Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 07:52:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckq_30390/04_2023/7ckq_30390_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckq_30390/04_2023/7ckq_30390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckq_30390/04_2023/7ckq_30390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckq_30390/04_2023/7ckq_30390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckq_30390/04_2023/7ckq_30390_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckq_30390/04_2023/7ckq_30390_updated.pdb" } resolution = 4.4 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 87 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 17082 2.51 5 N 4741 2.21 5 O 5505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C ARG 496": "NH1" <-> "NH2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C GLU 772": "OE1" <-> "OE2" Residue "C ARG 895": "NH1" <-> "NH2" Residue "C ARG 917": "NH1" <-> "NH2" Residue "C TYR 946": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 965": "NH1" <-> "NH2" Residue "C GLU 973": "OE1" <-> "OE2" Residue "C GLU 1005": "OE1" <-> "OE2" Residue "C ARG 1074": "NH1" <-> "NH2" Residue "C GLU 1079": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 209": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D GLU 407": "OE1" <-> "OE2" Residue "D GLU 671": "OE1" <-> "OE2" Residue "D ARG 697": "NH1" <-> "NH2" Residue "D ARG 748": "NH1" <-> "NH2" Residue "D ARG 846": "NH1" <-> "NH2" Residue "D GLU 983": "OE1" <-> "OE2" Residue "D ARG 1072": "NH1" <-> "NH2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ARG 224": "NH1" <-> "NH2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 297": "OE1" <-> "OE2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F ARG 343": "NH1" <-> "NH2" Residue "F GLU 344": "OE1" <-> "OE2" Residue "F GLU 350": "OE1" <-> "OE2" Residue "F ARG 358": "NH1" <-> "NH2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 88": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I GLU 131": "OE1" <-> "OE2" Residue "I GLU 208": "OE1" <-> "OE2" Residue "I GLU 227": "OE1" <-> "OE2" Residue "I GLU 253": "OE1" <-> "OE2" Residue "H GLU 39": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 27484 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1540 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1538 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 7446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 7446 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1010} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 972 Unresolved non-hydrogen angles: 1203 Unresolved non-hydrogen dihedrals: 824 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 16, 'ASN:plan1': 9, 'ASP:plan': 19, 'PHE:plan': 12, 'GLU:plan': 24, 'ARG:plan': 46} Unresolved non-hydrogen planarities: 615 Chain: "D" Number of atoms: 7854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 7854 Classifications: {'peptide': 1137} Incomplete info: {'truncation_to_alanine': 234} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 1085} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1126 Unresolved non-hydrogen angles: 1403 Unresolved non-hydrogen dihedrals: 926 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 10, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 7, 'GLU:plan': 40, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 638 Chain: "E" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 405 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2030 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 262} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 126 Chain: "1" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1028 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "2" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 756 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain breaks: 1 Chain: "G" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2187 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 12, 'TRANS': 263} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "I" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2184 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 12, 'TRANS': 263} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "H" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 463 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P4P': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P4P': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10941 SG CYS D 60 105.868 67.722 81.401 1.00 70.25 S ATOM 11048 SG CYS D 75 110.409 69.092 81.578 1.00 82.89 S ATOM 16179 SG CYS D 818 75.584 77.686 137.816 1.00 90.51 S ATOM 16628 SG CYS D 892 74.676 78.775 134.318 1.00 83.99 S ATOM 16671 SG CYS D 899 76.071 74.909 135.470 1.00 86.21 S ATOM 16687 SG CYS D 902 72.139 76.497 136.997 1.00 90.25 S Time building chain proxies: 14.47, per 1000 atoms: 0.53 Number of scatterers: 27484 At special positions: 0 Unit cell: (150, 139, 168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 66 16.00 P 87 15.00 Mg 1 11.99 O 5505 8.00 N 4741 7.00 C 17082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.34 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 75 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 902 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 892 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 899 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 818 " Number of angles added : 6 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 26 sheets defined 31.3% alpha, 7.5% beta 31 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 9.71 