Starting phenix.real_space_refine on Thu Dec 14 13:50:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu9_28609/12_2023/8eu9_28609_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu9_28609/12_2023/8eu9_28609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu9_28609/12_2023/8eu9_28609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu9_28609/12_2023/8eu9_28609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu9_28609/12_2023/8eu9_28609_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eu9_28609/12_2023/8eu9_28609_neut_updated.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 12 5.49 5 S 95 5.16 5 C 17928 2.51 5 N 4917 2.21 5 O 5565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q ASP 955": "OD1" <-> "OD2" Residue "Q TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 1154": "OE1" <-> "OE2" Residue "Q GLU 1176": "OE1" <-> "OE2" Residue "Q TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 1294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 1306": "OE1" <-> "OE2" Residue "Q GLU 1332": "OE1" <-> "OE2" Residue "R GLU 30": "OE1" <-> "OE2" Residue "R PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 101": "OD1" <-> "OD2" Residue "R GLU 156": "OE1" <-> "OE2" Residue "R TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 225": "OD1" <-> "OD2" Residue "R GLU 268": "OE1" <-> "OE2" Residue "R PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 643": "OE1" <-> "OE2" Residue "R PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 733": "OE1" <-> "OE2" Residue "R TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S ASP 69": "OD1" <-> "OD2" Residue "S PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 154": "OE1" <-> "OE2" Residue "S TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 119": "OE1" <-> "OE2" Residue "T GLU 187": "OE1" <-> "OE2" Residue "T TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 246": "OD1" <-> "OD2" Residue "T GLU 287": "OE1" <-> "OE2" Residue "T ASP 362": "OD1" <-> "OD2" Residue "T GLU 409": "OE1" <-> "OE2" Residue "U PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 132": "OE1" <-> "OE2" Residue "U GLU 282": "OE1" <-> "OE2" Residue "U GLU 283": "OE1" <-> "OE2" Residue "U ASP 315": "OD1" <-> "OD2" Residue "U GLU 376": "OE1" <-> "OE2" Residue "U PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 442": "OE1" <-> "OE2" Residue "U GLU 444": "OE1" <-> "OE2" Residue "V ASP 63": "OD1" <-> "OD2" Residue "V GLU 123": "OE1" <-> "OE2" Residue "V GLU 135": "OE1" <-> "OE2" Residue "V GLU 153": "OE1" <-> "OE2" Residue "V ASP 182": "OD1" <-> "OD2" Residue "V GLU 187": "OE1" <-> "OE2" Residue "V ASP 264": "OD1" <-> "OD2" Residue "V GLU 319": "OE1" <-> "OE2" Residue "V GLU 385": "OE1" <-> "OE2" Residue "V GLU 457": "OE1" <-> "OE2" Residue "W PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 282": "OE1" <-> "OE2" Residue "W TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 45": "OE1" <-> "OE2" Residue "X GLU 119": "OE1" <-> "OE2" Residue "X TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 287": "OE1" <-> "OE2" Residue "X ASP 376": "OD1" <-> "OD2" Residue "X GLU 457": "OE1" <-> "OE2" Residue "Y GLU 110": "OE1" <-> "OE2" Residue "Y ASP 177": "OD1" <-> "OD2" Residue "Y PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 302": "OD1" <-> "OD2" Residue "Y ASP 315": "OD1" <-> "OD2" Residue "Y TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 450": "OD1" <-> "OD2" Residue "Z PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 314": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 28517 Number of models: 1 Model: "" Number of chains: 16 Chain: "Q" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3413 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 22, 'TRANS': 403} Chain breaks: 6 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "R" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3489 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 28, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "T" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3338 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 17, 'TRANS': 419} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3333 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "V" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3388 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 424} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "W" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3389 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "X" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3376 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 423} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Y" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3412 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 248 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.50, per 1000 atoms: 0.51 Number of scatterers: 28517 At special positions: 0 Unit cell: (134.435, 194.555, 147.795, 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 95 16.00 P 12 15.00 O 5565 8.00 N 4917 7.00 C 17928 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.62 Conformation dependent library (CDL) restraints added in 4.7 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 152 helices and 31 sheets defined 37.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.68 Creating SS restraints... Processing helix chain 'Q' and resid 958 through 969 Processing helix chain 'Q' and resid 981 through 984 No H-bonds generated for 'chain 'Q' and resid 981 through 984' Processing helix chain 'Q' and resid 1000 through 1012 Processing helix chain 'Q' and resid 1087 through 1093 Processing helix chain 'Q' and resid 1102 through 1110 Processing helix chain 'Q' and resid 1122 through 1132 Processing helix chain 'Q' and resid 1139 through 1144 Processing helix chain 'Q' and resid 1148 through 1153 Processing helix chain 'Q' and resid 1170 through 1177 Processing helix chain 'Q' and resid 1186 through 1191 removed outlier: 3.587A pdb=" N LEU Q1190 " --> pdb=" O VAL Q1186 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU Q1191 " --> pdb=" O MET Q1187 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1186 through 1191' Processing helix chain 'Q' and resid 1194 through 1200 Processing helix chain 'Q' and resid 1203 through 1205 No H-bonds generated for 'chain 'Q' and resid 1203 through 1205' Processing helix chain 'Q' and resid 1228 through 1237 Processing helix chain 'Q' and resid 1240 through 1245 Processing helix chain 'Q' and resid 1251 through 1258 Processing helix chain 'Q' and resid 1265 through 1267 No H-bonds generated for 