Starting phenix.real_space_refine on Sat Jul 4 04:31:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8s9s_40245/07_2026/8s9s_40245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9s_40245/07_2026/8s9s_40245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8s9s_40245/07_2026/8s9s_40245.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8s9s_40245/07_2026/8s9s_40245.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s9s_40245/07_2026/8s9s_40245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9s_40245/07_2026/8s9s_40245.map" model { file = "/net/cci-nas-00/data/ceres_data/8s9s_40245/07_2026/8s9s_40245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9s_40245/07_2026/8s9s_40245.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 72 5.16 5 C 11530 2.51 5 N 3066 2.21 5 O 3338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18012 Number of models: 1 Model: "" Number of chains: 15 Chain: "1" Number of atoms: 7367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7367 Classifications: {'peptide': 930} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 886} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "2" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2306 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 276} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1833 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "4" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 867 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 10, 'TRANS': 133} Chain breaks: 2 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 5, 'ASN:plan1': 3, 'PHE:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 113 Chain: "5" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 795 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 97} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "6" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 774 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "7" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1054 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 124} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "8" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1533 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 8, 'TRANS': 183} Chain breaks: 1 Chain: "10" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1177 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 145} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "3" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 8 Chain: "6" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 3.63, per 1000 atoms: 0.20 Number of scatterers: 18012 At special positions: 0 Unit cell: (93.184, 123.968, 210.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 6 15.00 O 3338 8.00 N 3066 7.00 C 11530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 1 227 " - pdb=" SG CYS 1 237 " distance=2.02 Simple disulfide: pdb=" SG CYS 1 338 " - pdb=" SG CYS 1 368 " distance=2.03 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG 11001 " - " ASN 1 370 " " NAG A 1 " - " ASN 1 913 " " NAG B 1 " - " ASN 1 818 " " NAG C 1 " - " ASN10 182 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 894.3 milliseconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 26 sheets defined 40.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain '1' and resid 82 through 85 removed outlier: 3.689A pdb=" N GLY 1 85 " --> pdb=" O THR 1 82 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 82 through 85' Processing helix chain '1' and resid 222 through 227 removed outlier: 3.884A pdb=" N ALA 1 226 " --> pdb=" O HIS 1 222 " (cutoff:3.500A) Processing helix chain '1' and resid 261 through 265 Processing helix chain '1' and resid 446 through 450 Processing helix chain '1' and resid 463 through 468 removed outlier: 4.555A pdb=" N GLU 1 468 " --> pdb=" O GLY 1 464 " (cutoff:3.500A) Processing helix chain '1' and resid 469 through 471 No H-bonds generated for 'chain '1' and resid 469 through 471' Processing helix chain '1' and resid 479 through 500 removed outlier: 3.565A pdb=" N MET 1 483 " --> pdb=" O GLY 1 479 " (cutoff:3.500A) Processing helix chain '1' and resid 655 through 665 Processing helix chain '1' and resid 876 through 879 removed outlier: 3.578A pdb=" N ASP 1 879 " --> pdb=" O ALA 1 876 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 876 through 879' Processing helix chain '1' and resid 887 through 894 Processing helix chain '1' and resid 905 through 909 removed outlier: 3.628A pdb=" N PHE 1 909 " --> pdb=" O ALA 1 906 " (cutoff:3.500A) Processing helix chain '1' and resid 961 through 993 removed outlier: 3.824A pdb=" N SER 1 967 " --> pdb=" O VAL 1 963 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE 1 974 " --> pdb=" O PHE 1 970 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA 1 975 " --> pdb=" O GLY 1 971 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 25 Processing helix chain '2' and resid 29 through 44 Processing helix chain '2' and resid 50 through 67 removed outlier: 4.242A pdb=" N ILE 2 54 " --> pdb=" O ASP 2 50 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE 2 55 " --> pdb=" O ASP 2 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET 2 60 " --> pdb=" O TYR 2 56 " (cutoff:3.500A) Processing helix chain '2' and resid 69 through 83 removed outlier: 3.602A pdb=" N LEU 2 73 " --> pdb=" O ASP 2 69 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE 2 74 " --> pdb=" O ASP 2 70 " (cutoff:3.500A) Processing helix chain '2' and resid 86 through 99 Processing helix chain '2' and resid 102 through 117 removed outlier: 3.854A pdb=" N ALA 2 106 " --> pdb=" O ARG 2 102 " (cutoff:3.500A) Processing helix chain '2' and resid 121 through 134 Processing helix chain '2' and resid 136 through 149 Processing helix chain '2' and resid 154 through 169 Processing helix chain '2' and resid 170 through 185 Processing helix chain '2' and resid 188 through 203 removed outlier: 3.683A pdb=" N CYS 2 192 " --> pdb=" O ASN 2 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY 2 203 " --> pdb=" O LYS 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 204 through 222 removed outlier: 4.554A pdb=" N LEU 2 210 " --> pdb=" O GLU 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 242 Processing helix chain '2' and resid 246 through 275 removed outlier: 3.514A pdb=" N LYS 2 275 " --> pdb=" O ALA 2 271 " (cutoff:3.500A) Processing helix chain '2' and resid 279 through 290 removed outlier: 3.500A pdb=" N GLU 2 290 " --> pdb=" O GLU 2 286 " (cutoff:3.500A) Processing helix chain '3' and resid 10 through 17 removed outlier: 3.722A pdb=" N LEU 3 14 " --> pdb=" O SER 3 10 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 39 Processing helix chain '3' and resid 45 through 65 removed outlier: 3.541A pdb=" N VAL 3 49 " --> pdb=" O THR 3 45 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 68 No H-bonds generated for 'chain '3' and resid 66 through 68' Processing helix chain '3' and resid 69 through 81 Processing helix chain '3' and resid 104 through 116 Processing helix chain '3' and resid 118 through 132 Processing helix chain '3' and resid 145 through 147 No H-bonds generated for 'chain '3' and resid 145 through 147' Processing helix chain '3' and resid 148 through 153 Processing helix chain '3' and resid 167 through 178 Processing helix chain '3' and resid 179 through 187 Processing helix chain '3' and resid 214 through 228 Processing helix chain '3' and resid 232 through 235 Processing helix chain '3' and resid 236 through 243 removed outlier: 3.581A pdb=" N ALA 3 243 " --> pdb=" O GLU 3 239 " (cutoff:3.500A) Processing helix chain '4' and resid 67 through 91 removed outlier: 3.528A pdb=" N ASP 4 71 " --> pdb=" O LYS 4 67 " (cutoff:3.500A) Proline residue: 4 76 - end of helix Proline residue: 4 81 - end of helix removed outlier: 3.960A pdb=" N GLY 4 91 " --> pdb=" O MET 4 87 " (cutoff:3.500A) Processing helix chain '4' and resid 91 through 96 Processing helix chain '4' and resid 97 through 108 removed outlier: 3.875A pdb=" N VAL 4 102 " --> pdb=" O PRO 4 98 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG 4 108 " --> pdb=" O MET 4 104 " (cutoff:3.500A) Processing helix chain '4' and resid 110 through 115 Processing helix chain '4' and resid 115 through 123 Processing helix chain '4' and resid 127 through 155 removed outlier: 4.011A pdb=" N LEU 4 131 " --> pdb=" O SER 4 127 " (cutoff:3.500A) Processing helix chain '4' and resid 161 through 168 removed outlier: 4.697A pdb=" N ALA 4 166 " --> pdb=" O ASP 4 163 " (cutoff:3.500A) Processing helix chain '5' and resid 4 through 35 removed outlier: 3.596A pdb=" N GLY 5 8 " --> pdb=" O SER 5 4 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 64 removed outlier: 3.547A pdb=" N HIS 5 62 " --> pdb=" O TYR 5 58 " (cutoff:3.500A) Processing helix chain '5' and resid 80 through 85 removed outlier: 3.846A pdb=" N LEU 5 84 " --> pdb=" O THR 5 80 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG 5 85 " --> pdb=" O PHE 5 81 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 80 through 85' Processing helix chain '5' and resid 87 through 91 removed outlier: 3.654A pdb=" N TYR 5 91 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) Processing helix chain '5' and resid 95 through 101 removed outlier: 4.285A pdb=" N VAL 5 99 " --> pdb=" O HIS 5 95 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 45 Processing helix chain '6' and resid 48 through 71 Processing helix chain '6' and resid 73 through 77 removed outlier: 3.615A pdb=" N LYS 6 76 " --> pdb=" O ARG 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 81 through 87 removed outlier: 3.590A pdb=" N PHE 6 85 " --> pdb=" O ARG 6 81 " (cutoff:3.500A) Processing helix chain '6' and resid 88 through 108 removed outlier: 3.586A pdb=" N THR 6 95 " --> pdb=" O GLY 6 91 " (cutoff:3.500A) Processing helix chain '7' and resid 57 through 62 removed outlier: 4.015A pdb=" N TRP 7 61 " --> pdb=" O LYS 7 57 " (cutoff:3.500A) Processing helix chain '7' and resid 156 through 162 removed outlier: 4.215A pdb=" N MET 7 162 " --> pdb=" O THR 7 158 " (cutoff:3.500A) Processing helix chain '7' and resid 163 through 178 Proline residue: 7 172 - end of helix Processing helix chain '8' and resid 7 through 21 removed outlier: 3.543A pdb=" N TYR 8 21 " --> pdb=" O HIS 8 17 " (cutoff:3.500A) Processing helix chain '8' and resid 67 through 85 removed outlier: 4.018A pdb=" N LEU 8 71 " --> pdb=" O LEU 8 67 " (cutoff:3.500A) Processing helix chain '8' and resid 105 through 117 Processing helix chain '8' and resid 129 through 132 Processing helix chain '8' and resid 163 through 177 Processing helix chain '8' and resid 185 through 192 Processing helix chain '8' and resid 199 through 210 removed outlier: 3.904A pdb=" N ASN 8 203 " --> pdb=" O ASN 8 199 " (cutoff:3.500A) Processing helix chain '10' and resid 91 through 104 Processing helix chain '10' and resid 134 through 139 Processing helix chain '10' and resid 174 through 180 removed outlier: 3.626A pdb=" N GLU10 179 " --> pdb=" O VAL10 176 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU10 180 " --> pdb=" O ASP10 177 " (cutoff:3.500A) Processing helix chain '10' and resid 198 through 210 Processing sheet with id=AA1, first strand: chain '1' and resid 32 through 34 Processing sheet with id=AA2, first strand: chain '1' and resid 42 through 44 removed outlier: 7.018A pdb=" N ILE 1 63 " --> pdb=" O ARG 1 76 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG 1 76 " --> pdb=" O ILE 1 63 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA 1 65 " --> pdb=" O LEU 1 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 87 through 93 removed outlier: 6.886A pdb=" N VAL 1 100 " --> pdb=" O ASP 1 88 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N MET 1 90 " --> pdb=" O ILE 1 98 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE 1 98 " --> pdb=" O MET 1 90 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU 1 92 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP 1 96 " --> pdb=" O LEU 1 92 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N MET 1 107 " --> pdb=" O GLU 1 120 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU 1 120 " --> pdb=" O MET 1 107 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER 1 109 " --> pdb=" O ASN 1 118 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY 1 116 " --> pdb=" O GLU 1 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 128 through 135 removed outlier: 7.133A pdb=" N LEU 1 146 " --> pdb=" O GLN 1 129 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LEU 1 131 " --> pdb=" O ALA 1 144 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA 1 144 " --> pdb=" O LEU 1 131 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU 1 133 " --> pdb=" O TYR 1 142 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N TYR 1 142 " --> pdb=" O LEU 1 133 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY 1 135 " --> pdb=" O VAL 1 140 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL 1 140 " --> pdb=" O GLY 1 135 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU 1 151 " --> pdb=" O VAL 1 164 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL 1 164 " --> pdb=" O LEU 1 151 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU 1 153 " --> pdb=" O LYS 1 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 174 through 181 removed outlier: 5.162A pdb=" N TYR 1 175 " --> pdb=" O VAL 1 191 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL 1 191 " --> pdb=" O TYR 1 175 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET 1 177 " --> pdb=" O LEU 1 189 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR 1 181 " --> pdb=" O VAL 1 185 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL 1 185 " --> pdb=" O TYR 1 181 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASN 1 203 " --> pdb=" O ILE 1 209 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE 1 209 " --> pdb=" O ASN 1 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 228 through 230 Processing sheet with id=AA7, first strand: chain '1' and resid 275 through 277 removed outlier: 6.844A pdb=" N TYR 1 300 " --> pdb=" O ASN 1 315 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN 1 315 " --> pdb=" O TYR 1 300 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU 1 302 " --> pdb=" O LEU 1 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1' and resid 322 through 326 Processing sheet with id=AA9, first strand: chain '1' and resid 402 through 411 removed outlier: 6.553A pdb=" N GLN 1 424 " --> pdb=" O GLU 1 403 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU 1 405 " --> pdb=" O LEU 1 422 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU 1 422 " --> pdb=" O LEU 1 405 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE 1 407 " --> pdb=" O ARG 1 420 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG 1 420 " --> pdb=" O ILE 1 407 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL 1 409 " --> pdb=" O GLY 1 418 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY 1 418 " --> pdb=" O VAL 1 409 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU 1 430 " --> pdb=" O SER 1 444 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER 1 444 " --> pdb=" O LEU 1 430 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE 1 432 " --> pdb=" O LEU 1 442 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '1' and resid 452 through 458 removed outlier: 3.616A pdb=" N CYS 1 454 " --> pdb=" O VAL 1 539 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU 1 545 " --> pdb=" O LYS 1 558 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS 1 558 " --> pdb=" O LEU 1 545 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY 1 547 " --> pdb=" O LEU 1 556 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '1' and resid 572 through 576 removed outlier: 6.454A pdb=" N GLN 1 586 " --> pdb=" O GLN 1 575 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '1' and resid 623 through 632 removed outlier: 6.767A pdb=" N ILE 1 643 " --> pdb=" O LEU 1 624 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER 1 626 " --> pdb=" O LEU 1 641 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU 1 641 " --> pdb=" O SER 1 626 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU 1 628 " --> pdb=" O VAL 1 639 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL 1 639 " --> pdb=" O LEU 1 628 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '1' and resid 694 through 699 Processing sheet with id=AB5, first strand: chain '1' and resid 705 through 709 removed outlier: 5.661A pdb=" N ILE 1 707 " --> pdb=" O GLU 1 746 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU 1 746 " --> pdb=" O ILE 1 707 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N PHE 1 756 " --> pdb=" O SER 1 747 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N HIS 1 771 " --> pdb=" O LEU 1 761 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '1' and resid 723 through 727 removed outlier: 5.417A pdb=" N VAL 1 725 " --> pdb=" O LEU 1 732 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU 1 732 " --> pdb=" O VAL 1 725 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY 1 727 " --> pdb=" O SER 1 730 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '1' and resid 779 through 786 removed outlier: 4.451A pdb=" N TRP 1 796 " --> pdb=" O PRO 1 781 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '1' and resid 779 through 786 removed outlier: 4.451A pdb=" N TRP 1 796 " --> pdb=" O PRO 1 781 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '1' and resid 821 through 822 Processing sheet with id=AC1, first strand: chain '1' and resid 860 through 864 Processing sheet with id=AC2, first strand: chain '3' and resid 138 through 139 removed outlier: 3.888A pdb=" N THR 3 138 " --> pdb=" O VAL 3 166 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '7' and resid 84 through 89 removed outlier: 5.268A pdb=" N VAL 7 85 " --> pdb=" O GLY 7 49 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLY 7 49 " --> pdb=" O VAL 7 85 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N HIS 7 87 " --> pdb=" O ILE 7 47 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE 7 47 " --> pdb=" O HIS 7 87 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU 7 138 " --> pdb=" O GLU 7 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '7' and resid 74 through 77 removed outlier: 4.047A pdb=" N ALA 7 120 " --> pdb=" O LEU 7 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '8' and resid 4 through 6 removed outlier: 7.465A pdb=" N LYS 8 5 " --> pdb=" O PHE 8 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain '8' and resid 56 through 62 removed outlier: 3.902A pdb=" N ASN 8 27 " --> pdb=" O LEU 8 60 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL 8 26 " --> pdb=" O GLN 8 94 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLN 8 94 " --> pdb=" O VAL 8 26 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY 8 28 " --> pdb=" O TYR 8 92 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR 8 92 " --> pdb=" O GLY 8 28 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU 8 30 " --> pdb=" O ALA 8 90 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N ALA 8 123 " --> pdb=" O VAL 8 88 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA 8 90 " --> pdb=" O ALA 8 123 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE 8 125 " --> pdb=" O ALA 8 90 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR 8 92 " --> pdb=" O ILE 8 125 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL 8 127 " --> pdb=" O TYR 8 92 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLN 8 94 " --> pdb=" O VAL 8 127 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '10' and resid 82 through 87 removed outlier: 3.501A pdb=" N SER10 84 " --> pdb=" O LEU10 75 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS10 70 " --> pdb=" O HIS10 58 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS10 58 " --> pdb=" O LYS10 70 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU10 55 " --> pdb=" O PRO10 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '10' and resid 156 through 163 removed outlier: 3.515A pdb=" N VAL10 150 " --> pdb=" O GLN10 188 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2409 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2927 1.31 - 1.44: 4967 1.44 - 1.57: 10376 1.57 - 1.70: 13 1.70 - 1.83: 121 Bond restraints: 18404 Sorted by residual: bond pdb=" C11 PCW 3 303 " pdb=" O3 PCW 3 303 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C11 PCW 6 202 " pdb=" O3 PCW 6 202 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C11 PCW 3 302 " pdb=" O3 PCW 3 302 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C11 PCW 3 301 " pdb=" O3 PCW 3 301 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C11 PCW 11002 " pdb=" O3 PCW 11002 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.14e+01 ... (remaining 18399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.05: 24858 5.05 - 10.11: 78 10.11 - 15.16: 16 15.16 - 20.21: 2 20.21 - 25.27: 1 Bond angle restraints: 24955 Sorted by residual: angle pdb=" CA PRO 3 83 " pdb=" N PRO 3 83 " pdb=" CD PRO 3 83 " ideal model delta sigma weight residual 112.00 97.73 14.27 1.40e+00 5.10e-01 1.04e+02 angle pdb=" C19 PCW 3 302 " pdb=" C20 PCW 3 302 " pdb=" C21 PCW 3 302 " ideal model delta sigma weight residual 127.82 153.09 -25.27 3.00e+00 1.11e-01 7.09e+01 angle pdb=" O PRO 4 76 " pdb=" C PRO 4 76 " pdb=" N LEU 4 77 " ideal model delta sigma weight residual 122.22 115.09 7.13 1.29e+00 6.01e-01 3.05e+01 angle pdb=" C18 PCW 3 301 " pdb=" C19 PCW 3 301 " pdb=" C20 PCW 3 301 " ideal model delta sigma weight residual 127.82 112.22 15.60 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C18 PCW 3 302 " pdb=" C19 PCW 3 302 " pdb=" C20 PCW 3 302 " ideal model delta sigma weight residual 127.82 112.55 15.27 3.00e+00 1.11e-01 2.59e+01 ... (remaining 24950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 10460 35.12 - 70.23: 399 70.23 - 105.35: 35 105.35 - 140.47: 1 140.47 - 175.58: 7 Dihedral angle restraints: 10902 sinusoidal: 4327 harmonic: 6575 Sorted by residual: dihedral pdb=" N PCW 11002 " pdb=" C4 PCW 11002 " pdb=" C5 PCW 11002 " pdb=" O4P PCW 11002 " ideal model delta sinusoidal sigma weight residual -66.66 108.92 -175.58 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N PCW 6 202 " pdb=" C4 PCW 6 202 " pdb=" C5 PCW 6 202 " pdb=" O4P PCW 6 202 " ideal model delta sinusoidal sigma weight residual 293.34 132.79 160.55 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C2 PCW 3 303 " pdb=" C31 PCW 3 303 " pdb=" O2 PCW 3 303 " pdb=" C32 PCW 3 303 " ideal model delta sinusoidal sigma weight residual 175.43 16.62 158.81 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 10899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2257 0.050 - 0.100: 459 0.100 - 0.150: 80 0.150 - 0.200: 3 0.200 - 0.250: 6 Chirality restraints: 2805 Sorted by residual: chirality pdb=" C2 PCW 11002 " pdb=" C1 PCW 11002 " pdb=" C3 PCW 11002 " pdb=" O2 PCW 11002 " both_signs ideal model delta sigma weight residual False -2.32 -2.57 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C2 PCW 3 303 " pdb=" C1 PCW 3 303 " pdb=" C3 PCW 3 303 " pdb=" O2 PCW 3 303 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C2 PCW 3 301 " pdb=" C1 PCW 3 301 " pdb=" C3 PCW 3 301 " pdb=" O2 PCW 3 301 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2802 not shown) Planarity restraints: 3168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO 4 76 " 0.043 2.00e-02 2.50e+03 8.11e-02 6.58e+01 pdb=" C PRO 4 76 " -0.140 2.00e-02 2.50e+03 pdb=" O PRO 4 76 " 0.052 2.00e-02 2.50e+03 pdb=" N LEU 4 77 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO 4 98 " 0.029 2.00e-02 2.50e+03 5.60e-02 3.13e+01 pdb=" C PRO 4 98 " -0.097 2.00e-02 2.50e+03 pdb=" O PRO 4 98 " 0.036 2.00e-02 2.50e+03 pdb=" N THR 4 99 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN 3 82 " -0.094 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO 3 83 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO 3 83 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO 3 83 " -0.069 5.00e-02 4.00e+02 ... (remaining 3165 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 975 2.73 - 3.27: 18569 3.27 - 3.81: 30555 3.81 - 4.36: 34523 4.36 - 4.90: 59690 Nonbonded interactions: 144312 Sorted by model distance: nonbonded pdb=" OG SER10 140 " pdb=" OG SER10 143 " model vdw 2.184 3.040 nonbonded pdb=" O ALA 5 52 " pdb=" OG1 THR 5 56 " model vdw 2.195 3.040 nonbonded pdb=" O THR 3 137 " pdb=" OH TYR 6 110 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASP 5 82 " pdb=" NE2 HIS 8 62 " model vdw 2.205 3.120 nonbonded pdb=" OE2 GLU10 61 " pdb=" ND2 ASN10 67 " model vdw 2.221 3.120 ... (remaining 144307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.900 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 0.005 0.165 18413 Z= 0.231 Angle : 0.826 25.267 24980 Z= 0.383 Chirality : 0.043 0.250 2805 Planarity : 0.005 0.131 3164 Dihedral : 18.517 175.582 6648 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.59 % Allowed : 28.32 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2228 helix: 1.19 (0.19), residues: 784 sheet: -0.32 (0.24), residues: 492 loop : -0.71 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 7 119 TYR 0.021 0.001 TYR 1 912 PHE 0.016 0.001 PHE 2 230 TRP 0.055 0.002 TRP 2 158 HIS 0.003 0.001 HIS 2 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 (18404) covalent geometry : angle 0.82416 / 0.38 (24955) SS BOND : bond 0.00555 / 0.29 ( 2) SS BOND : angle 2.22133 / 1.26 ( 4) hydrogen bonds : bond 0.14717 / 10.19 ( 844) hydrogen bonds : angle 6.57104 / 4.60 ( 2409) link_BETA1-4 : bond 0.00203 / 0.10 ( 3) link_BETA1-4 : angle 1.90366 / 0.98 ( 9) link_NAG-ASN : bond 0.00149 / 0.07 ( 4) link_NAG-ASN : angle 2.12032 / 1.