Starting phenix.real_space_refine (version: dev) on Tue Feb 28 06:34:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdm_23775/02_2023/7mdm_23775_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdm_23775/02_2023/7mdm_23775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdm_23775/02_2023/7mdm_23775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdm_23775/02_2023/7mdm_23775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdm_23775/02_2023/7mdm_23775_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdm_23775/02_2023/7mdm_23775_updated.pdb" } resolution = 4.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.075 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 Process input model Symmetric amino acids flipped Residue "B GLU 48": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ASP 392": "OD1" <-> "OD2" Residue "B ASP 451": "OD1" <-> "OD2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C ASP 450": "OD1" <-> "OD2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 450": "OD1" <-> "OD2" Residue "D ASP 501": "OD1" <-> "OD2" Residue "D GLU 706": "OE1" <-> "OE2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E ARG 322": "NH1" <-> "NH2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A ASP 205": "OD1" <-> "OD2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 640": "OD1" <-> "OD2" Residue "A ASP 671": "OD1" <-> "OD2" Residue "A ASP 751": "OD1" <-> "OD2" Residue "F ASP 205": "OD1" <-> "OD2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 392": "OD1" <-> "OD2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 599": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 31986 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 5513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5513 Classifications: {'peptide': 701} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 662} Chain breaks: 2 Chain: "C" Number of atoms: 5527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5527 Classifications: {'peptide': 703} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 664} Chain breaks: 2 Chain: "D" Number of atoms: 5527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5527 Classifications: {'peptide': 703} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 664} Chain breaks: 2 Chain: "E" Number of atoms: 5532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5532 Classifications: {'peptide': 704} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 665} Chain breaks: 2 Chain: "A" Number of atoms: 5513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5513 Classifications: {'peptide': 701} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 662} Chain breaks: 2 Chain: "F" Number of atoms: 4212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4212 Classifications: {'peptide': 539} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 510} Chain breaks: 2 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" 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: 17.40, per 1000 atoms: 0.54 Number of scatterers: 31986 At special positions: 0 Unit cell: (104.52, 160.68, 171.6, 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 172 16.00 P 12 15.00 O 6082 8.00 N 5597 7.00 C 20123 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: 13.39 Conformation dependent library (CDL) restraints added in 5.2 seconds 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7616 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 173 helices and 34 sheets defined 36.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 131 through 139 Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 227 through 230 No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 320 through 333 removed outlier: 4.473A pdb=" N GLN B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N THR B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 449 through 456 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 492 Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 526 through 534 removed outlier: 3.969A pdb=" N ALA B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 567 Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 600 through 609 removed outlier: 3.602A pdb=" N ASP B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 removed outlier: 4.549A pdb=" N LYS B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 675 No H-bonds generated for 'chain 'B' and resid 672 through 675' Processing helix chain 'B' and resid 684 through 703 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 750 through 762 removed outlier: 3.543A pdb=" N ARG B 753 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 131 through 134 No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 213 through 225 removed outlier: 4.466A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 271 through 274 No H-bonds generated for 'chain 'C' and resid 271 through 274' Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 320 through 325 Processing helix chain 'C' and resid 328 through 331 No H-bonds generated for 'chain 'C' and resid 328 through 331' Processing helix chain 'C' and resid 374 through 383 removed outlier: 3.904A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 400 No H-bonds generated for 'chain 'C' and resid 397 through 400' Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 456 Processing helix chain 'C' and resid 483 through 498 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 567 Processing helix chain 'C' and resid 580 through 583 No H-bonds generated for 'chain 'C' and resid 580 through 583' Processing helix chain 'C' and resid 600 through 607 