Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 14 01:10:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh5_0001/10_2023/6gh5_0001.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh5_0001/10_2023/6gh5_0001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh5_0001/10_2023/6gh5_0001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh5_0001/10_2023/6gh5_0001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh5_0001/10_2023/6gh5_0001.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gh5_0001/10_2023/6gh5_0001.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 92 5.49 5 S 97 5.16 5 C 17442 2.51 5 N 5014 2.21 5 O 5671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 542": "NH1" <-> "NH2" Residue "C LEU 699": "CD1" <-> "CD2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C ARG 720": "NH1" <-> "NH2" Residue "C GLU 899": "OE1" <-> "OE2" Residue "C ARG 919": "NH1" <-> "NH2" Residue "C ARG 1033": "NH1" <-> "NH2" Residue "C ARG 1034": "NH1" <-> "NH2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C ARG 1106": "NH1" <-> "NH2" Residue "C PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1171": "NH1" <-> "NH2" Residue "C PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1211": "NH1" <-> "NH2" Residue "C TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1301": "NH1" <-> "NH2" Residue "C TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D ARG 551": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "D ARG 709": "NH1" <-> "NH2" Residue "D PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ARG 798": "NH1" <-> "NH2" Residue "D ARG 838": "NH1" <-> "NH2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 1148": "NH1" <-> "NH2" Residue "D ARG 1149": "NH1" <-> "NH2" Residue "D ARG 1242": "NH1" <-> "NH2" Residue "D ARG 1258": "NH1" <-> "NH2" Residue "D ARG 1341": "NH1" <-> "NH2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "D ARG 1369": "NH1" <-> "NH2" Residue "D ARG 1372": "NH1" <-> "NH2" Residue "E ARG 16": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 28316 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2302 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1733 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 79 Chain: "C" Number of atoms: 10034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10034 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 674 Unresolved non-hydrogen dihedrals: 478 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 7, 'GLU:plan': 27, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 362 Chain: "D" Number of atoms: 9790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 9790 Classifications: {'peptide': 1345} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 51, 'TRANS': 1290} Chain breaks: 4 Unresolved non-hydrogen bonds: 699 Unresolved non-hydrogen angles: 851 Unresolved non-hydrogen dihedrals: 604 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 12, 'GLU:plan': 25, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 466 Chain: "E" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 565 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "M" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2002 Classifications: {'peptide': 338} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 192} Link IDs: {'PTRANS': 10, 'TRANS': 327} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 652 Unresolved non-hydrogen angles: 837 Unresolved non-hydrogen dihedrals: 509 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'UNK:plan-1': 50, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 398 Chain: "F" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 944 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "G" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 946 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N ASP M 168 " occ=0.20 ... (3 atoms not shown) pdb=" CB ASP M 168 " occ=0.20 residue: pdb=" N GLU M 169 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLU M 169 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 Time building chain proxies: 14.71, per 1000 atoms: 0.52 Number of scatterers: 28316 At special positions: 0 Unit cell: (140.98, 167.48, 160.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 92 15.00 O 5671 8.00 N 5014 7.00 C 17442 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: 11.61 Conformation dependent library (CDL) restraints added in 4.1 seconds 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6768 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 38 sheets defined 38.7% alpha, 10.7% beta 29 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 9.52 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.743A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.696A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.714A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.569A pdb=" N ASP A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 261 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 295 through 307 removed outlier: 3.617A pdb=" N SER A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.628A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.883A pdb=" N GLU B 163 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'C' and resid 5 through 10 removed outlier: 4.006A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.625A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.734A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.877A pdb=" N GLY C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.047A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.844A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.551A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.521A