Creating SS restraints... Processing helix chain 'A' and resid 33 through 46 removed outlier: 3.676A pdb=" N ARG A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 83 Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 206 through 220 removed outlier: 4.099A pdb=" N ILE A 210 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ALA A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 44 removed outlier: 3.904A pdb=" N ILE B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 No H-bonds generated for 'chain 'B' and resid 79 through 82' Processing helix chain 'B' and resid 206 through 223 removed outlier: 3.730A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 44 through 50 Processing helix chain 'C' and resid 81 through 84 No H-bonds generated for 'chain 'C' and resid 81 through 84' Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 203 through 209 removed outlier: 3.721A pdb=" N ILE C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 240 Processing helix chain 'C' and resid 248 through 255 removed outlier: 3.920A pdb=" N LEU C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 287 removed outlier: 4.021A pdb=" N PHE C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 287 " --> pdb=" O ASN C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 393 Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 412 through 424 Processing helix chain 'C' and resid 428 through 435 Processing helix chain 'C' and resid 445 through 448 No H-bonds generated for 'chain 'C' and resid 445 through 448' Processing helix chain 'C' and resid 452 through 461 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.544A pdb=" N LYS C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 501 through 504 No H-bonds generated for 'chain 'C' and resid 501 through 504' Processing helix chain 'C' and resid 508 through 510 No H-bonds generated for 'chain 'C' and resid 508 through 510' Processing helix chain 'C' and resid 615 through 618 removed outlier: 4.119A pdb=" N VAL C 618 " --> pdb=" O PRO C 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 615 through 618' Processing helix chain 'C' and resid 621 through 624 No H-bonds generated for 'chain 'C' and resid 621 through 624' Processing helix chain 'C' and resid 636 through 645 Processing helix chain 'C' and resid 663 through 667 Processing helix chain 'C' and resid 779 through 782 No H-bonds generated for 'chain 'C' and resid 779 through 782' Processing helix chain 'C' and resid 856 through 862 Processing helix chain 'C' and resid 962 through 965 No H-bonds generated for 'chain 'C' and resid 962 through 965' Processing helix chain 'C' and resid 968 through 982 Processing helix chain 'C' and resid 997 through 1003 Processing helix chain 'C' and resid 1005 through 1008 No H-bonds generated for 'chain 'C' and resid 1005 through 1008' Processing helix chain 'C' and resid 1077 through 1086 removed outlier: 3.724A pdb=" N TYR C1086 " --> pdb=" O ALA C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1095 Processing helix chain 'C' and resid 1098 through 1100 No H-bonds generated for 'chain 'C' and resid 1098 through 1100' Processing helix chain 'C' and resid 1106 through 1112 Processing helix chain 'C' and resid 1126 through 1137 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 155 through 162 Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 184 through 195 Processing helix chain 'D' and resid 201 through 219 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 253 through 274 removed outlier: 3.589A pdb=" N ASP D 256 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU D 272 " --> pdb=" O LYS D 269 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP D 273 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D 274 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 296 Processing helix chain 'D' and resid 298 through 301 No H-bonds generated for 'chain 'D' and resid 298 through 301' Processing helix chain 'D' and resid 359 through 365 removed outlier: 3.842A pdb=" N GLU D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 377 Processing helix chain 'D' and resid 383 through 390 Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 420 through 422 No H-bonds generated for 'chain 'D' and resid 420 through 422' Processing helix chain 'D' and resid 442 through 445 No H-bonds generated for 'chain 'D' and resid 442 through 445' Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 522 through 526 Processing helix chain 'D' and resid 562 through 568 Processing helix chain 'D' and resid 617 through 631 Processing helix chain 'D' and resid 634 through 654 removed outlier: 3.667A pdb=" N SER D 637 " --> pdb=" O THR D 634 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE D 648 " --> pdb=" O ASN D 645 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR D 652 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 688 removed outlier: 4.063A pdb=" N GLU D 671 " --> pdb=" O ASP D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 717 removed outlier: 4.096A pdb=" N ILE D 702 " --> pdb=" O TYR D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 731 Processing helix chain 'D' and resid 738 through 745 removed outlier: 3.551A pdb=" N GLN D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU D 744 " --> pdb=" O ASN D 740 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 745 " --> pdb=" O PHE D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 807 removed outlier: 3.807A pdb=" N HIS D 781 " --> pdb=" O PHE D 777 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY D 782 " --> pdb=" O ILE D 778 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 