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 650 through 661 Processing helix chain 'C' and resid 674 through 676 No H-bonds generated for 'chain 'C' and resid 674 through 676' Processing helix chain 'C' and resid 684 through 702 Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 752 through 762 removed outlier: 3.972A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 762 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 86 through 92 removed outlier: 5.460A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 4.483A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 210 through 220 removed outlier: 4.156A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 271 through 274 No H-bonds generated for 'chain 'D' and resid 271 through 274' Processing helix chain 'D' and resid 282 through 296 removed outlier: 4.176A pdb=" N GLU D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 320 through 325 Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 397 through 402 removed outlier: 3.961A pdb=" N GLU D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 440 through 443 No H-bonds generated for 'chain 'D' and resid 440 through 443' Processing helix chain 'D' and resid 449 through 456 Processing helix chain 'D' and resid 483 through 494 Processing helix chain 'D' and resid 501 through 504 No H-bonds generated for 'chain 'D' and resid 501 through 504' Processing helix chain 'D' and resid 524 through 533 Processing helix chain 'D' and resid 544 through 551 removed outlier: 4.496A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 567 Processing helix chain 'D' and resid 579 through 583 Processing helix chain 'D' and resid 600 through 606 Processing helix chain 'D' and resid 650 through 660 Processing helix chain 'D' and resid 673 through 678 removed outlier: 4.517A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 703 Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 752 through 762 Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 86 through 92 removed outlier: 4.504A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 227 through 233 removed outlier: 4.372A pdb=" N PHE E 230 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS E 231 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 233 " --> pdb=" O PHE E 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 227 through 233' Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 271 through 274 No H-bonds generated for 'chain 'E' and resid 271 through 274' Processing helix chain 'E' and resid 282 through 295 removed outlier: 3.658A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 316 No H-bonds generated for 'chain 'E' and resid 314 through 316' Processing helix chain 'E' and resid 319 through 325 removed outlier: 3.508A pdb=" N VAL E 325 " --> pdb=" O ARG E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 333 Processing helix chain 'E' and resid 374 through 384 removed outlier: 5.259A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 424 Processing helix chain 'E' and resid 440 through 443 No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'E' and resid 449 through 456 Processing helix chain 'E' and resid 483 through 493 Processing helix chain 'E' and resid 501 through 506 Processing helix chain 'E' and resid 524 through 533 removed outlier: 3.664A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS E 529 " --> pdb=" O THR E 525 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 553 removed outlier: 4.180A pdb=" N PHE E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 568 Processing helix chain 'E' and resid 579 through 583 removed outlier: 3.887A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA E 583 " --> pdb=" O ASP E 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 579 through 583' Processing helix chain 'E' and resid 599 through 607 Processing helix chain 'E' and resid 613 through 615 No H-bonds generated for 'chain 'E' and resid 613 through 615' Processing helix chain 'E' and resid 650 through 662 removed outlier: 3.564A pdb=" N ARG E 662 " --> pdb=" O LYS E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 703 Processing helix chain 'E' and resid 733 through 739 Processing helix chain 'E' and resid 751 through 762 Processing helix chain 'A' and resid 44 through 47 No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 131 through 138 removed outlier: 5.067A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 213 through 225 removed outlier: 5.568A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 320 through 331 removed outlier: 5.036A pdb=" N GLN A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.849A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 456 Processing helix chain 'A' and resid 485 through 494 removed outlier: 4.261A pdb=" N GLU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.969A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 567 Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 600 through 609 removed outlier: 4.419A pdb=" N ASP A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 662 removed outlier: 3.763A pdb=" N ARG A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 No H-bonds generated for 'chain 'A' and resid 672 through 675' Processing helix chain 'A' and resid 684 through 703 removed outlier: 3.687A pdb=" N ILE A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 751 through 762 Processing helix chain 'F' and resid 213 through 224 removed outlier: 5.632A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 230 No H-bonds generated for 'chain 'F' and resid 227 through 230' Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 