'chain 'Q' and resid 1265 through 1267' Processing helix chain 'Q' and resid 1280 through 1282 No H-bonds generated for 'chain 'Q' and resid 1280 through 1282' Processing helix chain 'Q' and resid 1291 through 1296 Processing helix chain 'Q' and resid 1301 through 1310 Processing helix chain 'Q' and resid 1320 through 1322 No H-bonds generated for 'chain 'Q' and resid 1320 through 1322' Processing helix chain 'Q' and resid 1328 through 1336 Processing helix chain 'Q' and resid 1360 through 1363 No H-bonds generated for 'chain 'Q' and resid 1360 through 1363' Processing helix chain 'Q' and resid 1398 through 1407 removed outlier: 3.607A pdb=" N ARG Q1407 " --> pdb=" O GLN Q1403 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1428 through 1439 removed outlier: 3.526A pdb=" N ARG Q1435 " --> pdb=" O ARG Q1431 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN Q1438 " --> pdb=" O ASP Q1434 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS Q1439 " --> pdb=" O ARG Q1435 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 87 Processing helix chain 'R' and resid 90 through 95 Processing helix chain 'R' and resid 108 through 122 Processing helix chain 'R' and resid 144 through 154 Processing helix chain 'R' and resid 168 through 176 Processing helix chain 'R' and resid 216 through 230 Processing helix chain 'R' and resid 240 through 249 Processing helix chain 'R' and resid 257 through 262 removed outlier: 3.687A pdb=" N GLU R 262 " --> pdb=" O ASP R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 590 through 596 Processing helix chain 'R' and resid 606 through 610 Processing helix chain 'R' and resid 618 through 624 Proline residue: R 622 - end of helix No H-bonds generated for 'chain 'R' and resid 618 through 624' Processing helix chain 'R' and resid 628 through 631 Processing helix chain 'R' and resid 638 through 647 Processing helix chain 'R' and resid 659 through 666 Processing helix chain 'R' and resid 680 through 691 removed outlier: 3.509A pdb=" N PHE R 691 " --> pdb=" O GLU R 687 " (cutoff:3.500A) Processing helix chain 'R' and resid 709 through 719 Processing helix chain 'R' and resid 721 through 727 Processing helix chain 'R' and resid 731 through 736 Processing helix chain 'R' and resid 738 through 740 No H-bonds generated for 'chain 'R' and resid 738 through 740' Processing helix chain 'S' and resid 30 through 40 Processing helix chain 'S' and resid 63 through 82 Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'S' and resid 151 through 159 removed outlier: 3.908A pdb=" N LEU S 158 " --> pdb=" O GLU S 154 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG S 159 " --> pdb=" O TYR S 155 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 67 Processing helix chain 'T' and resid 85 through 96 Processing helix chain 'T' and resid 107 through 110 removed outlier: 3.504A pdb=" N LEU T 110 " --> pdb=" O GLY T 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 107 through 110' Processing helix chain 'T' and resid 117 through 128 Processing helix chain 'T' and resid 183 through 192 Processing helix chain 'T' and resid 219 through 221 No H-bonds generated for 'chain 'T' and resid 219 through 221' Processing helix chain 'T' and resid 249 through 255 Processing helix chain 'T' and resid 282 through 297 Processing helix chain 'T' and resid 313 through 315 No H-bonds generated for 'chain 'T' and resid 313 through 315' Processing helix chain 'T' and resid 318 through 329 removed outlier: 4.039A pdb=" N GLU T 329 " --> pdb=" O ASN T 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 356 through 358 No H-bonds generated for 'chain 'T' and resid 356 through 358' Processing helix chain 'T' and resid 361 through 366 removed outlier: 3.995A pdb=" N ARG T 366 " --> pdb=" O ASP T 362 " (cutoff:3.500A) Processing helix chain 'T' and resid 377 through 390 Processing helix chain 'T' and resid 397 through 409 Processing helix chain 'T' and resid 412 through 428 removed outlier: 4.632A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix Processing helix chain 'T' and resid 436 through 445 Processing helix chain 'T' and resid 449 through 458 Processing helix chain 'U' and resid 48 through 63 Processing helix chain 'U' and resid 81 through 92 Processing helix chain 'U' and resid 113 through 124 removed outlier: 3.921A pdb=" N SER U 124 " --> pdb=" O ALA U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 180 Processing helix chain 'U' and resid 241 through 248 Processing helix chain 'U' and resid 254 through 259 removed outlier: 3.777A pdb=" N THR U 259 " --> pdb=" O ALA U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 267 through 283 Processing helix chain 'U' and resid 298 through 300 No H-bonds generated for 'chain 'U' and resid 298 through 300' Processing helix chain 'U' and resid 303 through 310 Processing helix chain 'U' and resid 340 through 342 No H-bonds generated for 'chain 'U' and resid 340 through 342' Processing helix chain 'U' and resid 345 through 349 Processing helix chain 'U' and resid 361 through 375 Processing helix chain 'U' and resid 381 through 393 Processing helix chain 'U' and resid 396 through 412 removed outlier: 4.352A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 429 Processing helix chain 'U' and resid 433 through 442 Processing helix chain 'V' and resid 52 through 67 Processing helix chain 'V' and resid 85 through 96 Processing helix chain 'V' and resid 107 through 110 removed outlier: 3.576A pdb=" N LEU V 110 " --> pdb=" O GLY V 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 107 through 110' Processing helix chain 'V' and resid 117 through 128 Processing helix chain 'V' and resid 155 through 157 No H-bonds generated for 'chain 'V' and resid 155 through 157' Processing helix chain 'V' and resid 183 through 191 removed outlier: 3.890A pdb=" N SER V 188 " --> pdb=" O THR V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 249 through 257 Processing helix chain 'V' and resid 265 through 272 removed outlier: 3.853A pdb=" N LEU V 272 " --> pdb=" O MET V 268 " (cutoff:3.500A) Processing helix chain 'V' and resid 282 through 298 Processing helix chain 'V' and resid 313 through 315 No H-bonds generated for 'chain 'V' and resid 313 through 315' Processing helix chain 'V' and resid 318 through 329 removed outlier: 3.983A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU V 329 " --> pdb=" O ASN V 325 " (cutoff:3.500A) Processing helix chain 'V' and resid 356 through 358 No H-bonds generated for 'chain 'V' and resid 356 through 358' Processing helix chain 'V' and resid 361 through 364 No H-bonds generated for 'chain 'V' and resid 361 