Starting phenix.real_space_refine on Sun Mar 17 02:09:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jps_22421/03_2024/7jps_22421_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jps_22421/03_2024/7jps_22421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jps_22421/03_2024/7jps_22421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jps_22421/03_2024/7jps_22421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jps_22421/03_2024/7jps_22421_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jps_22421/03_2024/7jps_22421_neut_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 33 5.49 5 Mg 3 5.21 5 S 82 5.16 5 C 10402 2.51 5 N 2772 2.21 5 O 3059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A ASP 703": "OD1" <-> "OD2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A GLU 757": "OE1" <-> "OE2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A GLU 809": "OE1" <-> "OE2" Residue "A ASP 852": "OD1" <-> "OD2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B ASP 396": "OD1" <-> "OD2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C ASP 143": "OD1" <-> "OD2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 437": "OE1" <-> "OE2" Residue "C GLU 444": "OE1" <-> "OE2" Residue "C ASP 449": "OD1" <-> "OD2" Residue "C GLU 660": "OE1" <-> "OE2" Residue "C GLU 674": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 248": "NH1" <-> "NH2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ARG 271": "NH1" <-> "NH2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16352 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2787 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 12, 'TRANS': 338} Chain breaks: 3 Chain: "B" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1640 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain: "C" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4844 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 24, 'TRANS': 566} Chain breaks: 9 Chain: "D" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3297 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 13, 'TRANS': 391} Chain breaks: 2 Chain: "E" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3160 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 368} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "G" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.57, per 1000 atoms: 0.59 Number of scatterers: 16352 At special positions: 0 Unit cell: (93.09, 133.75, 163.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 82 16.00 P 33 15.00 Mg 3 11.99 O 3059 8.00 N 2772 7.00 C 10402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.19 Conformation dependent library (CDL) restraints added in 3.2 seconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 7 sheets defined 55.6% alpha, 5.5% beta 11 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 6.99 Creating SS restraints... Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 508 through 522 removed outlier: 3.571A pdb=" N LYS A 521 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 556 Processing helix chain 'A' and resid 576 through 587 removed outlier: 3.755A pdb=" N VAL A 579 " --> pdb=" O PRO A 576 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 580 " --> pdb=" O HIS A 577 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 587 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 604 Processing helix chain 'A' and resid 622 through 625 Processing helix chain 'A' and resid 631 through 639 Processing helix chain 'A' and resid 683 through 693 Processing helix chain 'A' and resid 702 through 715 Processing helix chain 'A' and resid 719 through 735 Processing helix chain 'A' and resid 748 through 758 removed outlier: 3.550A pdb=" N ASP A 756 " --> pdb=" O MET A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 768 Processing helix chain 'A' and resid 772 through 788 Processing helix chain 'A' and resid 795 through 809 removed outlier: 4.028A pdb=" N ALA A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 828 removed outlier: 4.037A pdb=" N ALA A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.649A pdb=" N ASN B 274 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 305 removed outlier: 3.710A pdb=" N GLN B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HIS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 329 Processing helix chain 'B' and resid 348 through 358 removed outlier: 3.800A pdb=" N ILE B 355 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 382 Processing helix chain 'B' and resid 403 through 413 Processing helix chain 'B' and resid 429 through 432 removed outlier: 3.615A pdb=" N MET B 432 " --> pdb=" O ALA B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 437 through 440 No H-bonds generated for 'chain 'B' and resid 437 through 440' Processing helix chain 'B' and resid 456 through 464 removed outlier: 4.413A pdb=" N TYR B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 464 " --> pdb=" O TYR B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 64 removed outlier: 4.155A pdb=" N LYS C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 86 removed outlier: 3.950A pdb=" N ASN C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 removed outlier: 3.937A