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 726 MET cc_start: 0.7853 (tpp) cc_final: 0.7587 (tpp) REVERT: 2 19 MET cc_start: 0.9416 (mmm) cc_final: 0.9194 (mmm) REVERT: 2 183 MET cc_start: 0.8860 (mtp) cc_final: 0.8467 (mtt) REVERT: 2 254 MET cc_start: 0.9200 (mtp) cc_final: 0.8816 (mmm) REVERT: 3 251 MET cc_start: 0.8701 (tpp) cc_final: 0.7833 (tmm) outliers start: 11 outliers final: 6 residues processed: 121 average time/residue: 0.1323 time to fit residues: 25.8921 Evaluate side-chains 98 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 2 residue 230 PHE Chi-restraints excluded: chain 8 residue 195 ASN Chi-restraints excluded: chain 8 residue 204 LYS Chi-restraints excluded: chain 10 residue 173 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.051285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.034482 restraints weight = 107856.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.035731 restraints weight = 49729.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.036500 restraints weight = 32870.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.036895 restraints weight = 26139.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.037192 restraints weight = 23288.007| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 18413 Z= 0.248 Angle : 0.643 7.478 24980 Z= 0.327 Chirality : 0.042 0.159 2805 Planarity : 0.004 0.064 3164 Dihedral : 11.546 166.905 2564 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.39 % Allowed : 24.79 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 2228 helix: 1.70 (0.19), residues: 797 sheet: -0.40 (0.24), residues: 511 loop : -0.71 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 273 TYR 0.018 0.002 TYR 1 943 PHE 0.021 0.001 PHE 2 230 TRP 0.025 0.002 TRP 2 158 HIS 0.004 0.001 HIS 5 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.25 (18404) covalent geometry : angle 0.64051 / 0.33 (24955) SS BOND : bond 0.00359 / 0.19 ( 2) SS BOND : angle 1.51696 / 0.81 ( 4) hydrogen bonds : bond 0.04190 / 2.84 ( 844) hydrogen bonds : angle 5.18291 / 3.64 ( 2409) link_BETA1-4 : bond 0.00143 / 0.07 ( 3) link_BETA1-4 : angle 1.74378 / 0.87 ( 9) link_NAG-ASN : bond 0.00480 / 0.24 ( 4) link_NAG-ASN : angle 2.07865 / 1.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 94 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 408 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8812 (pt0) REVERT: 1 726 MET cc_start: 0.8526 (tpp) cc_final: 0.7869 (tpp) REVERT: 2 19 MET cc_start: 0.9493 (mmm) cc_final: 0.9025 (mmm) REVERT: 2 183 MET cc_start: 0.9164 (mtp) cc_final: 0.8809 (mtt) REVERT: 2 226 MET cc_start: 0.7992 (ppp) cc_final: 0.7613 (ppp) REVERT: 2 254 MET cc_start: 0.9396 (mtp) cc_final: 0.8990 (mmm) REVERT: 3 6 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8355 (mp) REVERT: 3 251 MET cc_start: 0.8990 (tpp) cc_final: 0.7922 (tmm) REVERT: 4 175 GLU cc_start: 0.8409 (mp0) cc_final: 0.8120 (mp0) REVERT: 8 71 LEU cc_start: 0.9770 (OUTLIER) cc_final: 0.9481 (pp) REVERT: 8 85 HIS cc_start: 0.9475 (OUTLIER) cc_final: 0.9270 (m90) outliers start: 82 outliers final: 43 residues processed: 166 average time/residue: 0.1113 time to fit residues: 31.1093 Evaluate side-chains 138 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 91 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 107 MET Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 191 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 295 LEU Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 408 GLN Chi-restraints excluded: chain 1 residue 452 VAL Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 757 ILE Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 919 MET Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 978 ILE Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 93 THR Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 2 residue 280 TYR Chi-restraints excluded: chain 3 residue 6 LEU Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 12 ILE Chi-restraints excluded: chain 5 residue 60 ILE Chi-restraints excluded: chain 6 residue 56 LEU Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 78 ILE Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 173 VAL Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 108 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 185 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 775 GLN ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** 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 = 0.3491 r_free = 0.3491 target = 0.051565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.034695 restraints weight = 108966.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.035974 restraints weight = 49428.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.036771 restraints weight = 32464.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.037217 restraints weight = 25802.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.037482 restraints weight = 22789.160| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18413 Z= 0.172 Angle : 0.582 6.875 24980 Z= 0.295 Chirality : 0.042 0.164 2805 Planarity : 0.004 0.054 3164 Dihedral : 10.939 169.137 2553 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.18 % Allowed : 25.27 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2228 helix: 1.79 (0.18), residues: 813 sheet: -0.34 (0.24), residues: 502 loop : -0.68 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG10 204 TYR 0.014 0.001 TYR 1 943 PHE 0.013 0.001 PHE 2 230 TRP 0.042 0.001 TRP 2 158 HIS 0.004 0.001 HIS 8 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (18404) covalent geometry : angle 0.57999 / 0.29 (24955) SS BOND : bond 0.00196 / 0.10 ( 2) SS BOND : angle 1.33029 / 0.69 ( 4) hydrogen bonds : bond 0.03722 / 2.51 ( 844) hydrogen bonds : angle 4.89215 / 3.43 ( 2409) link_BETA1-4 : bond 0.00145 / 0.07 ( 3) link_BETA1-4 : angle 1.74574 / 0.90 ( 9) link_NAG-ASN : bond 0.00256 / 0.13 ( 4) link_NAG-ASN : angle 1.95717 / 1.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 96 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9231 (OUTLIER) cc_final: 0.8942 (m-40) REVERT: 1 408 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8912 (pt0) REVERT: 1 640 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9240 (tp) REVERT: 1 726 MET cc_start: 0.8440 (tpp) cc_final: 0.7890 (tpp) REVERT: 2 254 MET cc_start: 0.9415 (mtp) cc_final: 0.8998 (mmm) REVERT: 3 130 MET cc_start: 0.8931 (mmm) cc_final: 0.8504 (mmm) REVERT: 3 173 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8890 (m-80) REVERT: 3 251 MET cc_start: 0.8947 (tpp) cc_final: 0.7863 (tmm) REVERT: 5 70 MET cc_start: 0.9213 (mtp) cc_final: 0.8608 (mpp) REVERT: 7 118 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8304 (ppp) REVERT: 8 71 LEU cc_start: 0.9764 (OUTLIER) cc_final: 0.9470 (pp) outliers start: 78 outliers final: 47 residues processed: 166 average time/residue: 0.1151 time to fit residues: 31.7506 Evaluate side-chains 142 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 89 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 408 GLN Chi-restraints excluded: chain 1 residue 422 LEU Chi-restraints excluded: chain 1 residue 452 VAL Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 603 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 640 LEU Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 757 ILE Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 916 VAL Chi-restraints excluded: chain 1 residue 919 MET Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 978 ILE Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 34 VAL Chi-restraints excluded: chain 2 residue 93 THR Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 173 PHE Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 4 residue 48 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 60 ILE Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 68 LEU Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 118 MET Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 10 residue 112 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 219 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 775 GLN ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 199 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 = 0.3467 r_free = 0.3467 target = 0.050697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.033750 restraints weight = 109686.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.034981 restraints weight = 50252.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.035742 restraints weight = 33243.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.036193 restraints weight = 26602.