876 removed outlier: 3.643A pdb=" N ILE D 876 " --> pdb=" O LYS D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 903 No H-bonds generated for 'chain 'D' and resid 900 through 903' Processing helix chain 'D' and resid 920 through 927 Processing helix chain 'D' and resid 929 through 931 No H-bonds generated for 'chain 'D' and resid 929 through 931' Processing helix chain 'D' and resid 953 through 960 Processing helix chain 'D' and resid 1040 through 1050 Processing helix chain 'D' and resid 1052 through 1058 removed outlier: 3.797A pdb=" N ARG D1056 " --> pdb=" O GLN D1052 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N MET D1057 " --> pdb=" O LYS D1053 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D1058 " --> pdb=" O VAL D1054 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1052 through 1058' Processing helix chain 'D' and resid 1064 through 1066 No H-bonds generated for 'chain 'D' and resid 1064 through 1066' Processing helix chain 'D' and resid 1068 through 1072 Processing helix chain 'D' and resid 1094 through 1101 Processing helix chain 'D' and resid 1104 through 1107 No H-bonds generated for 'chain 'D' and resid 1104 through 1107' Processing helix chain 'D' and resid 1142 through 1152 Processing helix chain 'D' and resid 1163 through 1167 Processing helix chain 'E' and resid 16 through 31 removed outlier: 3.782A pdb=" N THR E 21 " --> pdb=" O TYR E 17 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'F' and resid 101 through 110 Processing helix chain 'F' and resid 117 through 129 removed outlier: 3.624A pdb=" N GLU F 129 " --> pdb=" O GLN F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 149 removed outlier: 3.994A pdb=" N GLU F 140 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 172 Processing helix chain 'F' and resid 186 through 203 removed outlier: 3.939A pdb=" N TRP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TRP F 193 " --> pdb=" O TYR F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 removed outlier: 3.883A pdb=" N THR F 218 " --> pdb=" O HIS F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 244 removed outlier: 4.160A pdb=" N ALA F 243 " --> pdb=" O PRO F 239 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 239 through 244' Processing helix chain 'F' and resid 252 through 260 removed outlier: 3.732A pdb=" N LYS F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE F 259 " --> pdb=" O GLU F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 293 through 305 Processing helix chain 'F' and resid 315 through 322 removed outlier: 4.532A pdb=" N PHE F 322 " --> pdb=" O LEU F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 335 No H-bonds generated for 'chain 'F' and resid 332 through 335' Processing helix chain 'F' and resid 343 through 358 Processing helix chain 'F' and resid 367 through 369 No H-bonds generated for 'chain 'F' and resid 367 through 369' Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 19 through 28 Processing helix chain 'G' and resid 50 through 53 Processing helix chain 'G' and resid 55 through 62 Processing helix chain 'G' and resid 66 through 72 Processing helix chain 'G' and resid 77 through 114 Processing helix chain 'G' and resid 149 through 162 removed outlier: 4.491A pdb=" N PHE G 158 " --> pdb=" O LYS G 154 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE G 159 " --> pdb=" O LEU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 243 Processing helix chain 'I' and resid 8 through 14 Processing helix chain 'I' and resid 19 through 28 Processing helix chain 'I' and resid 50 through 53 Processing helix chain 'I' and resid 55 through 62 Processing helix chain 'I' and resid 66 through 72 Processing helix chain 'I' and resid 77 through 114 Processing helix chain 'I' and resid 149 through 162 removed outlier: 4.656A pdb=" N LYS I 154 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU I 155 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA I 162 " --> pdb=" O ILE I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 243 removed outlier: 4.465A pdb=" N PHE I 230 " --> pdb=" O PRO I 226 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU I 231 " --> pdb=" O GLU I 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 36 Processing helix chain 'H' and resid 52 through 58 removed outlier: 3.772A pdb=" N TYR H 57 " --> pdb=" O ALA H 53 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 49 through 53 removed outlier: 3.581A pdb=" N GLY A 145 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA A 52 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 143 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'A' and resid 99 through 102 removed outlier: 3.989A pdb=" N VAL A 101 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE A 136 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 105 through 108 removed outlier: 3.530A pdb=" N GLY A 105 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 173 through 182 removed outlier: 3.913A pdb=" N SER A 174 " --> pdb=" O TRP A 199 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N TRP A 199 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL A 176 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP A 197 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TYR A 178 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N THR A 195 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL A 180 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS A 193 " --> pdb=" O VAL A 180 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 20 through 25 removed outlier: 3.643A pdb=" N GLN B 179 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 