through 364' Processing helix chain 'V' and resid 377 through 390 Processing helix chain 'V' and resid 397 through 409 Processing helix chain 'V' and resid 412 through 428 removed outlier: 3.845A pdb=" N LEU V 419 " --> pdb=" O ALA V 415 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA V 420 " --> pdb=" O LEU V 416 " (cutoff:3.500A) Proline residue: V 421 - end of helix Processing helix chain 'V' and resid 436 through 445 Processing helix chain 'V' and resid 449 through 458 Processing helix chain 'W' and resid 48 through 63 Processing helix chain 'W' and resid 81 through 91 Processing helix chain 'W' and resid 104 through 106 No H-bonds generated for 'chain 'W' and resid 104 through 106' Processing helix chain 'W' and resid 113 through 124 Processing helix chain 'W' and resid 173 through 180 Processing helix chain 'W' and resid 241 through 249 Processing helix chain 'W' and resid 267 through 282 Processing helix chain 'W' and resid 298 through 300 No H-bonds generated for 'chain 'W' and resid 298 through 300' Processing helix chain 'W' and resid 303 through 312 Processing helix chain 'W' and resid 340 through 342 No H-bonds generated for 'chain 'W' and resid 340 through 342' Processing helix chain 'W' and resid 345 through 350 Processing helix chain 'W' and resid 361 through 374 Processing helix chain 'W' and resid 381 through 393 Processing helix chain 'W' and resid 396 through 412 removed outlier: 4.045A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 429 Processing helix chain 'W' and resid 433 through 442 Processing helix chain 'W' and resid 444 through 446 No H-bonds generated for 'chain 'W' and resid 444 through 446' Processing helix chain 'X' and resid 45 through 47 No H-bonds generated for 'chain 'X' and resid 45 through 47' Processing helix chain 'X' and resid 52 through 67 Processing helix chain 'X' and resid 85 through 96 Processing helix chain 'X' and resid 107 through 109 No H-bonds generated for 'chain 'X' and resid 107 through 109' Processing helix chain 'X' and resid 117 through 128 removed outlier: 3.727A pdb=" N ALA X 128 " --> pdb=" O ASN X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 183 through 191 removed outlier: 4.037A pdb=" N GLU X 187 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN X 190 " --> pdb=" O GLU X 187 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG X 191 " --> pdb=" O SER X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 257 Processing helix chain 'X' and resid 266 through 272 Processing helix chain 'X' and resid 282 through 298 Processing helix chain 'X' and resid 313 through 315 No H-bonds generated for 'chain 'X' and resid 313 through 315' Processing helix chain 'X' and resid 318 through 327 removed outlier: 3.948A pdb=" N LYS X 326 " --> pdb=" O THR X 322 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 361 through 364 No H-bonds generated for 'chain 'X' and resid 361 through 364' Processing helix chain 'X' and resid 377 through 390 Processing helix chain 'X' and resid 397 through 409 Processing helix chain 'X' and resid 412 through 416 Processing helix chain 'X' and resid 419 through 428 Processing helix chain 'X' and resid 436 through 445 Processing helix chain 'X' and resid 449 through 457 Processing helix chain 'Y' and resid 48 through 63 Processing helix chain 'Y' and resid 81 through 92 Processing helix chain 'Y' and resid 104 through 106 No H-bonds generated for 'chain 'Y' and resid 104 through 106' Processing helix chain 'Y' and resid 113 through 122 Processing helix chain 'Y' and resid 173 through 181 Processing helix chain 'Y' and resid 241 through 249 removed outlier: 3.901A pdb=" N ASP Y 245 " --> pdb=" O LEU Y 241 " (cutoff:3.500A) Processing helix chain 'Y' and resid 253 through 259 removed outlier: 4.051A pdb=" N THR Y 259 " --> pdb=" O ALA Y 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 282 Processing helix chain 'Y' and resid 298 through 300 No H-bonds generated for 'chain 'Y' and resid 298 through 300' Processing helix chain 'Y' and resid 303 through 311 removed outlier: 3.773A pdb=" N ARG Y 311 " --> pdb=" O SER Y 307 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 342 No H-bonds generated for 'chain 'Y' and resid 340 through 342' Processing helix chain 'Y' and resid 345 through 350 removed outlier: 3.745A pdb=" N ARG Y 350 " --> pdb=" O ASP Y 346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 361 through 374 Processing helix chain 'Y' and resid 381 through 393 Processing helix chain 'Y' and resid 396 through 412 removed outlier: 3.947A pdb=" N ILE Y 403 " --> pdb=" O SER Y 399 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL Y 405 " --> pdb=" O ASN Y 401 " (cutoff:3.500A) Processing helix chain 'Y' and resid 420 through 429 Processing helix chain 'Y' and resid 433 through 442 Processing helix chain 'Y' and resid 444 through 446 No H-bonds generated for 'chain 'Y' and resid 444 through 446' Processing sheet with id= A, first strand: chain 'Q' and resid 949 through 954 removed outlier: 6.191A pdb=" N VAL Q1419 " --> pdb=" O ILE Q 950 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL Q 952 " --> pdb=" O VAL Q1419 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ARG Q1421 " --> pdb=" O VAL Q 952 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N CYS Q 954 " --> pdb=" O ARG Q1421 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU Q1423 " --> pdb=" O CYS Q 954 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'Q' and resid 1082 through 1085 removed outlier: 6.979A pdb=" N THR Q1220 " --> pdb=" O TYR Q1083 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU Q1085 " --> pdb=" O THR Q1220 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLU Q1222 " --> pdb=" O LEU Q1085 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'Q' and resid 1317 through 1319 removed outlier: 7.393A pdb=" N PHE Q1370 " --> pdb=" O VAL Q1318 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'R' and resid 16 through 18 removed outlier: 7.831A pdb=" N VAL R 276 " --> pdb=" O ASP R 17 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'R' and resid 40 through 43 removed outlier: 3.504A pdb=" N ARG R 50 " --> pdb=" O ASP R 43 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'R' and resid 700 through 702 removed outlier: 6.417A pdb=" N VAL R 668 " --> pdb=" O ASN R 701 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU R 185 " --> pdb=" O LEU R 669 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR R 671 " --> pdb=" O LEU R 185 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE R 187 " --> pdb=" O THR R 671 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 