pdb=" N ASP C 115 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 116 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 118 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 120 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU C 123 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 124 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN C 126 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN C 127 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 144 through 157 removed outlier: 3.515A pdb=" N LEU C 148 " --> pdb=" O MET C 144 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 192 Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.998A pdb=" N ILE C 235 " --> pdb=" O GLN C 231 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.800A pdb=" N ILE C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 262 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 268 No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.579A pdb=" N THR C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 315 removed outlier: 3.694A pdb=" N PHE C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 338 Processing helix chain 'C' and resid 340 through 344 removed outlier: 4.207A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 344 " --> pdb=" O LEU C 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 340 through 344' Processing helix chain 'C' and resid 348 through 356 removed outlier: 3.536A pdb=" N ASN C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 368 removed outlier: 3.584A pdb=" N ARG C 368 " --> pdb=" O GLU C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 removed outlier: 3.579A pdb=" N LYS C 378 " --> pdb=" O ARG C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 389 removed outlier: 4.001A pdb=" N VAL C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 425 removed outlier: 3.508A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 413 " --> pdb=" O HIS C 409 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 414 " --> pdb=" O MET C 410 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 415 " --> pdb=" O ASN C 411 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N CYS C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 444 removed outlier: 3.611A pdb=" N CYS C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 461 removed outlier: 3.557A pdb=" N VAL C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 481 removed outlier: 3.614A pdb=" N PHE C 479 " --> pdb=" O CYS C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 500 Processing helix chain 'C' and resid 548 through 566 removed outlier: 3.692A pdb=" N ASN C 554 " --> pdb=" O VAL C 550 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE C 559 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP C 560 " --> pdb=" O VAL C 556 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 562 " --> pdb=" O PHE C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 576 through 579 Processing helix chain 'C' and resid 584 through 591 removed outlier: 3.766A pdb=" N HIS C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 604 removed outlier: 3.672A pdb=" N ALA C 602 " --> pdb=" O ALA C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 608 No H-bonds generated for 'chain 'C' and resid 606 through 608' Processing helix chain 'C' and resid 628 through 636 removed outlier: 3.672A pdb=" N ALA C 632 " --> pdb=" O ASP C 628 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS C 634 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS C 636 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 659 removed outlier: 3.708A pdb=" N THR C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 658 " --> pdb=" O THR C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 689 removed outlier: 4.219A pdb=" N LEU C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 28 Processing helix chain 'D' and resid 41 through 56 Processing helix chain 'D' and resid 73 through 85 removed outlier: 3.677A pdb=" N ILE D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.707A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 92' Processing helix chain 'D' and resid 107 through 117 Processing helix chain 'D' and resid 121 through 124 No H-bonds generated for 'chain 'D' and resid 121 through 124' Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.534A pdb=" N LEU D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 166 removed outlier: 3.529A pdb=" N ALA D 165 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 204 through 208 Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 243 through 257 Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.613A pdb=" N GLU D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 289 removed outlier: 3.599A pdb=" N MET D 284 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 285 " --> pdb=" O MET D 281 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 309 removed outlier: 3.841A pdb=" N LEU D 308 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 320 removed outlier: 3.530A pdb=" N ILE D 317 " --> pdb=" O SER D 313 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 removed outlier: 3.672A pdb=" N ILE D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 