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.036436 restraints weight = 23501.544| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 18413 Z= 0.258 Angle : 0.637 7.376 24980 Z= 0.321 Chirality : 0.043 0.159 2805 Planarity : 0.004 0.049 3164 Dihedral : 10.644 172.467 2552 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.94 % Allowed : 24.46 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2228 helix: 1.80 (0.18), residues: 812 sheet: -0.42 (0.24), residues: 500 loop : -0.75 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 6 73 TYR 0.020 0.002 TYR 1 943 PHE 0.023 0.001 PHE 2 230 TRP 0.024 0.001 TRP 2 158 HIS 0.006 0.001 HIS 1 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.26 (18404) covalent geometry : angle 0.63458 / 0.32 (24955) SS BOND : bond 0.00249 / 0.13 ( 2) SS BOND : angle 1.31984 / 0.61 ( 4) hydrogen bonds : bond 0.03719 / 2.51 ( 844) hydrogen bonds : angle 4.94489 / 3.47 ( 2409) link_BETA1-4 : bond 0.00167 / 0.08 ( 3) link_BETA1-4 : angle 1.95070 / 0.99 ( 9) link_NAG-ASN : bond 0.00510 / 0.25 ( 4) link_NAG-ASN : angle 2.16749 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 92 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.8932 (m-40) REVERT: 1 109 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8160 (p) REVERT: 1 408 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8868 (pt0) REVERT: 1 640 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9250 (tp) REVERT: 2 158 TRP cc_start: 0.8795 (OUTLIER) cc_final: 0.8570 (m-10) REVERT: 2 254 MET cc_start: 0.9443 (mtp) cc_final: 0.8865 (mmm) REVERT: 3 130 MET cc_start: 0.8939 (mmm) cc_final: 0.8518 (mmm) REVERT: 3 251 MET cc_start: 0.8967 (tpp) cc_final: 0.7916 (tmm) REVERT: 7 117 LYS cc_start: 0.9203 (tppt) cc_final: 0.8958 (tppt) REVERT: 7 118 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8401 (ppp) REVERT: 8 16 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8660 (mm) REVERT: 8 71 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9492 (pp) outliers start: 111 outliers final: 70 residues processed: 193 average time/residue: 0.1096 time to fit residues: 35.3452 Evaluate side-chains 167 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 89 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 109 SER Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 146 LEU Chi-restraints excluded: chain 1 residue 191 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 372 THR Chi-restraints excluded: chain 1 residue 408 GLN Chi-restraints excluded: chain 1 residue 452 VAL Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 640 LEU Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 757 ILE Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 791 VAL Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 912 TYR Chi-restraints excluded: chain 1 residue 916 VAL Chi-restraints excluded: chain 1 residue 919 MET Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 965 ILE Chi-restraints excluded: chain 1 residue 966 SER Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 978 ILE Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 34 VAL Chi-restraints excluded: chain 2 residue 93 THR Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 2 residue 158 TRP Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 4 residue 48 LEU Chi-restraints excluded: chain 4 residue 165 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 60 ILE Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 31 THR Chi-restraints excluded: chain 6 residue 56 LEU Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 68 LEU Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 118 MET Chi-restraints excluded: chain 8 residue 16 LEU Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 78 ILE Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 183 THR Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 775 GLN ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 199 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 = 0.3486 r_free = 0.3486 target = 0.052380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.034678 restraints weight = 108074.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.035958 restraints weight = 49754.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.036772 restraints weight = 32872.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.037252 restraints weight = 26129.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.037485 restraints weight = 22996.617| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18413 Z= 0.155 Angle : 0.584 9.157 24980 Z= 0.293 Chirality : 0.041 0.154 2805 Planarity : 0.004 0.050 3164 Dihedral : 10.293 174.633 2552 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.71 % Allowed : 25.48 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.18), residues: 2228 helix: 1.84 (0.18), residues: 812 sheet: -0.30 (0.24), residues: 496 loop : -0.66 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 257 TYR 0.015 0.001 TYR 7 136 PHE 0.019 0.001 PHE 2 230 TRP 0.025 0.001 TRP 2 158 HIS 0.004 0.001 HIS 1 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (18404) covalent geometry : angle 0.58153 / 0.29 (24955) SS BOND : bond 0.00210 / 0.11 ( 2) SS BOND : angle 1.19360 / 0.59 ( 4) hydrogen bonds : bond 0.03453 / 2.32 ( 844) hydrogen bonds : angle 4.76359 / 3.34 ( 2409) link_BETA1-4 : bond 0.00183 / 0.09 ( 3) link_BETA1-4 : angle 1.88007 / 0.98 ( 9) link_NAG-ASN : bond 0.00221 / 0.11 ( 4) link_NAG-ASN : angle 2.03033 / 1.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 92 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9224 (OUTLIER) cc_final: 0.8924 (m-40) REVERT: 1 109 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8118 (p) REVERT: 1 408 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8906 (pt0) REVERT: 1 640 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9237 (tp) REVERT: 1 726 MET cc_start: 0.8368 (tpp) cc_final: 0.8062 (tpp) REVERT: 2 158 TRP cc_start: 0.8761 (OUTLIER) cc_final: 0.8521 (m-10) REVERT: 2 254 MET cc_start: 0.9453 (mtp) cc_final: 0.8870 (mmm) REVERT: 3 130 MET cc_start: 0.8907 (mmm) cc_final: 0.8317 (mmm) REVERT: 3 251 MET cc_start: 0.8972 (tpp) cc_final: 0.7919 (tmm) REVERT: 5 31 MET cc_start: 0.8516 (tpp) cc_final: 0.8295 (tpp) REVERT: 5 70 MET cc_start: 0.9179 (mtp) cc_final: 0.8522 (mpp) REVERT: 7 162 MET cc_start: 0.8080 (pmm) cc_final: 0.7790 (pmm) REVERT: 8 16 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8656 (mm) REVERT: 8 71 LEU cc_start: 0.9769 (OUTLIER) cc_final: 0.9495 (pp) REVERT: 8 134 MET cc_start: 0.8802 (mmt) cc_final: 0.7400 (tpp) REVERT: 10 142 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9351 (tt) outliers start: 88 outliers final: 57 residues processed: 172 average time/residue: 0.1082 time to fit residues: 31.3957 Evaluate side-chains 153 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 88 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 109 SER Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 408 GLN Chi-restraints excluded: chain 1 residue 422 LEU Chi-restraints excluded: chain 1 residue 436 LEU Chi-restraints excluded: chain 1 residue 452 VAL Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 640 LEU Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 757 ILE Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 784 ILE Chi-restraints excluded: chain 1 residue 791 VAL Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 912 TYR Chi-restraints excluded: chain 1 residue 919 MET Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 966 SER Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 978 ILE Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 93 THR Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 2 residue 158 TRP Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 4 residue 48 LEU Chi-restraints excluded: chain 4 residue 165 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 60 ILE Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 29 CYS Chi-restraints excluded: chain 6 residue 34 SER Chi-restraints excluded: chain 6 residue 36 LEU Chi-restraints excluded: chain 6 residue 68 LEU Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 8 residue 16 LEU Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 85 HIS Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 142 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 151 optimal weight: 40.0000 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 143 optimal weight: 30.0000 chunk 169 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 203 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 26 GLN ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 238 HIS ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.051837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.035093 restraints weight = 106662.