198 through 200 Processing sheet with id= H, first strand: chain 'T' and resid 368 through 372 removed outlier: 6.574A pdb=" N VAL T 336 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LEU T 77 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU T 338 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLY T 79 " --> pdb=" O LEU T 338 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 238 through 248 Processing sheet with id= J, first strand: chain 'T' and resid 175 through 181 removed outlier: 3.822A pdb=" N GLU T 146 " --> pdb=" O GLY T 169 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS T 171 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL T 144 " --> pdb=" O LYS T 171 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY T 142 " --> pdb=" O ILE T 200 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP T 198 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY T 213 " --> pdb=" O VAL T 199 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'T' and resid 344 through 346 Processing sheet with id= L, first strand: chain 'U' and resid 352 through 355 removed outlier: 6.595A pdb=" N VAL U 321 " --> pdb=" O VAL U 71 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL U 73 " --> pdb=" O VAL U 321 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET U 323 " --> pdb=" O VAL U 73 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'U' and resid 287 through 290 removed outlier: 3.746A pdb=" N GLU U 131 " --> pdb=" O VAL U 235 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS U 233 " --> pdb=" O THR U 133 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'U' and resid 166 through 171 removed outlier: 4.226A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN U 155 " --> pdb=" O ASP U 146 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP U 188 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY U 203 " --> pdb=" O VAL U 189 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP U 193 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE U 199 " --> pdb=" O ASP U 193 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'V' and resid 367 through 371 removed outlier: 6.986A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL V 336 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LEU V 77 " --> pdb=" O VAL V 336 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU V 338 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'V' and resid 239 through 248 Processing sheet with id= Q, first strand: chain 'V' and resid 176 through 181 removed outlier: 3.502A pdb=" N VAL V 166 " --> pdb=" O LEU V 181 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS V 165 " --> pdb=" O GLU V 150 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU V 146 " --> pdb=" O GLY V 169 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS V 171 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL V 144 " --> pdb=" O LYS V 171 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASP V 198 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY V 213 " --> pdb=" O VAL V 199 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR V 201 " --> pdb=" O ARG V 211 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ARG V 211 " --> pdb=" O TYR V 201 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU V 203 " --> pdb=" O VAL V 209 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL V 209 " --> pdb=" O GLU V 203 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'V' and resid 344 through 346 Processing sheet with id= S, first strand: chain 'W' and resid 352 through 355 removed outlier: 6.140A pdb=" N VAL W 321 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL W 73 " --> pdb=" O VAL W 321 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET W 323 " --> pdb=" O VAL W 73 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'W' and resid 231 through 240 Processing sheet with id= U, first strand: chain 'W' and resid 166 through 171 removed outlier: 4.042A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP W 188 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER W 191 " --> pdb=" O LYS W 201 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LYS W 201 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASP W 193 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE W 199 " --> pdb=" O ASP W 193 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'W' and resid 329 through 331 Processing sheet with id= W, first strand: chain 'X' and resid 368 through 371 removed outlier: 6.491A pdb=" N VAL X 336 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU X 77 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU X 338 " --> pdb=" O LEU X 77 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU X 308 " --> pdb=" O VAL X 337 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA X 339 " --> pdb=" O LEU X 308 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE X 310 " --> pdb=" O ALA X 339 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS X 103 " --> pdb=" O VAL X 307 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 245 through 248 Processing sheet with id= Y, first strand: chain 'X' and resid 238 through 241 removed outlier: 3.508A pdb=" N TYR X 140 " --> pdb=" O ILE X 202 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP X 198 " --> pdb=" O VAL X 144 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR X 201 " --> pdb=" O ARG X 211 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ARG X 211 " --> pdb=" O TYR X 201 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLU X 203 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL X 209 " --> pdb=" O GLU X 203 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'X' and resid 175 through 181 removed outlier: 4.001A pdb=" N HIS X 165 " --> pdb=" O GLU X 150 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU X 146 " --> pdb=" O GLY X 169 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS X 171 " --> pdb=" O VAL X 144 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL X 144 " --> pdb=" O LYS X 171 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'X' and resid 344 through 346 Processing sheet with id= AB, first strand: chain 'Y' and resid 352 through 355 removed outlier: 3.518A pdb=" N ILE Y 352 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL Y 321 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL Y 73 " --> pdb=" O VAL Y 321 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET Y 323 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Y' and resid 287 through 290 Processing sheet with id= AD, first strand: chain 'Y' and resid 135 through 139 removed outlier: 3.515A pdb=" N GLY Y 203 " --> pdb=" O VAL Y 189 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER Y 191 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS Y 201 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ASP Y 193 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE Y 199 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 307 through 310 removed outlier: 3.511A pdb=" N LEU Z 309 " --> pdb=" O LEU Z 316 " (cutoff:3.500A) 1019 hydrogen bonds defined for protein. 