pdb=" N LEU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 4.168A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.551A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 476 removed outlier: 4.053A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 removed outlier: 4.031A pdb=" N ASP C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 506 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.593A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.821A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix chain 'C' and resid 656 through 660 removed outlier: 4.157A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.598A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.603A pdb=" N ASN C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 713 removed outlier: 3.782A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.786A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 907 through 911 removed outlier: 4.245A pdb=" N ALA C 910 " --> pdb=" O GLY C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 979 removed outlier: 3.694A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.675A pdb=" N LEU C1000 " --> pdb=" O TRP C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1037 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.636A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1168 through 1176 Processing helix chain 'C' and resid 1191 through 1201 removed outlier: 3.618A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.686A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.852A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.776A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 193 through 207 removed outlier: 3.657A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 231 removed outlier: 3.914A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.555A pdb=" N LEU D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.820A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.648A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 406 through 417 removed outlier: 3.854A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 573 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 613 through 635 removed outlier: 3.814A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 702 removed outlier: 4.178A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 removed outlier: 3.554A pdb=" N GLY D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.555A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.968A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP D 785 " --> pdb=" O LYS D 781 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR D 786 " --> pdb=" O GLY D 782 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.740A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.524A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1223 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.570A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.472A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1309 through 1315 removed outlier: 3.564A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.618A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 3.822A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.801A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.749A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 119 through 130 removed outlier: 3.524A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 146 removed outlier: 3.508A pdb=" N ALA M 139 " --> pdb=" O ASP M 135 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP M 146 " --> pdb=" O THR M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 164 Processing helix chain 'M' and resid 171 through 184 removed outlier: 3.823A pdb=" N VAL M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 203 Processing helix chain 'M' and resid 212 through 223 removed outlier: 3.774A pdb=" N ALA M 216 " --> pdb=" O TRP M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 239 removed outlier: 3.915A pdb=" N ARG M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 255 removed outlier: 4.118A pdb=" N LYS M 247 " --> pdb=" O GLU M 243 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA M 249 " --> pdb=" O VAL M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 355 removed outlier: 3.518A pdb=" N LEU M 329 " --> pdb=" O GLU M 325 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP M 338 " --> pdb=" O GLU M 334 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR M 339 " --> pdb=" O SER M 335 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU M 341 " --> pdb=" O ASN M 337 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG M 342 " --> pdb=" O ASP M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 374 removed outlier: 4.156A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 388 Processing helix chain 'M' and resid 416 through 430 removed outlier: 3.815A pdb=" N ALA M 430 " --> pdb=" O LYS M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 438 through 449 removed outlier: 3.738A pdb=" N LEU M 442 " --> pdb=" O SER M 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 456 through 464 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 9.340A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 105 removed outlier: 3.581A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.902A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 19 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 61 removed outlier: 