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.036365 restraints weight = 48089.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.037151 restraints weight = 31530.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.037639 restraints weight = 25065.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.037910 restraints weight = 22012.954| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18413 Z= 0.116 Angle : 0.574 11.520 24980 Z= 0.285 Chirality : 0.041 0.166 2805 Planarity : 0.003 0.052 3164 Dihedral : 9.835 178.305 2552 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.01 % Allowed : 26.50 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.19), residues: 2228 helix: 1.86 (0.19), residues: 818 sheet: -0.24 (0.24), residues: 502 loop : -0.55 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 119 TYR 0.023 0.001 TYR 7 136 PHE 0.021 0.001 PHE 2 230 TRP 0.024 0.001 TRP 2 158 HIS 0.003 0.001 HIS 8 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (18404) covalent geometry : angle 0.57143 / 0.28 (24955) SS BOND : bond 0.00235 / 0.12 ( 2) SS BOND : angle 1.11552 / 0.58 ( 4) hydrogen bonds : bond 0.03269 / 2.18 ( 844) hydrogen bonds : angle 4.59885 / 3.22 ( 2409) link_BETA1-4 : bond 0.00126 / 0.06 ( 3) link_BETA1-4 : angle 1.82262 / 0.95 ( 9) link_NAG-ASN : bond 0.00114 / 0.06 ( 4) link_NAG-ASN : angle 1.97781 / 1.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 94 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9126 (OUTLIER) cc_final: 0.8887 (m-40) REVERT: 1 109 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8075 (p) REVERT: 1 408 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8932 (pt0) REVERT: 1 726 MET cc_start: 0.8353 (tpp) cc_final: 0.8070 (tpp) REVERT: 2 158 TRP cc_start: 0.8699 (OUTLIER) cc_final: 0.8462 (m-10) REVERT: 2 183 MET cc_start: 0.9104 (mtp) cc_final: 0.8788 (mtt) REVERT: 2 254 MET cc_start: 0.9455 (mtp) cc_final: 0.8845 (mmm) REVERT: 3 130 MET cc_start: 0.8899 (mmm) cc_final: 0.8181 (mmm) REVERT: 3 251 MET cc_start: 0.8919 (tpp) cc_final: 0.7864 (tmm) REVERT: 5 31 MET cc_start: 0.8524 (tpp) cc_final: 0.8308 (tpp) REVERT: 5 70 MET cc_start: 0.9198 (mtp) cc_final: 0.8560 (mpp) REVERT: 8 16 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8612 (mm) REVERT: 8 71 LEU cc_start: 0.9762 (OUTLIER) cc_final: 0.9479 (pp) REVERT: 8 134 MET cc_start: 0.8757 (mmt) cc_final: 0.7494 (tpp) outliers start: 75 outliers final: 51 residues processed: 163 average time/residue: 0.1160 time to fit residues: 30.8264 Evaluate side-chains 143 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 86 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 109 SER Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 408 GLN Chi-restraints excluded: chain 1 residue 422 LEU Chi-restraints excluded: chain 1 residue 436 LEU Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 791 VAL Chi-restraints excluded: chain 1 residue 823 SER Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 912 TYR Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 966 SER Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 60 MET Chi-restraints excluded: chain 2 residue 138 VAL Chi-restraints excluded: chain 2 residue 158 TRP Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 4 residue 48 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 60 ILE Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 36 LEU Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 151 LYS Chi-restraints excluded: chain 8 residue 16 LEU Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 124 LEU Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 187 LEU Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 99 optimal weight: 9.9990 chunk 219 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 150 optimal weight: 0.3980 chunk 114 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 775 GLN ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 199 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 = 0.3491 r_free = 0.3491 target = 0.051389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.034554 restraints weight = 108623.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.035825 restraints weight = 49237.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.036618 restraints weight = 32263.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.037062 restraints weight = 25632.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.037319 restraints weight = 22693.387| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18413 Z= 0.163 Angle : 0.587 9.780 24980 Z= 0.292 Chirality : 0.041 0.191 2805 Planarity : 0.003 0.052 3164 Dihedral : 9.616 179.077 2552 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.76 % Allowed : 25.75 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.18), residues: 2228 helix: 1.86 (0.19), residues: 823 sheet: -0.20 (0.24), residues: 496 loop : -0.56 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG10 204 TYR 0.027 0.001 TYR 7 136 PHE 0.020 0.001 PHE 2 230 TRP 0.025 0.001 TRP 2 158 HIS 0.006 0.001 HIS 8 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (18404) covalent geometry : angle 0.58388 / 0.29 (24955) SS BOND : bond 0.00219 / 0.11 ( 2) SS BOND : angle 1.19166 / 0.60 ( 4) hydrogen bonds : bond 0.03333 / 2.24 ( 844) hydrogen bonds : angle 4.62091 / 3.24 ( 2409) link_BETA1-4 : bond 0.00160 / 0.08 ( 3) link_BETA1-4 : angle 1.90598 / 0.98 ( 9) link_NAG-ASN : bond 0.00215 / 0.11 ( 4) link_NAG-ASN : angle 2.04376 / 1.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 89 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8912 (m-40) REVERT: 1 109 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8072 (p) REVERT: 1 293 LEU cc_start: 0.9842 (OUTLIER) cc_final: 0.9630 (tt) REVERT: 1 408 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8932 (pt0) REVERT: 1 567 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8241 (t0) REVERT: 1 726 MET cc_start: 0.8411 (tpp) cc_final: 0.8137 (tpp) REVERT: 2 158 TRP cc_start: 0.8716 (OUTLIER) cc_final: 0.8474 (m-10) REVERT: 2 183 MET cc_start: 0.9123 (mtp) cc_final: 0.8808 (mtt) REVERT: 2 254 MET cc_start: 0.9459 (mtp) cc_final: 0.8855 (mmm) REVERT: 3 130 MET cc_start: 0.8883 (mmm) cc_final: 0.8254 (mmm) REVERT: 3 251 MET cc_start: 0.8925 (tpp) cc_final: 0.7789 (tmm) REVERT: 5 31 MET cc_start: 0.8514 (tpp) cc_final: 0.8300 (tpp) REVERT: 5 70 MET cc_start: 0.9213 (mtp) cc_final: 0.8581 (mpp) REVERT: 8 16 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8698 (mm) REVERT: 8 71 LEU cc_start: 0.9765 (OUTLIER) cc_final: 0.9468 (pp) REVERT: 10 142 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9346 (tt) outliers start: 89 outliers final: 64 residues processed: 172 average time/residue: 0.1002 time to fit residues: 29.3613 Evaluate side-chains 162 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 89 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 109 SER Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 293 LEU Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 408 GLN Chi-restraints excluded: chain 1 residue 436 LEU Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 567 ASP Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 765 VAL Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 784 ILE Chi-restraints excluded: chain 1 residue 791 VAL Chi-restraints excluded: chain 1 residue 823 SER Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 912 TYR Chi-restraints excluded: chain 1 residue 916 VAL Chi-restraints excluded: chain 1 residue 919 MET Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 966 SER Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 34 VAL Chi-restraints excluded: chain 2 residue 148 LEU Chi-restraints excluded: chain 2 residue 158 TRP Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 2 residue 238 HIS Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 4 residue 48 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 60 ILE Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 29 CYS Chi-restraints excluded: chain 6 residue 34 SER Chi-restraints excluded: chain 6 residue 36 LEU Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 151 LYS Chi-restraints excluded: chain 8 residue 16 LEU Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 124 LEU Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 142 LEU Chi-restraints excluded: chain 10 residue 152 VAL Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 2 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 160 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 152 optimal weight: 50.0000 chunk 133 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 199 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 = 0.3474 r_free = 0.3474 target = 0.050860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.033987 restraints weight = 108662.