2958 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.87 Time building geometry restraints manager: 11.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8448 1.33 - 1.46: 5920 1.46 - 1.58: 14389 1.58 - 1.71: 18 1.71 - 1.83: 166 Bond restraints: 28941 Sorted by residual: bond pdb=" N SER S 50 " pdb=" CA SER S 50 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.21e-02 6.83e+03 7.01e+00 bond pdb=" N ASP R 29 " pdb=" CA ASP R 29 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.86e+00 bond pdb=" N PHE R 28 " pdb=" CA PHE R 28 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.34e-02 5.57e+03 6.57e+00 bond pdb=" N LYS S 49 " pdb=" CA LYS S 49 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.28e-02 6.10e+03 6.32e+00 bond pdb=" N LEU R 614 " pdb=" CA LEU R 614 " ideal model delta sigma weight residual 1.452 1.484 -0.033 1.30e-02 5.92e+03 6.31e+00 ... (remaining 28936 not shown) Histogram of bond angle deviations from ideal: 96.05 - 104.30: 410 104.30 - 112.56: 15533 112.56 - 120.82: 14064 120.82 - 129.07: 9050 129.07 - 137.33: 118 Bond angle restraints: 39175 Sorted by residual: angle pdb=" CB MET Q1288 " pdb=" CG MET Q1288 " pdb=" SD MET Q1288 " ideal model delta sigma weight residual 112.70 134.01 -21.31 3.00e+00 1.11e-01 5.04e+01 angle pdb=" CB MET S 147 " pdb=" CG MET S 147 " pdb=" SD MET S 147 " ideal model delta sigma weight residual 112.70 131.29 -18.59 3.00e+00 1.11e-01 3.84e+01 angle pdb=" CB MET X 122 " pdb=" CG MET X 122 " pdb=" SD MET X 122 " ideal model delta sigma weight residual 112.70 131.00 -18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" CB MET W 215 " pdb=" CG MET W 215 " pdb=" SD MET W 215 " ideal model delta sigma weight residual 112.70 130.37 -17.67 3.00e+00 1.11e-01 3.47e+01 angle pdb=" CA LEU Q1319 " pdb=" CB LEU Q1319 " pdb=" CG LEU Q1319 " ideal model delta sigma weight residual 116.30 136.81 -20.51 3.50e+00 8.16e-02 3.44e+01 ... (remaining 39170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 17163 35.38 - 70.76: 535 70.76 - 106.14: 60 106.14 - 141.52: 5 141.52 - 176.91: 3 Dihedral angle restraints: 17766 sinusoidal: 7193 harmonic: 10573 Sorted by residual: dihedral pdb=" C5' ADP X 501 " pdb=" O5' ADP X 501 " pdb=" PA ADP X 501 " pdb=" O2A ADP X 501 " ideal model delta sinusoidal sigma weight residual -60.00 116.91 -176.91 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP V 501 " pdb=" O5' ADP V 501 " pdb=" PA ADP V 501 " pdb=" O2A ADP V 501 " ideal model delta sinusoidal sigma weight residual -60.00 88.87 -148.87 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C5' ADP W 501 " pdb=" O5' ADP W 501 " pdb=" PA ADP W 501 " pdb=" O2A ADP W 501 " ideal model delta sinusoidal sigma weight residual -60.00 82.88 -142.88 1 2.00e+01 2.50e-03 4.31e+01 ... (remaining 17763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 4506 0.138 - 0.277: 100 0.277 - 0.415: 3 0.415 - 0.553: 0 0.553 - 0.691: 1 Chirality restraints: 4610 Sorted by residual: chirality pdb=" CB ILE U 125 " pdb=" CA ILE U 125 " pdb=" CG1 ILE U 125 " pdb=" CG2 ILE U 125 " both_signs ideal model delta sigma weight residual False 2.64 1.95 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CB ILE Y 149 " pdb=" CA ILE Y 149 " pdb=" CG1 ILE Y 149 " pdb=" CG2 ILE Y 149 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CG LEU Q1335 " pdb=" CB LEU Q1335 " pdb=" CD1 LEU Q1335 " pdb=" CD2 LEU Q1335 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 4607 not shown) Planarity restraints: 5022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP V 63 " 0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" CG ASP V 63 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASP V 63 " 0.025 2.00e-02 2.50e+03 pdb=" OD2 ASP V 63 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP X 182 " 0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO X 183 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO X 183 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO X 183 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS V 174 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C LYS V 174 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS V 174 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY V 175 " 0.018 2.00e-02 2.50e+03 ... (remaining 5019 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 3 2.20 - 2.88: 10550 2.88 - 3.55: 41105 3.55 - 4.23: 66655 4.23 - 4.90: 113643 Nonbonded interactions: 231956 Sorted by model distance: nonbonded pdb=" OD1 ASN T 325 " pdb=" NE ARG T 366 " model vdw 1.528 2.520 nonbonded pdb=" OD1 ASN T 325 " pdb=" CZ ARG T 366 " model vdw 2.125 3.270 nonbonded pdb=" O LEU R 647 " pdb=" OG SER R 652 " model vdw 2.173 2.440 nonbonded pdb=" OG SER T 355 " pdb=" O VAL T 359 " model vdw 2.229 2.440 nonbonded pdb=" O GLU Q1332 " pdb=" OG1 THR Q1336 " model vdw 2.274 2.440 ... (remaining 231951 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 'T' and (resid 22 or (resid 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 98 or (resid 99 through 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 187 or (resid 188 a \ nd (name N or name CA or name C or name O or name CB )) or resid 189 through 233 \ or (resid 234 and (name N or name CA or name C or name O or name CB )) or resid \ 235 through 259 or (resid 260 and (name N or name CA or name C or name O or nam \ e CB )) or resid 261 through 313 or (resid 314 and (name N or name CA or name C \ or name O or name CB )) or resid 315 through 337 or (resid 338 through 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 380 or \ (resid 381 and (name N or name CA or name C or name O or name CB )) or resid 382 \ through 440 or (resid 441 through 442 and (name N or name CA or name C or name \ O or name CB )) or resid 443 through 463 or resid 501)) selection = (chain 'V' and (resid 22 through 116 or (resid 117 and (name N or name CA or nam \ e C or name O or name CB )) or resid 118 through 154 or (resid 161 through 163 a \ nd (name N or name CA or name C or name O or name CB )) or resid 164 through 233 \ or (resid 234 and (name N or name CA or name C or name O or name CB )) or resid \ 235 through 259 or (resid 