331 " --> pdb=" O CYS D 327 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D 336 " --> pdb=" O MET D 332 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP D 337 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE D 338 " --> pdb=" O HIS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 358 removed outlier: 3.782A pdb=" N LYS D 355 " --> pdb=" O ASN D 351 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 382 removed outlier: 3.508A pdb=" N MET D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D 374 " --> pdb=" O PRO D 370 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN D 381 " --> pdb=" O GLU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 removed outlier: 3.617A pdb=" N MET D 412 " --> pdb=" O ASN D 408 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN D 413 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 416 " --> pdb=" O MET D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 430 Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 44 through 53 Processing helix chain 'E' and resid 69 through 84 removed outlier: 3.558A pdb=" N LEU E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU E 74 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 110 Processing helix chain 'E' and resid 127 through 133 removed outlier: 4.545A pdb=" N ARG E 131 " --> pdb=" O GLU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 Proline residue: E 139 - end of helix Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 162 through 165 No H-bonds generated for 'chain 'E' and resid 162 through 165' Processing helix chain 'E' and resid 184 through 191 removed outlier: 3.732A pdb=" N ILE E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 removed outlier: 3.576A pdb=" N ALA E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR E 207 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 214 " --> pdb=" O ILE E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 236 removed outlier: 3.538A pdb=" N LEU E 231 " --> pdb=" O HIS E 227 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Proline residue: E 234 - end of helix Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 250 through 267 Proline residue: E 259 - end of helix removed outlier: 3.828A pdb=" N LYS E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS E 263 " --> pdb=" O PRO E 259 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 283 removed outlier: 3.801A pdb=" N GLN E 282 " --> pdb=" O TRP E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 317 removed outlier: 3.506A pdb=" N ILE E 311 " --> pdb=" O LYS E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 328 removed outlier: 4.217A pdb=" N LYS E 325 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE E 327 " --> pdb=" O ASP E 324 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE E 328 " --> pdb=" O LYS E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 369 removed outlier: 3.552A pdb=" N ALA E 364 " --> pdb=" O ASP E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.674A pdb=" N ILE E 384 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR E 385 " --> pdb=" O PHE E 381 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 422 removed outlier: 3.691A pdb=" N ALA E 418 " --> pdb=" O ASP E 414 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE E 419 " --> pdb=" O PHE E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 431 No H-bonds generated for 'chain 'E' and resid 428 through 431' Processing sheet with id= A, first strand: chain 'A' and resid 530 through 533 removed outlier: 5.457A pdb=" N THR A 674 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N SER A 533 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N MET A 676 " --> pdb=" O SER A 533 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 616 through 620 removed outlier: 6.221A pdb=" N VAL A 648 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 619 " --> pdb=" O VAL A 648 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU A 650 " --> pdb=" O VAL A 619 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.700A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU B 388 " --> pdb=" O TYR B 419 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ILE B 421 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 390 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N SER B 423 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILE B 392 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE B 335 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU B 391 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 337 " --> pdb=" O LEU B 391 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 271 through 276 removed outlier: 6.907A pdb=" N ILE C 100 " --> pdb=" O CYS C 272 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLU C 274 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR C 102 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N PHE C 276 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA C 104 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU C 246 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ALA C 103 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 248 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU C 105 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE C 250 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL C 215 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE C 249 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL C 217 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY C 251 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU C 219 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR C 132 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE C 218 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 134 " --> pdb=" O ILE C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'D' and resid 61 through 65 removed outlier: 3.929A pdb=" N ASN D 61 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL D 154 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N ILE D 190 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE D 156 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU D 192 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU D 158 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D 95 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE D 157 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL D 97 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASP D 159 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU D 99 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 385 through 387 Processing sheet with id= G, first strand: chain 'E' and resid 175 through 178 removed outlier: 3.659A pdb=" N PHE E 34 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU E 177 " --> pdb=" O PHE E 34 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR E 36 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE E 33 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL E 154 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE E 35 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N PHE E 156 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU E 157 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU E 124 " --> pdb=" O LEU E 157 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 4.79 Time building geometry restraints manager: 7.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3109 1.33 - 1.45: 4144 1.45 - 1.58: 9296 1.58 - 1.70: 63 1.70 - 1.83: 125 Bond restraints: 16737 Sorted by residual: bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.51e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.28e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.65e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.52e+01 ... (remaining 16732 not shown) Histogram of bond angle deviations from ideal: 98.61 - 106.06: 483 106.06 - 113.50: 9170 113.50 - 120.95: 8194 120.95 - 128.39: 4754 128.39 - 135.84: 159 Bond angle restraints: 22760 Sorted by residual: angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 120.95 18.92 1.00e+00 1.00e+00 3.58e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.55 18.32 1.00e+00 1.00e+00 3.36e+02 angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 123.67 16.20 1.00e+00 1.00e+00 2.62e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 120.65 16.18 1.00e+00 1.00e+00 2.62e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 121.34 15.49 1.00e+00 1.00e+00 2.40e+02 ... (remaining 22755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 8838 17.60 - 35.19: 962 35.19 - 52.78: 239 52.78 - 70.38: 62 70.38 - 87.97: 38 Dihedral angle restraints: 10139 sinusoidal: 4403 harmonic: 5736 Sorted by residual: dihedral pdb=" CA GLN D 31 " pdb=" C GLN D 31 " pdb=" N SER D 32 " pdb=" CA SER D 32 " ideal model delta harmonic sigma weight residual 180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA HIS E 195 " pdb=" C HIS E 195 " pdb=" N PRO E 196 " pdb=" CA PRO E 196 " ideal model delta harmonic sigma weight residual 180.00 157.49 22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA VAL E 214 " pdb=" C VAL E 214 " pdb=" N PHE E 215 " pdb=" CA PHE E 215 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 10136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2309 0.097 - 0.194: 264 0.194 - 0.291: 21 0.291 - 0.387: 2 0.387 - 0.484: 2 Chirality restraints: 2598 Sorted by residual: chirality pdb=" CB THR E 410 " pdb=" CA THR E 410 " pdb=" OG1 THR E 410 " pdb=" CG2 THR E 410 " both_signs ideal model delta sigma weight residual False 2.55 2.07 0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.10 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CG LEU B 303 " pdb=" CB LEU B 303 " pdb=" CD1 LEU B 303 " pdb=" CD2 LEU B 303 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 2595 not shown) Planarity restraints: 2772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 369 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO C 370 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 370 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 370 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 152 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO D 153 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO D 153 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 153 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 412 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C