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.035235 restraints weight = 49523.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.036005 restraints weight = 32602.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.036421 restraints weight = 26043.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.036701 restraints weight = 23110.603| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18413 Z= 0.209 Angle : 0.620 11.501 24980 Z= 0.308 Chirality : 0.042 0.175 2805 Planarity : 0.004 0.054 3164 Dihedral : 9.361 175.177 2552 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.71 % Allowed : 25.64 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 2228 helix: 1.89 (0.19), residues: 824 sheet: -0.30 (0.24), residues: 498 loop : -0.61 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG10 204 TYR 0.019 0.001 TYR 7 136 PHE 0.019 0.001 PHE 2 230 TRP 0.026 0.001 TRP 2 158 HIS 0.004 0.001 HIS 8 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (18404) covalent geometry : angle 0.61684 / 0.31 (24955) SS BOND : bond 0.00385 / 0.19 ( 2) SS BOND : angle 1.36845 / 0.61 ( 4) hydrogen bonds : bond 0.03428 / 2.31 ( 844) hydrogen bonds : angle 4.70133 / 3.30 ( 2409) link_BETA1-4 : bond 0.00125 / 0.06 ( 3) link_BETA1-4 : angle 2.08448 / 1.06 ( 9) link_NAG-ASN : bond 0.00368 / 0.18 ( 4) link_NAG-ASN : angle 2.14387 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 92 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9257 (OUTLIER) cc_final: 0.8935 (m-40) REVERT: 1 109 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8152 (p) REVERT: 1 293 LEU cc_start: 0.9855 (OUTLIER) cc_final: 0.9650 (tt) REVERT: 1 408 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8873 (pt0) REVERT: 1 567 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8285 (t0) REVERT: 1 726 MET cc_start: 0.8496 (tpp) cc_final: 0.7871 (tpp) REVERT: 2 158 TRP cc_start: 0.8774 (OUTLIER) cc_final: 0.8502 (m-10) REVERT: 2 183 MET cc_start: 0.9162 (mtp) cc_final: 0.8842 (mtt) REVERT: 2 254 MET cc_start: 0.9463 (mtp) cc_final: 0.8869 (mmm) REVERT: 3 130 MET cc_start: 0.8924 (mmm) cc_final: 0.8250 (mmm) REVERT: 3 251 MET cc_start: 0.8963 (tpp) cc_final: 0.7853 (tmm) REVERT: 8 71 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9472 (pp) REVERT: 8 134 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7436 (tpp) REVERT: 10 142 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9345 (tt) outliers start: 88 outliers final: 71 residues processed: 174 average time/residue: 0.1045 time to fit residues: 30.5787 Evaluate side-chains 170 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 90 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 109 SER Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 293 LEU Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 1 residue 331 THR Chi-restraints excluded: chain 1 residue 408 GLN Chi-restraints excluded: chain 1 residue 436 LEU Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 567 ASP Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 761 LEU Chi-restraints excluded: chain 1 residue 765 VAL Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 784 ILE Chi-restraints excluded: chain 1 residue 791 VAL Chi-restraints excluded: chain 1 residue 823 SER Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 912 TYR Chi-restraints excluded: chain 1 residue 916 VAL Chi-restraints excluded: chain 1 residue 919 MET Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 965 ILE Chi-restraints excluded: chain 1 residue 966 SER Chi-restraints excluded: chain 1 residue 972 LEU Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 978 ILE Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 34 VAL Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 148 LEU Chi-restraints excluded: chain 2 residue 158 TRP Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 4 residue 48 LEU Chi-restraints excluded: chain 4 residue 162 SER Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 60 ILE Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 5 residue 100 LEU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 29 CYS Chi-restraints excluded: chain 6 residue 31 THR Chi-restraints excluded: chain 6 residue 34 SER Chi-restraints excluded: chain 6 residue 36 LEU Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 8 residue 52 THR Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 124 LEU Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 142 LEU Chi-restraints excluded: chain 10 residue 152 VAL Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 44 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 127 optimal weight: 0.0370 chunk 184 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 199 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 = 0.3493 r_free = 0.3493 target = 0.051454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.034667 restraints weight = 107818.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.035942 restraints weight = 48696.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.036736 restraints weight = 31949.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.037198 restraints weight = 25386.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.037441 restraints weight = 22421.173| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18413 Z= 0.130 Angle : 0.594 10.638 24980 Z= 0.294 Chirality : 0.041 0.160 2805 Planarity : 0.003 0.056 3164 Dihedral : 9.110 173.154 2552 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.80 % Allowed : 26.66 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.19), residues: 2228 helix: 1.90 (0.19), residues: 822 sheet: -0.19 (0.24), residues: 494 loop : -0.55 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG10 204 TYR 0.012 0.001 TYR 7 122 PHE 0.019 0.001 PHE 2 230 TRP 0.026 0.001 TRP 2 158 HIS 0.004 0.001 HIS 1 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (18404) covalent geometry : angle 0.59172 / 0.29 (24955) SS BOND : bond 0.00217 / 0.11 ( 2) SS BOND : angle 1.19889 / 0.58 ( 4) hydrogen bonds : bond 0.03286 / 2.20 ( 844) hydrogen bonds : angle 4.57324 / 3.21 ( 2409) link_BETA1-4 : bond 0.00233 / 0.12 ( 3) link_BETA1-4 : angle 1.99504 / 1.04 ( 9) link_NAG-ASN : bond 0.00124 / 0.06 ( 4) link_NAG-ASN : angle 2.01675 / 1.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 94 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8891 (m-40) REVERT: 1 109 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8124 (p) REVERT: 1 293 LEU cc_start: 0.9851 (OUTLIER) cc_final: 0.9641 (tt) REVERT: 1 408 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8896 (pt0) REVERT: 1 567 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8246 (t0) REVERT: 1 726 MET cc_start: 0.8473 (tpp) cc_final: 0.7863 (tpp) REVERT: 2 158 TRP cc_start: 0.8711 (OUTLIER) cc_final: 0.8492 (m-10) REVERT: 2 183 MET cc_start: 0.9133 (mtp) cc_final: 0.8809 (mtt) REVERT: 2 254 MET cc_start: 0.9460 (mtp) cc_final: 0.8867 (mmm) REVERT: 3 130 MET cc_start: 0.8911 (mmm) cc_final: 0.8576 (mmm) REVERT: 3 242 MET cc_start: 0.9128 (mmp) cc_final: 0.8826 (mmm) REVERT: 3 251 MET cc_start: 0.8947 (tpp) cc_final: 0.7838 (tmm) REVERT: 8 71 LEU cc_start: 0.9769 (OUTLIER) cc_final: 0.9471 (pp) REVERT: 8 134 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7331 (tpp) REVERT: 10 142 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9336 (tt) outliers start: 71 outliers final: 59 residues processed: 157 average time/residue: 0.1059 time to fit residues: 28.2352 Evaluate side-chains 159 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 91 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 109 SER Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 293 LEU Chi-restraints excluded: chain 1 residue 408 GLN Chi-restraints excluded: chain 1 residue 436 LEU Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 567 ASP Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 761 LEU Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 784 ILE Chi-restraints excluded: chain 1 residue 791 VAL Chi-restraints excluded: chain 1 residue 823 SER Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 912 TYR Chi-restraints excluded: chain 1 residue 916 VAL Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 966 SER Chi-restraints excluded: chain 1 residue 972 LEU Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 158 TRP Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 4 residue 48 LEU Chi-restraints excluded: chain 4 residue 165 LEU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 29 CYS Chi-restraints excluded: chain 6 residue 31 THR Chi-restraints excluded: chain 6 residue 34 SER Chi-restraints excluded: chain 6 residue 36 LEU Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 8 residue 52 THR Chi-restraints excluded: chain 8 residue 71 LEU Chi-restraints excluded: chain 8 residue 124 LEU Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 142 LEU Chi-restraints excluded: chain 10 residue 152 VAL Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 52 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 204 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 199 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 = 0.3471 r_free = 0.3471 target = 0.050770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.033875 restraints weight = 108771.