7.155A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.882A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 67 through 71 removed outlier: 4.006A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 67 through 71 removed outlier: 4.006A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.979A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 230 through 231 Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.621A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 256 Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.229A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 633 through 637 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.359A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 722 through 726 removed outlier: 7.011A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 4.224A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1068 Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 840 removed outlier: 3.938A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AC9, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD1, first strand: chain 'D' and resid 104 through 111 removed outlier: 6.348A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 350 through 357 Processing sheet with id=AD3, first strand: chain 'D' and resid 526 through 528 removed outlier: 3.542A pdb=" N LEU D 527 " --> pdb=" O LYS D 549 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 748 through 749 removed outlier: 3.525A pdb=" N SER D 753 " --> pdb=" O LYS D 749 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD6, first strand: chain 'D' and resid 959 through 961 Processing sheet with id=AD7, first strand: chain 'D' and resid 966 through 967 Processing sheet with id=AD8, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AD9, first strand: chain 'D' and resid 1059 through 1060 Processing sheet with id=AE1, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE2, first strand: chain 'M' and resid 287 through 288 removed outlier: 5.956A pdb=" N UNK M 277 " --> pdb=" O HIS M 391 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 13.42 Time building geometry restraints manager: 12.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.22: 776 1.22 - 1.41: 10343 1.41 - 1.60: 17155 1.60 - 1.79: 514 1.79 - 1.98: 104 Bond restraints: 28892 Sorted by residual: bond pdb=" C HIS C 526 " pdb=" O HIS C 526 " ideal model delta sigma weight residual 1.237 1.026 0.211 1.19e-02 7.06e+03 3.14e+02 bond pdb=" C TYR C 555 " pdb=" O TYR C 555 " ideal model delta sigma weight residual 1.236 1.436 -0.200 1.15e-02 7.56e+03 3.01e+02 bond pdb=" C VAL C1225 " pdb=" O VAL C1225 " ideal model delta sigma weight residual 1.236 1.410 -0.175 1.01e-02 9.80e+03 2.99e+02 bond pdb=" N GLY D 333 " pdb=" CA GLY D 333 " ideal model delta sigma weight residual 1.449 1.698 -0.248 1.45e-02 4.76e+03 2.93e+02 bond pdb=" CZ ARG D 99 " pdb=" NH1 ARG D 99 " ideal model delta sigma weight residual 1.323 1.560 -0.237 1.40e-02 5.10e+03 2.86e+02 ... (remaining 28887 not shown) Histogram of bond angle deviations from ideal: 65.55 - 82.56: 13 82.56 - 99.56: 302 99.56 - 116.57: 20857 116.57 - 133.57: 18498 133.57 - 150.58: 21 Bond angle restraints: 39691 Sorted by residual: angle pdb=" N ASP D 462 " pdb=" CA ASP D 462 " pdb=" C ASP D 462 " ideal model delta sigma weight residual 113.02 86.00 27.02 1.49e+00 4.50e-01 3.29e+02 angle pdb=" C GLU D 765 " pdb=" N GLY D 766 " pdb=" CA GLY D 766 " ideal model delta sigma weight residual 120.64 100.22 20.42 1.26e+00 6.30e-01 2.63e+02 angle pdb=" CB ILE A 61 " pdb=" CG1 ILE A 61 " pdb=" CD1 ILE A 61 " ideal model delta sigma weight residual 113.80 79.98 33.82 2.10e+00 2.27e-01 2.59e+02 angle pdb=" CG MET C 805 " pdb=" SD MET C 805 " pdb=" CE MET C 805 " ideal model delta sigma weight residual 100.90 65.55 35.35 2.20e+00 2.07e-01 2.58e+02 angle pdb=" N ASP M 186 " pdb=" CA ASP M 186 " pdb=" CB ASP M 186 " ideal model delta sigma weight residual 110.42 129.15 -18.73 1.18e+00 7.18e-01 2.52e+02 ... (remaining 39686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 16591 35.30 - 70.60: 629 70.60 - 105.90: 26 105.90 - 141.20: 3 141.20 - 176.50: 7 Dihedral angle restraints: 17256 sinusoidal: 6781 harmonic: 10475 Sorted by residual: dihedral pdb=" N TYR C 555 " pdb=" C TYR C 555 " pdb=" CA TYR C 555 " pdb=" CB TYR C 555 " ideal model delta harmonic sigma weight residual 122.80 159.58 -36.78 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" C TYR C 555 " pdb=" N TYR C 555 " pdb=" CA TYR C 555 " pdb=" CB TYR C 555 " ideal model delta harmonic sigma weight residual -122.60 -159.21 36.61 0 2.50e+00 1.60e-01 2.14e+02 dihedral pdb=" N GLU D 534 " pdb=" C GLU D 534 " pdb=" CA GLU D 534 " pdb=" CB GLU D 534 " ideal model delta harmonic sigma weight residual 122.80 159.04 -36.24 0 2.50e+00 1.60e-01 2.10e+02 ... (remaining 17253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.615: 4665 0.615 - 1.230: 98 1.230 - 1.844: 10 1.844 - 2.459: 0 2.459 - 3.074: 1 Chirality restraints: 4774 Sorted by residual: chirality pdb=" CG LEU C 699 " pdb=" CB LEU C 699 " pdb=" CD1 LEU C 699 " pdb=" CD2 LEU C 699 " both_signs ideal model delta sigma weight residual False -2.59 0.48 -3.07 2.00e-01 2.50e+01 2.36e+02 chirality pdb=" CA GLU D 534 " pdb=" N GLU D 534 " pdb=" C GLU D 534 " pdb=" CB GLU D 534 " both_signs ideal model delta sigma weight residual False 2.51 0.87 1.64 2.00e-01 2.50e+01 6.71e+01 chirality pdb=" CA TYR C 555 " pdb=" N TYR C 555 " pdb=" C TYR C 555 " pdb=" CB TYR C 555 " both_signs ideal model delta sigma weight residual False 2.51 0.88 1.63 2.00e-01 2.50e+01 6.67e+01 ... (remaining 4771 not shown) Planarity restraints: 