291 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 320 through 331 removed outlier: 5.163A pdb=" N GLN F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU F 328 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 386 removed outlier: 3.855A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS F 386 " --> pdb=" O GLN F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 402 No H-bonds generated for 'chain 'F' and resid 399 through 402' Processing helix chain 'F' and resid 408 through 423 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 456 Processing helix chain 'F' and resid 460 through 462 No H-bonds generated for 'chain 'F' and resid 460 through 462' Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 removed outlier: 4.383A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 534 removed outlier: 3.626A pdb=" N LYS F 529 " --> pdb=" O THR F 525 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 552 removed outlier: 3.785A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 569 removed outlier: 3.589A pdb=" N ALA F 569 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 582 No H-bonds generated for 'chain 'F' and resid 579 through 582' Processing helix chain 'F' and resid 600 through 607 Processing helix chain 'F' and resid 650 through 663 removed outlier: 4.324A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 676 Processing helix chain 'F' and resid 684 through 703 Processing helix chain 'F' and resid 734 through 740 Processing helix chain 'F' and resid 750 through 762 removed outlier: 3.559A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 27 through 30 Processing sheet with id= B, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= C, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.638A pdb=" N PHE B 152 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 241 through 243 removed outlier: 3.636A pdb=" N ILE B 342 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 469 through 471 removed outlier: 3.935A pdb=" N ILE B 540 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 575 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 577 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 27 through 30 Processing sheet with id= G, first strand: chain 'C' and resid 38 through 41 removed outlier: 7.081A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU C 41 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU C 72 " --> pdb=" O LEU C 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.771A pdb=" N GLN C 103 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 153 through 156 Processing sheet with id= J, first strand: chain 'C' and resid 241 through 244 removed outlier: 7.021A pdb=" N ARG C 365 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N TYR C 244 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C 367 " --> pdb=" O TYR C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 265 through 269 removed outlier: 3.520A pdb=" N PHE C 267 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 302 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP C 304 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE C 342 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE C 303 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N MET C 344 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 619 through 623 removed outlier: 4.131A pdb=" N VAL C 514 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C 518 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN C 641 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TYR C 517 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE C 643 " --> pdb=" O TYR C 517 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 538 through 542 Processing sheet with id= N, first strand: chain 'C' and resid 114 through 118 removed outlier: 4.134A pdb=" N HIS C 115 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU C 167 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 38 through 41 removed outlier: 6.966A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.757A pdb=" N GLN D 103 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 153 through 155 Processing sheet with id= R, first strand: chain 'D' and resid 241 through 244 removed outlier: 7.554A pdb=" N ARG D 365 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N TYR D 244 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL D 367 " --> pdb=" O TYR D 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.500A pdb=" N PHE D 267 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE D 302 " --> pdb=" O PHE D 267 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 539 through 543 removed outlier: 6.735A pdb=" N VAL D 573 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE D 542 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE D 575 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 514 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D 640 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU D 515 " --> pdb=" O ASP D 640 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU D 642 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N TYR D 517 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR D 644 " --> pdb=" O TYR D 517 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.679A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 38 through 41 removed outlier: 6.787A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU E 41 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU E 72 " --> pdb=" O LEU E 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'E' and resid 57 through 59 