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.035123 restraints weight = 49772.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.035891 restraints weight = 32803.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.036325 restraints weight = 26208.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.036573 restraints weight = 23213.383| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18413 Z= 0.225 Angle : 0.640 13.259 24980 Z= 0.317 Chirality : 0.042 0.165 2805 Planarity : 0.004 0.057 3164 Dihedral : 9.027 170.990 2552 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.28 % Allowed : 26.18 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.18), residues: 2228 helix: 1.91 (0.19), residues: 824 sheet: -0.26 (0.24), residues: 488 loop : -0.59 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 6 73 TYR 0.018 0.001 TYR 1 943 PHE 0.019 0.001 PHE 2 230 TRP 0.027 0.001 TRP 2 158 HIS 0.004 0.001 HIS 5 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 (18404) covalent geometry : angle 0.63724 / 0.32 (24955) SS BOND : bond 0.00229 / 0.12 ( 2) SS BOND : angle 1.34348 / 0.62 ( 4) hydrogen bonds : bond 0.03429 / 2.31 ( 844) hydrogen bonds : angle 4.68007 / 3.28 ( 2409) link_BETA1-4 : bond 0.00066 / 0.03 ( 3) link_BETA1-4 : angle 2.11657 / 1.07 ( 9) link_NAG-ASN : bond 0.00379 / 0.19 ( 4) link_NAG-ASN : angle 2.15930 / 1.24 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 90 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 61 ASN cc_start: 0.9227 (OUTLIER) cc_final: 0.8912 (m-40) REVERT: 1 109 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8145 (p) REVERT: 1 293 LEU cc_start: 0.9858 (OUTLIER) cc_final: 0.9653 (tt) REVERT: 1 408 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8849 (pt0) REVERT: 1 567 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8280 (t0) REVERT: 1 726 MET cc_start: 0.8506 (tpp) cc_final: 0.8086 (tpp) REVERT: 2 158 TRP cc_start: 0.8791 (OUTLIER) cc_final: 0.8540 (m-10) REVERT: 2 183 MET cc_start: 0.9178 (mtp) cc_final: 0.8942 (mtm) REVERT: 2 254 MET cc_start: 0.9478 (mtp) cc_final: 0.8895 (mmm) REVERT: 3 130 MET cc_start: 0.8925 (mmm) cc_final: 0.8601 (mmm) REVERT: 3 251 MET cc_start: 0.8977 (tpp) cc_final: 0.7875 (tmm) REVERT: 8 134 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7311 (tpp) REVERT: 10 142 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9345 (tt) outliers start: 80 outliers final: 66 residues processed: 164 average time/residue: 0.1006 time to fit residues: 28.0014 Evaluate side-chains 164 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 90 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 58 THR Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 93 HIS Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 100 VAL Chi-restraints excluded: chain 1 residue 109 SER Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 1 residue 197 VAL Chi-restraints excluded: chain 1 residue 229 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 276 VAL Chi-restraints excluded: chain 1 residue 293 LEU Chi-restraints excluded: chain 1 residue 408 GLN Chi-restraints excluded: chain 1 residue 436 LEU Chi-restraints excluded: chain 1 residue 535 MET Chi-restraints excluded: chain 1 residue 567 ASP Chi-restraints excluded: chain 1 residue 588 THR Chi-restraints excluded: chain 1 residue 591 VAL Chi-restraints excluded: chain 1 residue 614 VAL Chi-restraints excluded: chain 1 residue 632 MET Chi-restraints excluded: chain 1 residue 662 LEU Chi-restraints excluded: chain 1 residue 740 LEU Chi-restraints excluded: chain 1 residue 759 ILE Chi-restraints excluded: chain 1 residue 761 LEU Chi-restraints excluded: chain 1 residue 782 VAL Chi-restraints excluded: chain 1 residue 784 ILE Chi-restraints excluded: chain 1 residue 791 VAL Chi-restraints excluded: chain 1 residue 823 SER Chi-restraints excluded: chain 1 residue 851 ILE Chi-restraints excluded: chain 1 residue 857 THR Chi-restraints excluded: chain 1 residue 896 ILE Chi-restraints excluded: chain 1 residue 912 TYR Chi-restraints excluded: chain 1 residue 916 VAL Chi-restraints excluded: chain 1 residue 919 MET Chi-restraints excluded: chain 1 residue 963 VAL Chi-restraints excluded: chain 1 residue 966 SER Chi-restraints excluded: chain 1 residue 972 LEU Chi-restraints excluded: chain 1 residue 976 THR Chi-restraints excluded: chain 1 residue 978 ILE Chi-restraints excluded: chain 1 residue 982 LEU Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 148 LEU Chi-restraints excluded: chain 2 residue 158 TRP Chi-restraints excluded: chain 2 residue 219 LEU Chi-restraints excluded: chain 2 residue 290 GLU Chi-restraints excluded: chain 3 residue 91 THR Chi-restraints excluded: chain 3 residue 107 LEU Chi-restraints excluded: chain 3 residue 176 VAL Chi-restraints excluded: chain 4 residue 48 LEU Chi-restraints excluded: chain 4 residue 162 SER Chi-restraints excluded: chain 4 residue 165 LEU Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 29 CYS Chi-restraints excluded: chain 6 residue 31 THR Chi-restraints excluded: chain 6 residue 34 SER Chi-restraints excluded: chain 6 residue 36 LEU Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 97 VAL Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 8 residue 52 THR Chi-restraints excluded: chain 8 residue 124 LEU Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 10 residue 112 ILE Chi-restraints excluded: chain 10 residue 138 VAL Chi-restraints excluded: chain 10 residue 142 LEU Chi-restraints excluded: chain 10 residue 152 VAL Chi-restraints excluded: chain 10 residue 191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.8612 > 50: distance: 57 - 142: 16.215 distance: 60 - 139: 23.396 distance: 71 - 127: 22.638 distance: 74 - 124: 27.596 distance: 86 - 110: 26.224 distance: 89 - 107: 33.418 distance: 99 - 103: 25.983 distance: 103 - 104: 54.914 distance: 104 - 105: 29.238 distance: 105 - 106: 47.355 distance: 105 - 107: 60.861 distance: 107 - 108: 47.546 distance: 108 - 109: 30.210 distance: 108 - 111: 51.695 distance: 109 - 110: 20.865 distance: 109 - 116: 16.604 distance: 111 - 112: 32.385 distance: 112 - 113: 35.215 distance: 113 - 114: 41.197 distance: 114 - 115: 35.412 distance: 116 - 117: 19.877 distance: 117 - 118: 27.292 distance: 117 - 120: 18.048 distance: 118 - 119: 26.711 distance: 118 - 124: 11.473 distance: 120 - 121: 21.745 distance: 121 - 122: 41.643 distance: 121 - 123: 29.048 distance: 124 - 125: 51.309 distance: 125 - 126: 27.019 distance: 125 - 128: 27.810 distance: 126 - 127: 21.614 distance: 126 - 135: 23.978 distance: 128 - 129: 9.180 distance: 129 - 130: 23.955 distance: 129 - 131: 16.238 distance: 130 - 132: 12.411 distance: 131 - 133: 36.132 distance: 132 - 134: 26.826 distance: 133 - 134: 24.560 distance: 135 - 136: 29.120 distance: 136 - 137: 28.238 distance: 137 - 138: 33.427 distance: 137 - 139: 20.632 distance: 138 - 192: 26.694 distance: 139 - 140: 41.625 distance: 140 - 141: 40.240 distance: 140 - 143: 21.834 distance: 141 - 142: 30.384 distance: 141 - 147: 17.479 distance: 143 - 144: 15.001 distance: 143 - 145: 26.595 distance: 144 - 146: 11.956 distance: 147 - 148: 14.440 distance: 148 - 149: 32.699 distance: 148 - 151: 14.526 distance: 149 - 150: 14.210 distance: 149 - 156: 8.487 distance: 151 - 152: 22.236 distance: 152 - 153: 24.168 distance: 153 - 154: 18.983 distance: 153 - 155: 16.083 distance: 156 - 157: 27.216 distance: 157 - 158: 25.161 distance: 157 - 160: 16.989 distance: 158 - 159: 31.708 distance: 158 - 162: 15.424 distance: 160 - 161: 22.847 distance: 162 - 163: 9.034 distance: 163 - 164: 5.429 distance: 163 - 166: 8.448 distance: 164 - 165: 10.614 distance: 164 - 168: 5.306 distance: 166 - 167: 17.946 distance: 168 - 169: 9.593 distance: 169 - 170: 10.928 distance: 169 - 172: 11.083 distance: 170 - 171: 19.580 distance: 170 - 174: 16.231 distance: 172 - 173: 9.919