TYR C 412 " 0.063 2.00e-02 2.50e+03 pdb=" O TYR C 412 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE C 413 " -0.021 2.00e-02 2.50e+03 ... (remaining 2769 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.71: 431 2.71 - 3.32: 18354 3.32 - 3.92: 31096 3.92 - 4.53: 41364 4.53 - 5.14: 61998 Nonbonded interactions: 153243 Sorted by model distance: nonbonded pdb=" O1B ATP A 901 " pdb="MG MG A 902 " model vdw 2.102 2.170 nonbonded pdb=" O1B ATP E 501 " pdb="MG MG E 502 " model vdw 2.110 2.170 nonbonded pdb=" O3G ATP A 901 " pdb="MG MG A 902 " model vdw 2.111 2.170 nonbonded pdb=" O3G ATP E 501 " pdb="MG MG E 502 " model vdw 2.174 2.170 nonbonded pdb=" O LEU B 316 " pdb=" OH TYR B 454 " model vdw 2.236 2.440 ... (remaining 153238 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 'F' and (resid 1 through 11 or resid 13)) selection = (chain 'G' and (resid 1 through 2 or resid 4 through 13)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.010 Extract box with map and model: 8.150 Check model and map are aligned: 0.000 Set scattering table: 0.130 Process input model: 50.830 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4824 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 0.081 16737 Z= 0.397 Angle : 1.195 18.915 22760 Z= 0.705 Chirality : 0.062 0.484 2598 Planarity : 0.007 0.112 2772 Dihedral : 16.818 87.973 6381 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.16), residues: 1888 helix: -1.62 (0.13), residues: 1051 sheet: -0.75 (0.39), residues: 156 loop : -1.54 (0.21), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP E 162 HIS 0.015 0.002 HIS C 81 PHE 0.045 0.004 PHE A 637 TYR 0.032 0.003 TYR C 375 ARG 0.023 0.002 ARG E 417 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 2.259 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: A 494 ARG cc_start: 0.6024 (mmt-90) cc_final: 0.5124 (mtt180) REVERT: A 566 ILE cc_start: 0.6767 (mp) cc_final: 0.6560 (mm) REVERT: D 29 CYS cc_start: 0.6658 (m) cc_final: 0.5791 (m) REVERT: D 50 LEU cc_start: 0.7852 (mt) cc_final: 0.7509 (tp) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.3069 time to fit residues: 166.3127 Evaluate side-chains 205 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 78 optimal weight: 40.0000 chunk 151 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 0.0370 chunk 112 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN A 516 ASN ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN A 769 ASN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 127 ASN C 242 HIS ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN C 399 GLN C 409 HIS C 411 ASN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5106 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16737 Z= 0.200 Angle : 0.616 8.253 22760 Z= 0.322 Chirality : 0.041 0.194 2598 Planarity : 0.004 0.055 2772 Dihedral : 13.348 85.777 2470 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.23 % Allowed : 3.10 % Favored : 96.67 % 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: -0.92 (0.18), residues: 1888 helix: -0.17 (0.15), residues: 1073 sheet: -0.18 (0.41), residues: 146 loop : -1.27 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 648 HIS 0.007 0.001 HIS C 81 PHE 0.026 0.002 PHE B 380 TYR 0.033 0.002 TYR C 609 ARG 0.028 0.001 ARG C 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 264 time to evaluate : 2.103 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: A 494 ARG cc_start: 0.6497 (mmt-90) cc_final: 0.5245 (mtt180) REVERT: A 530 MET cc_start: 0.3942 (tpt) cc_final: 0.2337 (tpt) REVERT: A 647 LEU cc_start: 0.6956 (tp) cc_final: 0.6638 (tp) REVERT: C 144 MET cc_start: 0.7885 (mmm) cc_final: 0.7667 (mmm) REVERT: C 610 LEU cc_start: 0.7117 (mt) cc_final: 0.6762 (mp) REVERT: D 355 LYS cc_start: 0.7171 (mppt) cc_final: 0.6841 (tptt) REVERT: E 216 TYR cc_start: 0.4516 (t80) cc_final: 0.4178 (t80) outliers start: 4 outliers final: 1 residues processed: 267 average time/residue: 0.3059 time to fit residues: 119.6826 Evaluate side-chains 178 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN A 582 GLN ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 HIS ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 HIS C 557 ASN ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 HIS D 19 GLN D 46 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5566 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 16737 Z= 0.362 Angle : 0.777 7.853 22760 Z= 0.408 Chirality : 0.045 0.252 2598 Planarity : 0.005 0.044 2772 Dihedral : 13.995 88.238 2470 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.11 % Allowed : 4.85 % Favored : 95.03 % 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: -0.90 (0.19), residues: 1888 helix: -0.27 (0.15), residues: 1067 sheet: 0.21 (0.41), residues: 147 loop : -1.11 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP C 648 HIS 0.009 0.002 HIS C 242 PHE 0.032 0.003 PHE B 380 TYR 0.026 0.003 TYR C 609 ARG 0.005 0.001 ARG D 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 231 time to evaluate : 1.588 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: A 494 ARG cc_start: 0.6859 (mmt-90) cc_final: 0.5655 (mtt180) REVERT: A 530 MET cc_start: 0.5215 (tpt) cc_final: 