4889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C1276 " 0.018 2.00e-02 2.50e+03 1.06e-01 2.80e+02 pdb=" CG TRP C1276 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP C1276 " 0.123 2.00e-02 2.50e+03 pdb=" CD2 TRP C1276 " -0.181 2.00e-02 2.50e+03 pdb=" NE1 TRP C1276 " 0.111 2.00e-02 2.50e+03 pdb=" CE2 TRP C1276 " -0.127 2.00e-02 2.50e+03 pdb=" CE3 TRP C1276 " 0.047 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1276 " -0.112 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1276 " 0.065 2.00e-02 2.50e+03 pdb=" CH2 TRP C1276 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 380 " -0.071 2.00e-02 2.50e+03 1.10e-01 2.11e+02 pdb=" CG PHE D 380 " 0.097 2.00e-02 2.50e+03 pdb=" CD1 PHE D 380 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 380 " 0.104 2.00e-02 2.50e+03 pdb=" CE1 PHE D 380 " -0.066 2.00e-02 2.50e+03 pdb=" CE2 PHE D 380 " -0.191 2.00e-02 2.50e+03 pdb=" CZ PHE D 380 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 115 " 0.128 2.00e-02 2.50e+03 7.03e-02 1.23e+02 pdb=" CG TRP D 115 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 115 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP D 115 " -0.076 2.00e-02 2.50e+03 pdb=" NE1 TRP D 115 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP D 115 " 0.059 2.00e-02 2.50e+03 pdb=" CE3 TRP D 115 " -0.116 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 115 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 115 " 0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP D 115 " 0.077 2.00e-02 2.50e+03 ... (remaining 4886 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 177 2.46 - 3.07: 19488 3.07 - 3.68: 41568 3.68 - 4.29: 62237 4.29 - 4.90: 96609 Nonbonded interactions: 220079 Sorted by model distance: nonbonded pdb=" CD1 ILE D 316 " pdb=" N THR D 317 " model vdw 1.847 3.540 nonbonded pdb=" O GLY C1260 " pdb=" NH1 ARG D 346 " model vdw 1.882 2.520 nonbonded pdb=" CA GLY C1260 " pdb=" NH1 ARG D 346 " model vdw 1.994 3.520 nonbonded pdb=" O HIS D 113 " pdb=" CB HIS D 113 " model vdw 2.030 2.752 nonbonded pdb=" CD1 ILE D 316 " pdb=" O THR D 317 " model vdw 2.049 3.460 ... (remaining 220074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.030 Extract box with map and model: 5.280 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 82.170 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 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 : 0.033 0.383 28892 Z= 2.221 Angle : 3.297 39.068 39691 Z= 1.968 Chirality : 0.221 3.074 4774 Planarity : 0.019 0.160 4889 Dihedral : 17.287 176.499 10488 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 2.30 % Allowed : 11.02 % Favored : 86.68 % Rotamer: Outliers : 4.29 % Allowed : 8.51 % Favored : 87.20 % Cbeta Deviations : 9.84 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 2.08 % Twisted General : 0.55 % 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: -4.34 (0.11), residues: 3567 helix: -3.21 (0.10), residues: 1267 sheet: -1.73 (0.27), residues: 316 loop : -2.91 (0.11), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 615 time to evaluate : 3.178 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 outliers start: 111 outliers final: 27 residues processed: 697 average time/residue: 0.4450 time to fit residues: 473.9125 Evaluate side-chains 354 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 327 time to evaluate : 3.572 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2749 time to fit residues: 17.6856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 5.9990 chunk 279 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 289 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 335 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 132 HIS C 193 ASN C 519 ASN C 526 HIS C 554 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 799 ASN C 856 ASN C 952 GLN C1080 ASN C1116 HIS C1136 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 GLN D 560 ASN D 716 GLN D 897 HIS D1249 ASN D1259 GLN M 127 GLN M 157 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 28892 Z= 0.317 Angle : 0.852 15.926 39691 Z= 0.444 Chirality : 0.048 0.293 4774 Planarity : 0.006 0.131 4889 Dihedral : 17.864 176.696 4804 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 1.07 % Allowed : 8.05 % Favored : 90.89 % Rotamer: Outliers : 3.09 % Allowed : 14.31 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % 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: -2.69 (0.12), residues: 3567 helix: -1.08 (0.13), residues: 1288 sheet: -1.02 (0.28), residues: 284 loop : -2.47 (0.12), residues: 1995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 345 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 28 residues processed: 409 average time/residue: 0.3925 time to fit residues: 255.0931 Evaluate side-chains 294 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 266 time to evaluate : 2.879 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2781 time to fit residues: 17.6551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 278 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 335 optimal weight: 0.9990 chunk 362 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 chunk 332 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS C 618 GLN C1257 GLN ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 157 GLN D 861 ASN D1295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28892 Z= 0.290 Angle : 0.753 15.324 39691 Z= 0.389 Chirality : 0.045 0.238 4774 Planarity : 0.005 0.079 4889 Dihedral : 17.679 178.986 4804 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.11 % Favored : 89.91 % Rotamer: Outliers : 2.44 % Allowed : 15.62 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.09 % 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: -1.87 (0.13), residues: 3567 helix: 0.00 (0.14), residues: 1276 sheet: -0.80 (0.28), residues: 292 loop : -2.25 (0.12), residues: 1999 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 304 time to evaluate : 3.371 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 outliers start: 63 outliers final: 22 residues processed: 354 average time/residue: 0.4243 time to fit residues: 239.7097 Evaluate side-chains 279 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 257 time to evaluate : 3.418 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2989 time to fit residues: 16.1403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 331 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 336 optimal weight: 4.9990 chunk 356 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 319 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 447 HIS C 554 HIS ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN D 861 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28892 Z= 0.359 Angle : 0.760 15.932 39691 Z= 0.391 Chirality : 0.046 0.325 4774 Planarity : 0.005 0.079 4889 Dihedral : 17.564 177.979 4804 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 1.04 % Allowed : 8.97 % Favored : 89.99 % Rotamer: Outliers : 1.89 % Allowed : 18.02 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.09 % 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: -1.51 (0.14), residues: 3567 helix: 0.45 (0.15), residues: 1277 sheet: -0.60 (0.28), residues: 305 loop : -2.17 (0.13), residues: 1985 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 269 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 23 residues processed: 308 average time/residue: 0.4175 time to fit residues: 207.0685 Evaluate side-chains 263 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 240 time to evaluate : 3.174 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3061 time to fit residues: 16.7229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 10.0000 chunk 202 optimal weight: 0.0170 chunk 5 optimal weight: 3.9990 chunk 265 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 304 optimal weight: 0.7980 chunk 246 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 320 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 519 ASN C 554 HIS C 952 GLN ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 364 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28892 Z= 0.185 Angle : 0.693 14.609 39691 Z= 0.352 Chirality : 0.043 0.284 4774 Planarity : 0.004 0.081 4889 Dihedral : 17.377 177.641 4804 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 1.01 % Allowed : 8.63 % Favored : 90.36 % Rotamer: Outliers : 1.89 % Allowed : 17.87 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % 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: -1.20 (0.14), residues: 3567 helix: 0.87 (0.15), residues: 1274 sheet: -0.46 (0.29), residues: 301 loop : -2.09 (0.13), residues: 1992 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 284 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 25 residues processed: 318 average time/residue: 0.4160 time to fit residues: 213.4644 Evaluate side-chains 271 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 246 time to evaluate : 2.948 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3020 time to fit residues: 17.7684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 3.9990 chunk 321 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 357 optimal weight: 20.0000 chunk 296 optimal weight: 50.0000 chunk 165 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 513 GLN C 526 HIS C 554 HIS ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS D 861 ASN M 229 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 28892 Z= 0.418 Angle : 0.759 15.882 39691 Z= 0.389 Chirality : 0.046 0.268 4774 Planarity : 0.005 0.079 4889 Dihedral : 17.412 177.917 4804 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 1.04 % Allowed : 9.34 % Favored : 89.63 % Rotamer: Outliers : 1.70 % Allowed : 19.41 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.09 % 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: -1.21 (0.14), residues: 3567 helix: 0.82 (0.15), residues: 1283 sheet: -0.39 (0.29), residues: 295 loop : -2.09 (0.13), residues: 1989 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 263 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 18 residues processed: 296 average time/residue: 0.4207 time to fit residues: 202.5972 Evaluate side-chains 257 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 239 time to evaluate : 3.306 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2770 time to fit residues: 13.9253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 20.0000 chunk 40 optimal weight: 0.4980 chunk 203 optimal weight: 10.0000 chunk 260 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 300 optimal weight: 40.0000 chunk 199 optimal weight: 1.9990 chunk 355 optimal weight: 50.0000 chunk 222 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 554 HIS ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN E 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28892 Z= 0.303 Angle : 0.719 15.093 39691 Z= 0.366 Chirality : 0.044 0.247 4774 Planarity : 0.004 0.081 4889 Dihedral : 17.368 177.990 4804 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.95 % Allowed : 8.94 % Favored : 90.10 % Rotamer: Outliers : 1.35 % Allowed : 19.95 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % 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: -1.13 (0.14), residues: 3567 helix: 0.94 (0.15), residues: 1294 sheet: -0.48 (0.29), residues: 312 loop : -2.07 (0.13), residues: 1961 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 263 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 290 average time/residue: 0.4207 time to fit residues: 198.8977 Evaluate side-chains 267 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 249 time to evaluate : 2.963 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2742 time to fit residues: 13.6415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 220 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 279 optimal weight: 0.3980 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 554 HIS ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28892 Z= 0.294 Angle : 0.724 15.093 39691 Z= 0.368 Chirality : 0.044 0.263 4774 Planarity : 0.004 0.081 4889 Dihedral : 17.315 177.875 4804 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.25 % Favored : 89.77 % Rotamer: Outliers : 1.01 % Allowed : 20.11 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % 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: -1.10 (0.14), residues: 3567 helix: 0.98 (0.15), residues: 1295 sheet: -0.56 (0.28), residues: 322 loop : -2.06 (0.13), residues: 1950 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 249 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 266 average time/residue: 0.4285 time to fit residues: 184.3597 Evaluate side-chains 250 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 237 time to evaluate : 3.022 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2718 time to fit residues: 10.6670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 323 optimal weight: 6.9990 chunk 340 optimal weight: 30.0000 chunk 310 optimal weight: 4.9990 chunk 331 optimal weight: 10.0000 chunk 199 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 101 optimal weight: 30.0000 chunk 299 optimal weight: 5.9990 chunk 313 optimal weight: 8.9990 chunk 330 optimal weight: 0.0980 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 28892 Z= 0.382 Angle : 0.758 15.628 39691 Z= 0.387 Chirality : 0.045 0.274 4774 Planarity : 0.005 0.083 4889 Dihedral : 17.349 178.643 4804 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 1.01 % Allowed : 9.59 % Favored : 89.40 % Rotamer: Outliers : 0.73 % Allowed : 20.61 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % 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: -1.14 (0.14), residues: 3567 helix: 0.93 (0.15), residues: 1295 sheet: -0.60 (0.29), residues: 319 loop : -2.07 (0.14), residues: 1953 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 250 average time/residue: 0.4369 time to fit residues: 178.2465 Evaluate side-chains 244 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 235 time to evaluate : 3.255 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3577 time to fit residues: 9.6941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 217 optimal weight: 3.9990 chunk 350 optimal weight: 40.0000 chunk 213 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 243 optimal weight: 7.9990 chunk 367 optimal weight: 20.0000 chunk 338 optimal weight: 2.9990 chunk 292 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN C 554 HIS ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 560 ASN E 43 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28892 Z= 0.301 Angle : 0.732 15.245 39691 Z= 0.370 Chirality : 0.044 0.249 4774 Planarity : 0.004 0.082 4889 Dihedral : 17.299 178.493 4804 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 1.04 % Allowed : 9.20 % Favored : 89.77 % Rotamer: Outliers : 0.43 % Allowed : 20.73 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % 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: -1.10 (0.14), residues: 3567 helix: 0.99 (0.15), residues: 1301 sheet: -0.69 (0.29), residues: 328 loop : -2.05 (0.14), residues: 1938 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7134 Ramachandran restraints generated. 3567 Oldfield, 0 Emsley, 3567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 247 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 255 average time/residue: 0.4292 time to fit residues: 177.9501 Evaluate side-chains 241 residues out of total 3073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 236 time to evaluate : 3.087 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2732 time to fit residues: 6.8403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 232 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 293 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 301 optimal weight: 40.0000 chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.124803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079123 restraints weight = 68058.357| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.37 r_work: 0.2864 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28892 Z= 0.208 Angle : 0.712 14.847 39691 Z= 0.359 Chirality : 0.043 0.302 4774 Planarity : 0.004 0.082 4889 Dihedral : 17.206 178.211 4804 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 1.01 % Allowed : 8.89 % Favored : 90.10 % Rotamer: Outliers : 0.23 % Allowed : 21.38 % Favored : 78.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.03 % Twisted Proline : 0.69 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3567 helix: 1.15 (0.15), residues: 1293 sheet: -0.53 (0.29), residues: 313 loop : -2.02 (0.14), residues: 1961 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6148.75 seconds wall clock time: 111 minutes 37.42 seconds (6697.42 seconds total)