55 through 57 Processing sheet with id= H, first strand: chain 'B' and resid 105 through 108 removed outlier: 3.505A pdb=" N LEU B 130 " --> pdb=" O GLY B 105 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 62 through 66 Processing sheet with id= J, first strand: chain 'C' and resid 69 through 71 Processing sheet with id= K, first strand: chain 'C' and resid 137 through 140 Processing sheet with id= L, first strand: chain 'C' and resid 144 through 148 removed outlier: 3.783A pdb=" N SER C 147 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 562 through 565 removed outlier: 3.638A pdb=" N ASP C 562 " --> pdb=" O TYR C 547 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 592 through 595 removed outlier: 3.780A pdb=" N ILE C 592 " --> pdb=" O VAL C 603 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 603 " --> pdb=" O ILE C 592 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR C 601 " --> pdb=" O ALA C 594 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 708 through 711 removed outlier: 3.554A pdb=" N VAL C 692 " --> pdb=" O ASP C 708 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 1032 through 1036 removed outlier: 6.671A pdb=" N ILE C 955 " --> pdb=" O GLY C 762 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 924 through 926 Processing sheet with id= R, first strand: chain 'C' and resid 789 through 800 removed outlier: 4.285A pdb=" N SER C 789 " --> pdb=" O ARG C 917 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG C 917 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR C 795 " --> pdb=" O VAL C 911 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL C 911 " --> pdb=" O TYR C 795 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER C 797 " --> pdb=" O VAL C 909 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 909 " --> pdb=" O SER C 797 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN C 907 " --> pdb=" O ALA C 799 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 908 " --> pdb=" O PHE C 893 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL C 914 " --> pdb=" O ILE C 887 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE C 887 " --> pdb=" O VAL C 914 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 94 through 96 Processing sheet with id= T, first strand: chain 'D' and resid 339 through 342 removed outlier: 3.906A pdb=" N GLY D 340 " --> pdb=" O VAL D 457 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER D 342 " --> pdb=" O MET D 455 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET D 455 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 426 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN D 424 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 344 through 346 removed outlier: 5.721A pdb=" N ILE D 436 " --> pdb=" O VAL D 345 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 135 through 138 removed outlier: 3.568A pdb=" N VAL D 135 " --> pdb=" O SER D 169 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 169 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLN D 167 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 209 through 211 removed outlier: 3.808A pdb=" N ILE G 135 " --> pdb=" O THR G 192 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE G 190 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 220 through 223 removed outlier: 4.099A pdb=" N TYR G 222 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL G 270 " --> pdb=" O TYR G 222 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS G 273 " --> pdb=" O TYR G 252 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 209 through 211 removed outlier: 3.734A pdb=" N ILE I 135 " --> pdb=" O THR I 192 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE I 190 " --> pdb=" O THR I 137 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS I 189 " --> pdb=" O THR I 173 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE I 255 " --> pdb=" O TYR I 170 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA I 172 " --> pdb=" O GLU I 253 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE I 174 " --> pdb=" O VAL I 251 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL I 251 " --> pdb=" O PHE I 174 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS I 273 " --> pdb=" O TYR I 252 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE I 256 " --> pdb=" O ARG I 269 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 21 through 26 removed outlier: 4.201A pdb=" N LYS H 4 " --> pdb=" O THR H 48 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR H 48 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLN H 8 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE H 44 " --> pdb=" O GLN H 8 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 10.00 Time building geometry restraints manager: 12.