0.3486 (tpt) REVERT: A 700 PHE cc_start: 0.6121 (m-10) cc_final: 0.5916 (m-10) REVERT: B 381 LYS cc_start: 0.6538 (mmmt) cc_final: 0.6337 (mmmt) REVERT: B 462 ASN cc_start: 0.1906 (m-40) cc_final: 0.1126 (t0) REVERT: D 178 ASP cc_start: 0.6658 (p0) cc_final: 0.6336 (p0) outliers start: 2 outliers final: 0 residues processed: 232 average time/residue: 0.3113 time to fit residues: 106.7528 Evaluate side-chains 162 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 GLN ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN B 406 GLN ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 HIS ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 HIS C 702 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN D 378 HIS E 62 ASN ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.6723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16737 Z= 0.384 Angle : 0.814 11.383 22760 Z= 0.425 Chirality : 0.046 0.226 2598 Planarity : 0.005 0.062 2772 Dihedral : 14.615 88.018 2470 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 28.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.20 % 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: -1.54 (0.18), residues: 1888 helix: -0.87 (0.14), residues: 1078 sheet: 0.13 (0.41), residues: 155 loop : -1.30 (0.26), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 648 HIS 0.009 0.002 HIS C 585 PHE 0.033 0.003 PHE B 380 TYR 0.043 0.003 TYR D 174 ARG 0.008 0.001 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 1.757 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: A 494 ARG cc_start: 0.6846 (mmt-90) cc_final: 0.5306 (mtt180) REVERT: A 595 ASN cc_start: 0.4151 (OUTLIER) cc_final: 0.2884 (m-40) REVERT: A 632 ILE cc_start: 0.6616 (mp) cc_final: 0.6207 (mp) REVERT: B 381 LYS cc_start: 0.6396 (mmmt) cc_final: 0.5939 (mmmt) REVERT: B 462 ASN cc_start: 0.2296 (m-40) cc_final: 0.1906 (t0) REVERT: D 174 TYR cc_start: 0.6519 (m-10) cc_final: 0.5720 (m-80) outliers start: 3 outliers final: 1 residues processed: 193 average time/residue: 0.2777 time to fit residues: 80.8373 Evaluate side-chains 140 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 95 optimal weight: 0.2980 chunk 167 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.7207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16737 Z= 0.284 Angle : 0.684 8.068 22760 Z= 0.354 Chirality : 0.042 0.214 2598 Planarity : 0.004 0.036 2772 Dihedral : 14.251 78.960 2470 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 24.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.11 % Allowed : 3.56 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.19), residues: 1888 helix: -0.48 (0.15), residues: 1072 sheet: 0.15 (0.42), residues: 154 loop : -1.25 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 648 HIS 0.007 0.001 HIS B 426 PHE 0.019 0.002 PHE E 215 TYR 0.033 0.002 TYR D 174 ARG 0.004 0.001 ARG A 728 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 1.732 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: A 494 ARG cc_start: 0.6472 (mmt-90) cc_final: 0.4868 (mtt180) REVERT: A 632 ILE cc_start: 0.6614 (mp) cc_final: 0.5657 (mm) REVERT: D 29 CYS cc_start: 0.7339 (m) cc_final: 0.6978 (m) outliers start: 2 outliers final: 1 residues processed: 189 average time/residue: 0.2795 time to fit residues: 79.7309 Evaluate side-chains 140 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 HIS D 354 GLN E 62 ASN E 193 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5604 moved from start: 0.7267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16737 Z= 0.182 Angle : 0.602 9.499 22760 Z= 0.309 Chirality : 0.041 0.282 2598 Planarity : 0.003 0.036 2772 Dihedral : 13.711 81.185 2470 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 1888 helix: 0.09 (0.15), residues: 1084 sheet: 0.45 (0.41), residues: 156 loop : -1.23 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 648 HIS 0.008 0.001 HIS B 426 PHE 0.016 0.001 PHE E 215 TYR 0.013 0.001 TYR C 408 ARG 0.005 0.000 ARG A 728 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.807 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: A 494 ARG cc_start: 0.6466 (mmt-90) cc_final: 0.4766 (mtt180) REVERT: A 632 ILE cc_start: 0.6535 (mp) cc_final: 0.5464 (mm) REVERT: C 136 LEU cc_start: 0.3434 (mt) cc_final: 0.2896 (tp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2760 time to fit residues: 77.3626 Evaluate side-chains 132 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 105 optimal weight: 0.2980 chunk 157 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 moved from start: 0.7725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16737 Z= 0.236 Angle : 0.649 12.477 22760 Z= 0.334 Chirality : 0.041 0.180 2598 Planarity : 0.004 0.040 2772 Dihedral : 13.834 81.953 2470 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: -0.65 (0.19), residues: 1888 helix: 0.02 (0.15), residues: 1085 sheet: 0.13 (0.39), residues: 170 loop : -1.19 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 433 HIS 0.008 0.001 HIS B 426 PHE 0.021 0.002 PHE E 215 TYR 0.025 0.002 TYR D 174 ARG 0.004 0.001 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.853 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: A 494 ARG cc_start: 0.6497 (mmt-90) cc_final: 0.4744 (mtt180) REVERT: A 632 ILE cc_start: 0.6836 (mp) cc_final: 0.5870 (mm) REVERT: B 294 TYR cc_start: 0.6518 (m-10) cc_final: 0.6182 (m-10) REVERT: C 181 MET cc_start: 0.2298 (mtp) cc_final: 0.1530 (mtp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2595 time to fit residues: 67.4076 Evaluate side-chains 137 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5713 moved from start: 0.8094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16737 Z= 0.235 Angle : 0.649 11.282 22760 Z= 0.333 Chirality : 0.041 0.181 2598 Planarity : 0.004 0.040 2772 Dihedral : 13.835 84.554 2470 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -0.63 (0.19), residues: 1888 helix: 0.01 (0.15), residues: 1090 sheet: 0.08 (0.39), residues: 170 loop : -1.13 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 433 HIS 0.006 0.001 HIS C 81 PHE 0.029 0.002 PHE C 497 TYR 0.021 0.002 TYR D 174 ARG 0.004 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.933 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: A 530 MET cc_start: 0.4969 (tpt) cc_final: 0.3374 (tpt) REVERT: A 632 ILE cc_start: 0.6843 (mp) cc_final: 0.5884 (mm) REVERT: B 294 TYR cc_start: 0.6503 (m-10) cc_final: 0.6210 (m-10) REVERT: D 328 LEU cc_start: 0.7129 (mt) cc_final: 0.6901 (mt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2627 time to fit residues: 67.7665 Evaluate side-chains 126 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 136 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS D 400 GLN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5574 moved from start: 0.7988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16737 Z= 0.160 Angle : 0.599 11.268 22760 Z= 0.303 Chirality : 0.040 0.174 2598 Planarity : 0.003 0.039 2772 Dihedral : 13.479 81.231 2470 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -0.09 (0.20), residues: 1888 helix: 0.47 (0.16), residues: 1083 sheet: 0.24 (0.39), residues: 170 loop : -0.91 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 301 HIS 0.006 0.001 HIS D 46 PHE 0.022 0.001 PHE C 497 TYR 0.012 0.001 TYR D 226 ARG 0.004 0.000 ARG C 436 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.4805 (tpt) cc_final: 0.3177 (tpt) REVERT: A 632 ILE cc_start: 0.6736 (mp) cc_final: 0.5615 (mm) REVERT: B 294 TYR cc_start: 0.6491 (m-10) cc_final: 0.6127 (m-10) REVERT: B 432 MET cc_start: 0.6646 (pmm) cc_final: 0.6361 (pmm) REVERT: E 265 MET cc_start: 0.6095 (tpp) cc_final: 0.5830 (tpp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2801 time to fit residues: 75.2406 Evaluate side-chains 129 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 HIS ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 moved from start: 0.8238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16737 Z= 0.195 Angle : 0.621 11.066 22760 Z= 0.315 Chirality : 0.040 0.182 2598 Planarity : 0.004 0.093 2772 Dihedral : 13.551 84.553 2470 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.29 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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 (0.20), residues: 1888 helix: 0.47 (0.16), residues: 1090 sheet: 0.22 (0.39), residues: 169 loop : -0.95 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 433 HIS 0.011 0.001 HIS B 426 PHE 0.024 0.002 PHE C 497 TYR 0.026 0.001 TYR D 174 ARG 0.025 0.001 ARG D 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.037 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: A 530 MET cc_start: 0.5078 (tpt) cc_final: 0.3493 (tpt) REVERT: A 632 ILE cc_start: 0.6619 (mp) cc_final: 0.5689 (mm) REVERT: B 294 TYR cc_start: 0.6465 (m-10) cc_final: 0.6136 (m-10) REVERT: B 432 MET cc_start: 0.6592 (pmm) cc_final: 0.6191 (pmm) REVERT: E 265 MET cc_start: 0.6553 (tpp) cc_final: 0.6208 (tpp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2914 time to fit residues: 74.8846 Evaluate side-chains 129 residues out of total 1774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 134 optimal weight: 0.0670 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 HIS ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN B 426 HIS ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 96 GLN D 400 GLN E 62 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.063491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.052549 restraints weight = 172411.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.053430 restraints weight = 128565.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.054133 restraints weight = 104215.185| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.8287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16737 Z= 0.162 Angle : 0.608 13.123 22760 Z= 0.304 Chirality : 0.040 0.338 2598 Planarity : 0.003 0.052 2772 Dihedral : 13.397 84.046 2470 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.13 (0.20), residues: 1888 helix: 0.66 (0.16), residues: 1086 sheet: 0.35 (0.39), residues: 168 loop : -0.87 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 301 HIS 0.010 0.001 HIS B 426 PHE 0.029 0.001 PHE D 344 TYR 0.021 0.001 TYR D 174 ARG 0.015 0.000 ARG D 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2978.71 seconds wall clock time: 55 minutes 26.67 seconds (3326.67 seconds total)