260 and (name N or name CA or name C or name O or nam \ e CB )) or resid 261 through 262 or (resid 263 and (name N or name CA or name C \ or name O or name CB )) or resid 264 through 273 or (resid 274 and (name N or na \ me CA or name C or name O or name CB )) or resid 275 through 337 or (resid 338 t \ hrough 339 and (name N or name CA or name C or name O or name CB )) or resid 340 \ through 380 or (resid 381 and (name N or name CA or name C or name O or name CB \ )) or resid 382 through 440 or (resid 441 through 442 and (name N or name CA or \ name C or name O or name CB )) or resid 443 through 455 or (resid 456 and (name \ N or name CA or name C or name O or name CB )) or resid 457 through 462 or (res \ id 463 and (name N or name CA or name C or name O or name CB )) or resid 501)) selection = (chain 'X' and (resid 22 or (resid 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 98 or (resid 99 through 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 116 or (resid 117 a \ nd (name N or name CA or name C or name O or name CB )) or resid 118 through 154 \ or (resid 161 through 163 and (name N or name CA or name C or name O or name CB \ )) or resid 164 through 187 or (resid 188 and (name N or name CA or name C or n \ ame O or name CB )) or resid 189 through 262 or (resid 263 and (name N or name C \ A or name C or name O or name CB )) or resid 264 through 273 or (resid 274 and ( \ name N or name CA or name C or name O or name CB )) or resid 275 through 313 or \ (resid 314 and (name N or name CA or name C or name O or name CB )) or resid 315 \ through 455 or (resid 456 and (name N or name CA or name C or name O or name CB \ )) or resid 457 through 462 or (resid 463 and (name N or name CA or name C or n \ ame O or name CB )) or resid 501)) } ncs_group { reference = (chain 'U' and (resid 18 through 162 or (resid 163 through 164 and (name N or na \ me CA or name C or name O or name CB )) or resid 165 through 170 or (resid 171 a \ nd (name N or name CA or name C or name O or name CB )) or resid 172 through 181 \ or (resid 182 and (name N or name CA or name C or name O or name CB )) or resid \ 183 through 232 or (resid 233 and (name N or name CA or name C or name O or nam \ e CB )) or resid 234 through 297 or (resid 298 and (name N or name CA or name C \ or name O or name CB )) or resid 299 through 459 or resid 501)) selection = (chain 'W' and (resid 18 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 44 or (resid 45 and (name N or nam \ e CA or name C or name O or name CB )) or resid 46 through 133 or (resid 134 and \ (name N or name CA or name C or name O or name CB )) or resid 135 through 170 o \ r (resid 171 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 72 through 200 or (resid 201 and (name N or name CA or name C or name O or name \ CB )) or resid 202 through 210 or resid 221 through 232 or (resid 233 and (name \ N or name CA or name C or name O or name CB )) or resid 234 through 297 or (resi \ d 298 and (name N or name CA or name C or name O or name CB )) or resid 299 thro \ ugh 412 or (resid 413 and (name N or name CA or name C or name O or name CB )) o \ r resid 414 through 459 or resid 501)) selection = (chain 'Y' and (resid 18 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 44 or (resid 45 and (name N or nam \ e CA or name C or name O or name CB )) or resid 46 through 133 or (resid 134 and \ (name N or name CA or name C or name O or name CB )) or resid 135 through 162 o \ r (resid 163 through 164 and (name N or name CA or name C or name O or name CB ) \ ) or resid 165 through 181 or (resid 182 and (name N or name CA or name C or nam \ e O or name CB )) or resid 183 through 200 or (resid 201 and (name N or name CA \ or name C or name O or name CB )) or resid 202 through 210 or resid 221 through \ 412 or (resid 413 and (name N or name CA or name C or name O or name CB )) or re \ sid 414 through 459 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.570 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: 23.070 Check model and map are aligned: 0.400 Set scattering table: 0.270 Process input model: 70.960 Find NCS groups from input model: 2.230 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.006 0.074 28941 Z= 0.384 Angle : 1.056 21.307 39175 Z= 0.549 Chirality : 0.056 0.691 4610 Planarity : 0.007 0.108 5022 Dihedral : 17.255 176.906 10936 Min Nonbonded Distance : 1.528 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 20.55 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.12), residues: 3618 helix: -1.39 (0.11), residues: 1469 sheet: -0.25 (0.22), residues: 559 loop : -1.22 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP Y 280 HIS 0.011 0.002 HIS V 27 PHE 0.042 0.002 PHE R 281 TYR 0.036 0.003 TYR R 151 ARG 0.017 0.001 ARG X 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1225 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1225 time to evaluate : 3.862 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 outliers start: 0 outliers final: 0 residues processed: 1225 average time/residue: 0.4766 time to fit residues: 880.4825 Evaluate side-chains 1013 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1013 time to evaluate : 3.161 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 283 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 172 optimal weight: 0.3980 chunk 211 optimal weight: 1.9990 chunk 328 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1100 ASN Q1256 ASN R 607 HIS R 659 GLN R 666 ASN T 94 GLN T 250 HIS U 36 GLN U 274 ASN U 408 GLN V 94 GLN V 124 ASN ** V 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 238 HIS W 362 GLN X 29 HIS ** X 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 256 ASN Y 34 ASN Y 47 GLN Y 223 GLN Y 310 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28941 Z= 0.240 Angle : 0.679 13.114 39175 Z= 0.340 Chirality : 0.045 0.225 4610 Planarity : 0.005 0.067 5022 Dihedral : 8.274 172.595 4000 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.30 % Allowed : 23.35 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 3618 helix: 0.06 (0.13), residues: 1476 sheet: 0.12 (0.22), residues: 548 loop : -0.97 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 280 HIS 0.007 0.001 HIS V 27 PHE 0.021 0.002 PHE S 124 TYR 0.028 0.002 TYR W 439 ARG 0.007 0.001 ARG T 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1050 time to evaluate : 3.118 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 outliers start: 134 outliers final: 63 residues processed: 1122 average time/residue: 0.4865 time to fit residues: 822.1093 Evaluate side-chains 1038 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 975 time to evaluate : 3.508 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.2762 time to fit residues: 36.6599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 182 optimal weight: 0.7980 chunk 102 optimal weight: 0.0570 chunk 273 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 329 optimal weight: 0.0010 chunk 355 optimal weight: 0.9980 chunk 293 optimal weight: 4.9990 chunk 326 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 264 optimal weight: 6.9990 overall best weight: 0.