removed outlier: 3.573A pdb=" N GLN E 103 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 151 through 155 removed outlier: 3.612A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 241 through 243 removed outlier: 3.570A pdb=" N ILE E 241 " --> pdb=" O VAL E 343 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 642 through 645 removed outlier: 8.507A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 645 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR E 517 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'A' and resid 27 through 30 Processing sheet with id= AB, first strand: chain 'A' and resid 66 through 70 removed outlier: 3.657A pdb=" N GLN A 103 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= AD, first strand: chain 'A' and resid 151 through 154 removed outlier: 3.723A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 365 through 368 removed outlier: 3.944A pdb=" N LEU A 242 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 367 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR A 244 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 469 through 471 removed outlier: 3.903A pdb=" N GLU A 470 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 514 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 265 through 268 Processing sheet with id= AH, first strand: chain 'F' and resid 643 through 645 removed outlier: 3.745A pdb=" N ILE F 643 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 828 hydrogen bonds defined for protein. 2433 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: 10.17 Time building geometry restraints manager: 13.93 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: 9073 1.33 - 1.46: 5643 1.46 - 1.58: 17504 1.58 - 1.70: 19 1.70 - 1.82: 277 Bond restraints: 32516 Sorted by residual: bond pdb=" C CYS A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.334 1.404 -0.071 8.40e-03 1.42e+04 7.11e+01 bond pdb=" CA GLU E 314 " pdb=" C GLU E 314 " ideal model delta sigma weight residual 1.523 1.589 -0.066 1.80e-02 3.09e+03 1.35e+01 bond pdb=" C ASN B 460 " pdb=" N PRO B 461 " ideal model delta sigma weight residual 1.334 1.407 -0.074 2.34e-02 1.83e+03 9.87e+00 bond pdb=" C ASN A 460 " pdb=" N PRO A 461 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.54e+00 bond pdb=" C ASN D 460 " pdb=" N PRO D 461 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.34e+00 ... (remaining 32511 not shown) Histogram of bond angle deviations from ideal: 97.46 - 105.23: 771 105.23 - 113.00: 16965 113.00 - 120.77: 15597 120.77 - 128.54: 10407 128.54 - 136.31: 202 Bond angle restraints: 43942 Sorted by residual: angle pdb=" C SER F 326 " pdb=" N GLN F 327 " pdb=" CA GLN F 327 " ideal model delta sigma weight residual 121.54 135.92 -14.38 1.91e+00 2.74e-01 5.67e+01 angle pdb=" N LYS F 211 " pdb=" CA LYS F 211 " pdb=" C LYS F 211 " ideal model delta sigma weight residual 114.56 105.37 9.19 1.27e+00 6.20e-01 5.24e+01 angle pdb=" C SER A 326 " pdb=" N GLN A 327 " pdb=" CA GLN A 327 " ideal model delta sigma weight residual 121.54 134.60 -13.06 1.91e+00 2.74e-01 4.67e+01 angle pdb=" CB MET F 740 " pdb=" CG MET F 740 " pdb=" SD MET F 740 " ideal model delta sigma weight residual 112.70 131.30 -18.60 3.00e+00 1.11e-01 3.84e+01 angle pdb=" N ILE D 369 " pdb=" CA ILE D 369 " pdb=" C ILE D 369 " ideal model delta sigma weight residual 112.96 106.95 6.01 1.00e+00 1.00e+00 3.61e+01 ... (remaining 43937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.98: 19630 32.98 - 65.97: 521 65.97 - 98.95: 35 98.95 - 131.94: 6 131.94 - 164.92: 1 Dihedral angle restraints: 20193 sinusoidal: 8483 harmonic: 11710 Sorted by residual: dihedral pdb=" CA ARG B 95 " pdb=" C ARG B 95 " pdb=" N LEU B 96 " pdb=" CA LEU B 96 " ideal model delta harmonic sigma weight residual 180.00 129.94 50.06 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 104.92 -164.92 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" CA LEU A 331 " pdb=" C LEU A 331 " pdb=" N MET A 332 " pdb=" CA MET A 332 " ideal model delta harmonic sigma weight residual 180.00 147.39 32.61 0 5.00e+00 4.00e-02 4.25e+01 ... (remaining 20190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4160 0.089 - 0.179: 712 0.179 - 0.268: 79 0.268 - 0.358: 21 0.358 - 0.447: 6 Chirality restraints: 4978 Sorted by residual: chirality pdb=" CB VAL A 108 " pdb=" CA VAL A 108 " pdb=" CG1 VAL A 108 " pdb=" CG2 VAL A 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CB ILE E 303 " pdb=" CA ILE E 303 " pdb=" CG1 ILE E 303 " pdb=" CG2 ILE E 303 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB ILE E 241 " pdb=" CA ILE E 241 " pdb=" CG1 ILE E 241 " pdb=" CG2 ILE E 241 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 4975 not shown) Planarity restraints: 5767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 495 " 0.057 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO C 496 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 496 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 496 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 327 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C GLN B 327 " -0.057 2.00e-02 2.50e+03 pdb=" O GLN B 327 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 328 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 95 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ARG B 95 " -0.056 2.00e-02 2.50e+03 pdb=" O ARG B 95 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 96 " 0.019 2.00e-02 2.50e+03 ... (remaining 5764 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7606 2.79 - 3.32: 30925 3.32 - 3.84: 58124 3.84 - 4.37: 65280 4.37 - 4.90: 103118 Nonbonded interactions: 265053 Sorted by model distance: nonbonded pdb=" O VAL D 258 " pdb=" OG1 THR D 262 " model vdw 2.261 2.440 nonbonded pdb=" O ILE D 274 " pdb=" OG SER D 282 " model vdw 2.274 2.440 nonbonded pdb=" O MET A 757 " pdb=" OG1 THR A 761 " model vdw 2.280 2.440 nonbonded pdb=" O LEU D 381 " pdb=" OG1 THR D 385 " model vdw 2.293 2.440 nonbonded pdb=" O PRO D 246 " pdb=" OG1 THR D 249 " model vdw 2.296 2.440 ... (remaining 265048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 25 through 582 or resid 598 through 763 or resid 901)) selection = (chain 'D' and (resid 25 through 582 or resid 598 through 763 or resid 901)) selection = (chain 'E' and (resid 25 through 582 or resid 598 through 763 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 172 5.16 5 C 20123 2.51 5 N 5597 2.21 5 O 6082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.040 Extract box with map and model: 6.230 Check model and map are aligned: 0.460 Process input model: 77.660 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.270 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 32516 Z= 0.327 Angle : 1.189 18.595 43942 Z= 0.623 Chirality : 0.070 0.447 4978 Planarity : 0.008 0.086 5767 Dihedral : 15.375 164.919 12577 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.11), residues: 4015 helix: -2.92 (0.09), residues: 1644 sheet: -1.61 (0.23), residues: 442 loop : -1.87 (0.13), residues: 1929 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1035 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1036 average time/residue: 0.5139 time to fit residues: 804.6332 Evaluate side-chains 622 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 622 time to evaluate : 4.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 340 optimal weight: 8.9990 chunk 305 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 315 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 365 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 660 ASN B 760 GLN C 129 ASN ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN C 406 HIS C 458 GLN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN E 401 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS A 499 HIS F 226 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 32516 Z= 0.224 Angle : 0.746 8.989 43942 Z= 0.376 Chirality : 0.047 0.303 4978 Planarity : 0.006 0.084 5767 Dihedral : 8.133 158.461 4446 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.38 % Favored : 93.60 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.12), residues: 4015 helix: -1.88 (0.11), residues: 1678 sheet: -1.42 (0.23), residues: 457 loop : -1.57 (0.14), residues: 1880 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 773 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 779 average time/residue: 0.5042 time to fit residues: 606.3357 Evaluate side-chains 551 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 549 time to evaluate : 4.286 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3253 time to fit residues: 7.0141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 203 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 249 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 366 optimal weight: 9.9990 chunk 396 optimal weight: 0.9980 chunk 326 optimal weight: 3.9990 chunk 363 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN E 568 GLN E 692 GLN A 90 ASN ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS A 692 GLN F 199 ASN F 260 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 32516 Z= 0.232 Angle : 0.736 9.347 43942 Z= 0.371 Chirality : 0.048 0.211 4978 Planarity : 0.005 0.072 5767 Dihedral : 7.947 170.776 4446 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.13), residues: 4015 helix: -1.44 (0.12), residues: 1658 sheet: -1.33 (0.23), residues: 461 loop : -1.42 (0.14), residues: 1896 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 733 time to evaluate : 4.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 735 average time/residue: 0.4933 time to fit residues: 560.6047 Evaluate side-chains 541 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 539 time to evaluate : 4.021 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2901 time to fit residues: 6.0624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 362 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 246 optimal weight: 0.9980 chunk 367 optimal weight: 4.9990 chunk 389 optimal weight: 20.0000 chunk 192 optimal weight: 0.9990 chunk 348 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 HIS ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 GLN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN E 384 HIS E 401 ASN E 538 ASN ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS F 533 ASN F 624 ASN ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 32516 Z= 0.416 Angle : 0.914 10.569 43942 Z= 0.474 Chirality : 0.052 0.266 4978 Planarity : 0.007 0.095 5767 Dihedral : 8.540 169.410 4446 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 42.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.69 % Favored : 91.28 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.12), residues: 4015 helix: -1.73 (0.11), residues: 1633 sheet: -1.67 (0.22), residues: 502 loop : -1.60 (0.14), residues: 1880 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 661 time to evaluate : 4.