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9134 1.35 - 1.48: 6664 1.48 - 1.61: 12110 1.61 - 1.74: 63 1.74 - 1.87: 124 Bond restraints: 28095 Sorted by residual: bond pdb=" C ASP C 551 " pdb=" N PRO C 552 " ideal model delta sigma weight residual 1.336 1.384 -0.048 1.20e-02 6.94e+03 1.57e+01 bond pdb=" C1C P4P G 300 " pdb=" P P4P G 300 " ideal model delta sigma weight residual 1.795 1.867 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1A P4P G 300 " pdb=" P P4P G 300 " ideal model delta sigma weight residual 1.795 1.866 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1B P4P I 300 " pdb=" P P4P I 300 " ideal model delta sigma weight residual 1.795 1.866 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1A P4P I 300 " pdb=" P P4P I 300 " ideal model delta sigma weight residual 1.795 1.866 -0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 28090 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.36: 1232 106.36 - 113.28: 15326 113.28 - 120.21: 10128 120.21 - 127.13: 11564 127.13 - 134.05: 375 Bond angle restraints: 38625 Sorted by residual: angle pdb=" N GLU D 834 " pdb=" CA GLU D 834 " pdb=" C GLU D 834 " ideal model delta sigma weight residual 109.52 120.06 -10.54 1.55e+00 4.16e-01 4.63e+01 angle pdb=" N ILE D 836 " pdb=" CA ILE D 836 " pdb=" C ILE D 836 " ideal model delta sigma weight residual 109.58 116.61 -7.03 1.29e+00 6.01e-01 2.97e+01 angle pdb=" C GLU H 13 " pdb=" N VAL H 14 " pdb=" CA VAL H 14 " ideal model delta sigma weight residual 122.13 129.82 -7.69 1.85e+00 2.92e-01 1.73e+01 angle pdb=" C LYS H 38 " pdb=" N GLU H 39 " pdb=" CA GLU H 39 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.72e+01 angle pdb=" N GLN D 989 " pdb=" CA GLN D 989 " pdb=" C GLN D 989 " ideal model delta sigma weight residual 114.56 109.32 5.24 1.27e+00 6.20e-01 1.70e+01 ... (remaining 38620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 16150 35.53 - 71.06: 479 71.06 - 106.59: 25 106.59 - 142.12: 4 142.12 - 177.65: 2 Dihedral angle restraints: 16660 sinusoidal: 6299 harmonic: 10361 Sorted by residual: dihedral pdb=" CA PRO H 49 " pdb=" C PRO H 49 " pdb=" N VAL H 50 " pdb=" CA VAL H 50 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LYS C 702 " pdb=" C LYS C 702 " pdb=" N VAL C 703 " pdb=" CA VAL C 703 " ideal model delta harmonic sigma weight residual 180.00 157.48 22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA GLY C 866 " pdb=" C GLY C 866 " pdb=" N GLU C 867 " pdb=" CA GLU C 867 " ideal model delta harmonic sigma weight residual 180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 16657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 4014 0.075 - 0.150: 527 0.150 - 0.225: 40 0.225 - 0.301: 6 0.301 - 0.376: 1 Chirality restraints: 4588 Sorted by residual: chirality pdb=" CB ILE I 255 " pdb=" CA ILE I 255 " pdb=" CG1 ILE I 255 " pdb=" CG2 ILE I 255 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB ILE G 255 " pdb=" CA ILE G 255 " pdb=" CG1 ILE G 255 " pdb=" CG2 ILE G 255 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB THR D 142 " pdb=" CA THR D 142 " pdb=" OG1 THR D 142 " pdb=" CG2 THR D 142 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 4585 not shown) Planarity restraints: 4763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 234 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO D 235 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 988 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C GLN D 988 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN D 988 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN D 989 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 475 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO C 476 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 476 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 476 " 0.033 5.00e-02 4.00e+02 ... (remaining 4760 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 862 2.70 - 3.25: 24593 3.25 - 3.80: 44070 3.80 - 4.35: 53575 4.35 - 4.90: 86632 Nonbonded interactions: 209732 Sorted by model distance: nonbonded pdb=" O GLN A 179 " pdb=" OG1 THR A 195 " model vdw 2.153 2.440 nonbonded pdb=" OD2 ASP D 451 " pdb="MG MG D1501 " model vdw 2.181 2.170 nonbonded pdb=" OG SER I 181 " pdb=" OE1 GLU I 184 " model vdw 2.298 2.440 nonbonded pdb=" O ARG B 42 " pdb=" OG SER B 46 " model vdw 2.326 2.440 nonbonded pdb=" O ILE G 134 " pdb=" OG1 THR G 210 " model vdw 2.333 2.440 ... (remaining 209727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 15 or (resid 16 through 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 40 or (resid 41 through \ 42 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name NE or name CZ )) or resid 43 through 56 or (resid 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 67 or (resid 68 and (na \ me N or name CA or name C or name O or name CB )) or resid 69 through 97 or (res \ id 98 and (name N or name CA or name C or name O or name CB )) or resid 99 or (r \ esid 100 and (name N or name CA or name C or name O or name CB )) or resid 101 o \ r (resid 102 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 03 through 131 or (resid 132 and (name N or name CA or name C or name O or name \ CB )) or resid 133 through 162 or (resid 163 and (name N or name CA or name C or \ name O or name CB )) or resid 164 through 200 or (resid 201 and (name N or name \ CA or name C or name O or name CB )) or resid 202 through 206 or (resid 207 and \ (name N or name CA or name C or name O or name CB )) or resid 208 through 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB or name CG )) \ or (resid 213 through 215 and (name N or name CA or name C or name O or name CB \ )) or resid 216 through 225)) selection = (chain 'B' and (resid 6 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or (resid 11 and (name N or name CA or name C or name O \ or name CB or name OG1)) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 16 or (resid 17 throug \ h 19 and (name N or name CA or name C or name O or name CB )) or resid 20 throug \ h 22 or (resid 23 and (name N or name CA or name C or name O or name CB )) or re \ sid 24 through 29 or (resid 30 and (name N or name CA or name C or name O or nam \ e CB )) or resid 31 through 33 or (resid 34 and (name N or name CA or name C or \ name O or name CB or name OG1)) or resid 35 through 47 or (resid 48 and (name N \ or name CA or name C or name O or name CB )) or resid 49 through 75 or (resid 76 \ through 77 and (name N or name CA or name C or name O or name CB or name OG1)) \ or resid 78 or (resid 79 and (name N or name CA or name C or name O or name CB o \ r name CG1)) or resid 80 through 105 or (resid 106 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 107 through 121 or (resid 122 an \ d (name N or name CA or name C or name O or name CB )) or resid 123 or (resid 12 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 125 through \ 128 or (resid 129 and (name N or name CA or name C or name O or name CB or name \ OG1)) or (resid 130 and (name N or name CA or name C or name O or name CB )) or \ resid 131 through 140 or (resid 141 and (name N or name CA or name C or name O o \ r name CB or name OG1)) or resid 142 through 147 or (resid 148 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ )) or resid 149 through 165 or (resid 166 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2)) or resid 16 \ 7 through 170 or (resid 171 and (name N or name CA or name C or name O or name C \ B or name OG1)) or resid 172 through 178 or (resid 179 and (name N or name CA or \ name C or name O or name CB )) or resid 180 through 183 or (resid 184 and (name \ N or name CA or name C or name O or name CB )) or resid 185 through 190 or (res \ id 191 and (name N or name CA or name C or name O or name CB )) or resid 192 thr \ ough 225)) } ncs_group { reference = (chain 'G' and (resid 2 through 11 or (resid 12 through 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 through 38 or (resid 39 and (nam \ e N or name CA or name C or name O or name CB )) or resid 40 through 46 or (resi \ d 47 and (name N or name CA or name C or name O or name CB )) or resid 48 throug \ h 49 or (resid 50 and (name N or name CA or name C or name O or name CB )) or re \ sid 51 through 144 or (resid 145 and (name N or name CA or name C or name O or n \ ame CB )) or resid 146 through 266 or (resid 267 and (name N or name CA or name \ C or name O or name CB )) or resid 268 through 271 or (resid 272 and (name N or \ name CA or name C or name O or name CB )) or resid 273 through 277 or resid 300) \ ) selection = (chain 'I' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 6 or (resid 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 9 or (resid 10 and (name N o \ r name CA or name C or name O or name CB )) or resid 11 through 146 or (resid 14 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 148 through \ 154 or (resid 155 and (name N or name CA or name C or name O or name CB )) or re \ sid 156 or (resid 157 and (name N or name CA or name C or name O or name CB )) o \ r resid 158 through 275 or (resid 276 through 277 and (name N or name CA or name \ C or name O or name CB )) or resid 300)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 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: 2.010 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: 8.310 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 79.100 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 28095 Z= 0.203 Angle : 0.690 10.544 38625 Z= 0.379 Chirality : 0.049 0.376 4588 Planarity : 0.005 0.068 4763 Dihedral : 15.781 177.650 9972 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.59 % Favored : 94.38 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.10), residues: 3558 helix: -3.47 (0.08), residues: 1251 sheet: -1.92 (0.27), residues: 309 loop : -3.22 (0.11), residues: 1998 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 799 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 804 average time/residue: 0.4380 time to fit residues: 534.9633 Evaluate side-chains 509 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 507 time to evaluate : 3.027 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2525 time to fit residues: 4.9362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 0.3980 chunk 275 optimal weight: 5.9990 chunk 153 optimal weight: 0.0770 chunk 94 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 330 optimal weight: 8.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 63 HIS B 114 HIS B 190 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 419 GLN C 475 ASN ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 ASN C 862 HIS C 915 GLN ** C 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS D 180 GLN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 GLN D 677 GLN D 743 GLN ** D 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1052 GLN D1058 GLN ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN I 167 ASN I 197 ASN I 199 GLN I 259 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 28095 Z= 0.186 Angle : 0.568 12.160 38625 Z= 0.295 Chirality : 0.042 0.206 4588 Planarity : 0.005 0.060 4763 Dihedral : 15.142 179.775 4673 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.92 % Favored : 95.05 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.12), residues: 3558 helix: -1.69 (0.13), residues: 1263 sheet: -1.71 (0.26), residues: 363 loop : -2.69 (0.12), residues: 1932 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 623 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 623 average time/residue: 0.3944 time to fit residues: 389.0909 Evaluate side-chains 465 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 464 time to evaluate : 3.205 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2398 time to fit residues: 5.1179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 275 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 331 optimal weight: 9.9990 chunk 357 optimal weight: 0.4980 chunk 294 optimal weight: 0.3980 chunk 328 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 265 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS B 63 HIS C 38 GLN C 475 ASN ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 ASN ** C 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN D 677 GLN D 740 ASN F 142 ASN ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 ASN I 232 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 28095 Z= 0.177 Angle : 0.553 13.246 38625 Z= 0.283 Chirality : 0.042 0.214 4588 Planarity : 0.004 0.077 4763 Dihedral : 15.116 180.000 4673 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.13), residues: 3558 helix: -0.96 (0.14), residues: 1282 sheet: -1.23 (0.27), residues: 342 loop : -2.43 (0.12), residues: 1934 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 577 time to evaluate : 3.