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1204 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 610 HIS ** R 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 ASN U 272 GLN ** V 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 289 ASN ** V 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 124 ASN ** X 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28941 Z= 0.212 Angle : 0.677 12.273 39175 Z= 0.335 Chirality : 0.045 0.377 4610 Planarity : 0.004 0.068 5022 Dihedral : 7.995 171.460 4000 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 2.67 % Allowed : 26.91 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3618 helix: 0.54 (0.13), residues: 1474 sheet: 0.13 (0.21), residues: 571 loop : -0.85 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 711 HIS 0.005 0.001 HIS Y 242 PHE 0.034 0.002 PHE Q1127 TYR 0.024 0.002 TYR R 34 ARG 0.008 0.001 ARG X 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 994 time to evaluate : 2.972 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: 83 outliers final: 40 residues processed: 1036 average time/residue: 0.4884 time to fit residues: 761.8771 Evaluate side-chains 989 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 949 time to evaluate : 3.257 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3045 time to fit residues: 26.5362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 325 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 221 optimal weight: 0.4980 chunk 330 optimal weight: 2.9990 chunk 349 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 313 optimal weight: 0.9990 chunk 94 optimal weight: 0.0570 overall best weight: 0.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1192 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 607 HIS R 627 GLN R 666 ASN ** R 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 23 HIS ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 242 HIS U 272 GLN V 256 ASN ** V 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 245 GLN Y 63 ASN Y 223 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28941 Z= 0.216 Angle : 0.662 11.398 39175 Z= 0.329 Chirality : 0.045 0.217 4610 Planarity : 0.004 0.066 5022 Dihedral : 7.740 168.712 4000 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 2.99 % Allowed : 27.71 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3618 helix: 0.71 (0.13), residues: 1479 sheet: 0.14 (0.21), residues: 570 loop : -0.83 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 711 HIS 0.006 0.001 HIS R 745 PHE 0.036 0.001 PHE R 104 TYR 0.023 0.002 TYR R 34 ARG 0.014 0.001 ARG S 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 980 time to evaluate : 3.221 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: 93 outliers final: 54 residues processed: 1023 average time/residue: 0.4848 time to fit residues: 746.9163 Evaluate side-chains 996 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 942 time to evaluate : 3.307 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.2897 time to fit residues: 32.9108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 291 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 298 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 178 optimal weight: 0.8980 chunk 314 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1192 ASN ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 592 HIS R 666 ASN ** R 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 23 HIS ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 272 GLN ** U 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 453 ASN X 245 GLN Y 252 GLN Y 274 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 28941 Z= 0.332 Angle : 0.710 12.696 39175 Z= 0.361 Chirality : 0.047 0.229 4610 Planarity : 0.005 0.065 5022 Dihedral : 7.775 169.445 4000 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 2.92 % Allowed : 28.16 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3618 helix: 0.59 (0.13), residues: 1483 sheet: 0.02 (0.21), residues: 578 loop : -0.88 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP R 586 HIS 0.012 0.001 HIS Y 153 PHE 0.032 0.002 PHE Q1127 TYR 0.025 0.002 TYR R 34 ARG 0.015 0.001 ARG R 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 999 time to evaluate : 3.128 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 outliers start: 91 outliers final: 52 residues processed: 1048 average time/residue: 0.4780 time to fit residues: 750.5352 Evaluate side-chains 1006 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 954 time to evaluate : 2.988 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.3170 time to fit residues: 33.1632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 117 optimal weight: 2.9990 chunk 315 optimal weight: 0.0470 chunk 69 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 350 optimal weight: 0.9980 chunk 290 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 ASN U 36 GLN U 272 GLN U 401 ASN V 260 GLN ** V 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 190 GLN Y 119 GLN Y 223 GLN Y 274 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28941 Z= 0.223 Angle : 0.695 13.082 39175 Z= 0.347 Chirality : 0.045 0.185 4610 Planarity : 0.005 0.095 5022 Dihedral : 7.497 164.950 4000 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 1.99 % Allowed : 29.77 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3618 helix: 0.67 (0.13), residues: 1477 sheet: -0.00 (0.21), residues: 587 loop : -0.88 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 586 HIS 0.009 0.001 HIS R 745 PHE 0.028 0.001 PHE Q1127 TYR 0.031 0.002 TYR T 323 ARG 0.009 0.001 ARG R 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 969 time to evaluate : 3.561 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 outliers start: 62 outliers final: 35 residues processed: 989 average time/residue: 0.4956 time to fit residues: 737.0093 Evaluate side-chains 971 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 936 time to evaluate : 3.620 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3140 time to fit residues: 24.5371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 