) cc_final: 0.7589 (mm-30) REVERT: D 110 GLU cc_start: 0.9194 (tp30) cc_final: 0.8939 (tp30) REVERT: F 18 HIS cc_start: 0.6729 (OUTLIER) cc_final: 0.6511 (t-90) REVERT: H 39 TYR cc_start: 0.8636 (t80) cc_final: 0.8410 (t80) REVERT: H 56 MET cc_start: 0.9019 (tpp) cc_final: 0.8814 (tpp) REVERT: H 65 ASP cc_start: 0.9092 (t70) cc_final: 0.8806 (t0) REVERT: H 96 ARG cc_start: 0.8762 (mtm-85) cc_final: 0.8472 (mtm-85) REVERT: I 1219 SER cc_start: 0.6825 (OUTLIER) cc_final: 0.5909 (m) REVERT: I 1222 MET cc_start: 0.7647 (mmm) cc_final: 0.6517 (mmm) outliers start: 6 outliers final: 4 residues processed: 120 average time/residue: 0.3412 time to fit residues: 56.1062 Evaluate side-chains 117 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain I residue 1077 LYS Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1219 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6621 > 50: distance: 0 - 1: 4.811 distance: 1 - 2: 23.798 distance: 1 - 4: 51.313 distance: 2 - 9: 39.884 distance: 4 - 5: 38.211 distance: 5 - 6: 55.075 distance: 6 - 7: 57.315 distance: 7 - 8: 56.347 distance: 9 - 10: 46.961 distance: 9 - 15: 40.064 distance: 10 - 11: 10.387 distance: 10 - 13: 30.982 distance: 11 - 12: 43.155 distance: 11 - 16: 17.796 distance: 13 - 14: 41.518 distance: 14 - 15: 39.313 distance: 16 - 17: 37.337 distance: 17 - 18: 39.037 distance: 17 - 20: 38.288 distance: 18 - 19: 34.065 distance: 18 - 26: 43.983 distance: 20 - 21: 5.405 distance: 21 - 22: 23.860 distance: 21 - 23: 32.938 distance: 22 - 24: 43.731 distance: 24 - 25: 53.248 distance: 26 - 27: 20.805 distance: 27 - 28: 51.452 distance: 27 - 30: 32.715 distance: 28 - 29: 5.844 distance: 28 - 37: 37.634 distance: 30 - 31: 39.988 distance: 31 - 32: 40.039 distance: 32 - 33: 50.950 distance: 33 - 34: 40.975 distance: 34 - 36: 39.934 distance: 37 - 38: 29.001 distance: 38 - 39: 46.931 distance: 38 - 41: 31.836 distance: 39 - 40: 42.227 distance: 39 - 49: 47.395 distance: 41 - 42: 36.212 distance: 42 - 43: 40.303 distance: 42 - 44: 47.511 distance: 43 - 45: 3.836 distance: 44 - 46: 38.676 distance: 45 - 47: 10.232 distance: 46 - 47: 49.094 distance: 47 - 48: 28.906 distance: 49 - 50: 24.690 distance: 50 - 51: 43.170 distance: 50 - 53: 41.631 distance: 51 - 52: 19.741 distance: 51 - 60: 35.875 distance: 53 - 54: 58.553 distance: 54 - 55: 40.556 distance: 57 - 59: 20.732 distance: 60 - 61: 40.726 distance: 60 - 66: 34.512 distance: 61 - 62: 17.278 distance: 61 - 64: 30.777 distance: 62 - 63: 32.373 distance: 62 - 67: 47.389 distance: 64 - 65: 39.242 distance: 65 - 66: 55.932 distance: 71 - 72: 56.251 distance: 72 - 73: 39.612 distance: 73 - 78: 35.103 distance: 74 - 97: 36.437 distance: 75 - 76: 41.599 distance: 75 - 77: 38.964