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 580 average time/residue: 0.3826 time to fit residues: 355.9900 Evaluate side-chains 430 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 429 time to evaluate : 3.238 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2410 time to fit residues: 5.0509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 10.0000 chunk 248 optimal weight: 0.9980 chunk 171 optimal weight: 0.0870 chunk 36 optimal weight: 7.9990 chunk 158 optimal weight: 8.9990 chunk 222 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 351 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 314 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 81 HIS C 475 ASN C 642 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 GLN D 740 ASN F 142 ASN ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 28095 Z= 0.163 Angle : 0.537 10.099 38625 Z= 0.277 Chirality : 0.041 0.173 4588 Planarity : 0.004 0.070 4763 Dihedral : 15.028 179.222 4673 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.13), residues: 3558 helix: -0.58 (0.14), residues: 1291 sheet: -1.40 (0.26), residues: 373 loop : -2.24 (0.13), residues: 1894 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 565 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 567 average time/residue: 0.3826 time to fit residues: 351.2717 Evaluate side-chains 434 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 433 time to evaluate : 3.108 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2518 time to fit residues: 4.7239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 300 optimal weight: 8.9990 chunk 243 optimal weight: 30.0000 chunk 0 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 315 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN C 475 ASN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN D 255 ASN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN D 677 GLN ** D 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.093 28095 Z= 0.342 Angle : 0.706 15.689 38625 Z= 0.364 Chirality : 0.046 0.527 4588 Planarity : 0.005 0.074 4763 Dihedral : 15.316 178.240 4673 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.52 % Favored : 93.45 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.13), residues: 3558 helix: -0.63 (0.14), residues: 1296 sheet: -1.62 (0.25), residues: 378 loop : -2.12 (0.13), residues: 1884 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 551 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 552 average time/residue: 0.3841 time to fit residues: 343.9337 Evaluate side-chains 416 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 415 time to evaluate : 3.170 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2330 time to fit residues: 4.6646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 3.9990 chunk 316 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 206 optimal weight: 0.2980 chunk 86 optimal weight: 10.0000 chunk 352 optimal weight: 7.9990 chunk 292 optimal weight: 0.0070 chunk 163 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 184 optimal weight: 8.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN C 280 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 GLN D 740 ASN F 142 ASN ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 28095 Z= 0.173 Angle : 0.569 9.114 38625 Z= 0.292 Chirality : 0.043 0.191 4588 Planarity : 0.004 0.061 4763 Dihedral : 15.210 179.590 4673 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.00 % Favored : 94.97 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.14), residues: 3558 helix: -0.47 (0.14), residues: 1340 sheet: -1.66 (0.26), residues: 364 loop : -2.06 (0.14), residues: 1854 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 565 time to evaluate : 3.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 566 average time/residue: 0.3939 time to fit residues: 360.7427 Evaluate side-chains 421 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 420 time to evaluate : 3.163 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2465 time to fit residues: 4.7490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 257 optimal weight: 8.9990 chunk 199 optimal weight: 0.7980 chunk 296 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 350 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 161 optimal weight: 0.0870 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 720 GLN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 ASN G 52 HIS ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 28095 Z= 0.182 Angle : 0.577 9.708 38625 Z= 0.295 Chirality : 0.043 0.166 4588 Planarity : 0.004 0.059 4763 Dihedral : 15.178 179.345 4673 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.90 % Favored : 94.07 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.14), residues: 3558 helix: -0.30 (0.14), residues: 1327 sheet: -1.66 (0.26), residues: 372 loop : -1.94 (0.14), residues: 1859 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 559 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 560 average time/residue: 0.3840 time to fit residues: 347.4555 Evaluate side-chains 433 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 432 time to evaluate : 3.140 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2349 time to fit residues: 4.7308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 209 optimal weight: 7.9990 chunk 105 optimal weight: 0.0040 chunk 68 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 223 optimal weight: 0.6980 chunk 239 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 275 optimal weight: 6.