337 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 348 optimal weight: 0.9990 chunk 218 optimal weight: 0.6980 chunk 212 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS R 607 HIS ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 ASN T 250 HIS U 36 GLN U 272 GLN U 299 HIS ** U 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 119 GLN X 190 GLN Y 274 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28941 Z= 0.266 Angle : 0.712 13.476 39175 Z= 0.360 Chirality : 0.047 0.225 4610 Planarity : 0.005 0.104 5022 Dihedral : 7.455 164.853 4000 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.15 % Favored : 95.83 % Rotamer: Outliers : 2.09 % Allowed : 30.60 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3618 helix: 0.63 (0.13), residues: 1474 sheet: 0.02 (0.21), residues: 577 loop : -0.91 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 586 HIS 0.007 0.001 HIS R 745 PHE 0.029 0.002 PHE Q1127 TYR 0.029 0.002 TYR V 414 ARG 0.013 0.001 ARG T 431 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 952 time to evaluate : 3.442 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: 65 outliers final: 36 residues processed: 979 average time/residue: 0.4879 time to fit residues: 718.2468 Evaluate side-chains 969 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 933 time to evaluate : 3.255 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3141 time to fit residues: 24.8229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 215 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 208 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 32 optimal weight: 30.0000 chunk 274 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 250 HIS U 36 GLN U 272 GLN ** U 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 190 GLN ** X 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 223 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28941 Z= 0.216 Angle : 0.699 13.499 39175 Z= 0.351 Chirality : 0.045 0.186 4610 Planarity : 0.004 0.065 5022 Dihedral : 7.295 161.443 4000 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.10 % Rotamer: Outliers : 1.35 % Allowed : 31.25 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.14 (0.14), residues: 3618 helix: 0.70 (0.13), residues: 1476 sheet: 0.06 (0.21), residues: 586 loop : -0.86 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 586 HIS 0.006 0.001 HIS Y 242 PHE 0.029 0.001 PHE Q1127 TYR 0.028 0.002 TYR T 323 ARG 0.010 0.001 ARG W 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 966 time to evaluate : 3.308 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 outliers start: 42 outliers final: 26 residues processed: 985 average time/residue: 0.5020 time to fit residues: 749.4209 Evaluate side-chains 955 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 929 time to evaluate : 3.254 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3401 time to fit residues: 19.8226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 317 optimal weight: 4.9990 chunk 334 optimal weight: 0.8980 chunk 304 optimal weight: 1.9990 chunk 325 optimal weight: 0.5980 chunk 195 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 255 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 293 optimal weight: 0.0270 chunk 307 optimal weight: 7.9990 chunk 324 optimal weight: 5.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 ASN ** T 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN U 272 GLN ** U 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 190 GLN Y 274 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28941 Z= 0.227 Angle : 0.720 13.331 39175 Z= 0.362 Chirality : 0.046 0.214 4610 Planarity : 0.004 0.065 5022 Dihedral : 7.223 161.669 4000 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.15 % Favored : 95.83 % Rotamer: Outliers : 0.67 % Allowed : 32.53 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3618 helix: 0.68 (0.13), residues: 1475 sheet: 0.01 (0.21), residues: 574 loop : -0.83 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 586 HIS 0.010 0.001 HIS W 242 PHE 0.029 0.001 PHE Q1127 TYR 0.026 0.002 TYR T 323 ARG 0.015 0.001 ARG T 371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 951 time to evaluate : 3.568 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: 21 outliers final: 6 residues processed: 962 average time/residue: 0.4955 time to fit residues: 718.4059 Evaluate side-chains 934 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 928 time to evaluate : 3.574 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3244 time to fit residues: 9.7079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.4718 > 50: distance: 66 - 70: 13.028 distance: 70 - 71: 26.552 distance: 71 - 72: 14.057 distance: 71 - 74: 16.079 distance: 72 - 73: 41.865 distance: 72 - 81: 3.447 distance: 74 - 75: 12.882 distance: 75 - 76: 15.936 distance: 75 - 77: 18.850 distance: 76 - 78: 13.868 distance: 77 - 79: 11.510 distance: 78 - 80: 5.644 distance: 79 - 80: 6.183 distance: 81 - 82: 15.757 distance: 82 - 83: 30.521 distance: 82 - 85: 28.925 distance: 83 - 84: 20.880 distance: 83 - 87: 10.276 distance: 85 - 86: 24.587 distance: 87 - 88: 19.690 distance: 88 - 89: 14.495 distance: 88 - 91: 28.567 distance: 89 - 90: 19.484 distance: 89 - 93: 12.489 distance: 91 - 92: 28.941 distance: 93 - 94: 27.421 distance: 94 - 95: 27.879 distance: 94 - 97: 22.353 distance: 95 - 96: 16.935 distance: 95 - 101: 7.800 distance: 97 - 98: 10.531 distance: 98 - 99: 32.869 distance: 98 - 100: 18.200 distance: 101 - 102: 12.212 distance: 102 - 103: 19.539 distance: 102 - 105: 12.870 distance: 103 - 104: 16.024 distance: 103 - 109: 9.813 distance: 105 - 106: 15.151 distance: 105 - 107: 17.579 distance: 106 - 108: 21.643 distance: 109 - 110: 18.642 distance: 110 - 111: 28.746 distance: 110 - 113: 16.927 distance: 111 - 112: 13.013 distance: 111 - 115: 16.986 distance: 113 - 114: 29.973 distance: 116 - 117: 6.259 distance: 116 - 119: 23.415 distance: 117 - 118: 32.171 distance: 117 - 123: 13.614 distance: 119 - 120: 15.667 distance: 120 - 121: 20.216 distance: 121 - 122: 20.728 distance: 123 - 124: 17.409 distance: 123 - 129: 19.766 distance: 124 - 125: 29.655 distance: 124 - 127: 3.709 distance: 125 - 126: 16.334 distance: 127 - 128: 17.795 distance: 128 - 129: 6.088 distance: 131 - 132: 18.875 distance: 131 - 134: 9.643 distance: 132 - 133: 25.875 distance: 132 - 136: 13.806 distance: 134 - 135: 51.596 distance: 137 - 138: 9.310 distance: 137 - 140: 19.561 distance: 138 - 139: 16.915 distance: 138 - 144: 7.709 distance: 139 - 168: 25.290 distance: 140 - 141: 15.027 distance: 141 - 142: 14.025 distance: 142 - 143: 15.733