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN C 642 ASN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 ASN ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 28095 Z= 0.164 Angle : 0.574 9.941 38625 Z= 0.292 Chirality : 0.043 0.213 4588 Planarity : 0.004 0.064 4763 Dihedral : 15.140 179.316 4673 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.14 % Favored : 94.83 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 3558 helix: -0.23 (0.15), residues: 1337 sheet: -1.43 (0.26), residues: 374 loop : -1.87 (0.14), residues: 1847 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 564 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 565 average time/residue: 0.3760 time to fit residues: 347.8699 Evaluate side-chains 446 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 445 time to evaluate : 3.250 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2386 time to fit residues: 4.7401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 2.9990 chunk 336 optimal weight: 0.4980 chunk 306 optimal weight: 6.9990 chunk 326 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 142 optimal weight: 0.0070 chunk 256 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 309 optimal weight: 5.9990 chunk 325 optimal weight: 5.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 ASN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 GLN ** D 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 28095 Z= 0.207 Angle : 0.605 11.832 38625 Z= 0.309 Chirality : 0.043 0.202 4588 Planarity : 0.004 0.069 4763 Dihedral : 15.211 178.575 4673 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.30 % Favored : 93.68 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3558 helix: -0.23 (0.15), residues: 1330 sheet: -1.60 (0.25), residues: 399 loop : -1.85 (0.14), residues: 1829 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 542 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 543 average time/residue: 0.3818 time to fit residues: 340.0864 Evaluate side-chains 427 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 426 time to evaluate : 3.280 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2830 time to fit residues: 5.1816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 0.9990 chunk 345 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 chunk 164 optimal weight: 8.9990 chunk 240 optimal weight: 0.9980 chunk 362 optimal weight: 6.9990 chunk 333 optimal weight: 0.0370 chunk 288 optimal weight: 0.7980 chunk 29 optimal weight: 0.0170 chunk 223 optimal weight: 0.5980 chunk 177 optimal weight: 0.6980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 GLN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 ASN G 52 HIS ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.6389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 28095 Z= 0.164 Angle : 0.598 9.859 38625 Z= 0.301 Chirality : 0.043 0.187 4588 Planarity : 0.004 0.073 4763 Dihedral : 15.216 179.746 4673 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3558 helix: -0.21 (0.15), residues: 1333 sheet: -1.46 (0.26), residues: 385 loop : -1.78 (0.14), residues: 1840 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 538 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 539 average time/residue: 0.3705 time to fit residues: 330.9051 Evaluate side-chains 439 residues out of total 3126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 438 time to evaluate : 3.360 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2540 time to fit residues: 5.1748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 9.9990 chunk 307 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 266 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 289 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 296 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN C 642 ASN C1062 GLN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 GLN ** D 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1164 ASN ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.113466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096994 restraints weight = 106008.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.099231 restraints weight = 69175.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.100812 restraints weight = 49062.811| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 28095 Z= 0.205 Angle : 0.608 11.129 38625 Z= 0.310 Chirality : 0.044 0.382 4588 Planarity : 0.004 0.060 4763 Dihedral : 15.225 179.031 4673 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.24 % Favored : 93.73 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3558 helix: -0.24 (0.14), residues: 1334 sheet: -1.36 (0.26), residues: 375 loop : -1.76 (0.14), residues: 1849 =============================================================================== Job complete usr+sys time: 6570.93 seconds wall clock time: 119 minutes 11.86 seconds (7151.86 seconds total)