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 664 average time/residue: 0.5073 time to fit residues: 520.0323 Evaluate side-chains 467 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 465 time to evaluate : 3.822 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2954 time to fit residues: 6.7176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 324 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 290 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 332 optimal weight: 0.9990 chunk 269 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 chunk 198 optimal weight: 7.9990 chunk 349 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS F 641 GLN ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 32516 Z= 0.221 Angle : 0.760 10.076 43942 Z= 0.378 Chirality : 0.049 0.241 4978 Planarity : 0.006 0.103 5767 Dihedral : 8.183 178.497 4446 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 29.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.13), residues: 4015 helix: -1.35 (0.12), residues: 1642 sheet: -1.50 (0.23), residues: 482 loop : -1.40 (0.15), residues: 1891 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 688 time to evaluate : 3.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 690 average time/residue: 0.5132 time to fit residues: 551.1766 Evaluate side-chains 515 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 4.109 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 131 optimal weight: 8.9990 chunk 350 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 228 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 389 optimal weight: 7.9990 chunk 323 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 128 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 GLN D 660 ASN E 103 GLN ** E 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS F 533 ASN ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 32516 Z= 0.280 Angle : 0.781 9.942 43942 Z= 0.396 Chirality : 0.049 0.250 4978 Planarity : 0.006 0.086 5767 Dihedral : 8.002 165.383 4446 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 33.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.13), residues: 4015 helix: -1.37 (0.12), residues: 1640 sheet: -1.59 (0.23), residues: 487 loop : -1.40 (0.14), residues: 1888 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 666 time to evaluate : 4.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.5055 time to fit residues: 521.6950 Evaluate side-chains 486 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 4.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 375 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 chunk 328 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 388 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 HIS ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS F 533 ASN ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 32516 Z= 0.245 Angle : 0.774 10.350 43942 Z= 0.387 Chirality : 0.050 0.266 4978 Planarity : 0.006 0.103 5767 Dihedral : 7.761 144.566 4446 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 32.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.17 (0.13), residues: 4015 helix: -1.34 (0.12), residues: 1647 sheet: -1.47 (0.23), residues: 479 loop : -1.39 (0.14), residues: 1889 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 675 time to evaluate : 3.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 675 average time/residue: 0.5038 time to fit residues: 526.9993 Evaluate side-chains 504 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 3.914 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 240 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 0.0670 chunk 246 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 192 optimal weight: 0.0470 chunk 36 optimal weight: 6.9990 chunk 305 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 32516 Z= 0.198 Angle : 0.768 11.268 43942 Z= 0.376 Chirality : 0.050 0.279 4978 Planarity : 0.005 0.093 5767 Dihedral : 7.278 121.943 4446 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.82 % Favored : 92.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.13), residues: 4015 helix: -1.21 (0.12), residues: 1676 sheet: -1.21 (0.24), residues: 447 loop : -1.37 (0.14), residues: 1892 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 718 time to evaluate : 3.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 718 average time/residue: 0.5223 time to fit residues: 582.4444 Evaluate side-chains 518 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 3.743 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 353 optimal weight: 0.0670 chunk 372 optimal weight: 6.9990 chunk 339 optimal weight: 7.9990 chunk 361 optimal weight: 0.0870 chunk 217 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 284 optimal weight: 5.9990 chunk 111 optimal weight: 0.0770 chunk 327 optimal weight: 0.4980 chunk 342 optimal weight: 1.9990 chunk 360 optimal weight: 8.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 32516 Z= 0.190 Angle : 0.775 11.596 43942 Z= 0.381 Chirality : 0.050 0.280 4978 Planarity : 0.005 0.071 5767 Dihedral : 6.990 121.274 4446 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.13), residues: 4015 helix: -1.15 (0.12), residues: 1671 sheet: -1.08 (0.24), residues: 453 loop : -1.33 (0.15), residues: 1891 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 0.5144 time to fit residues: 562.0622 Evaluate side-chains 516 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 3.798 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 237 optimal weight: 0.9980 chunk 382 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 266 optimal weight: 10.0000 chunk 401 optimal weight: 0.7980 chunk 369 optimal weight: 0.2980 chunk 319 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 246 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS E 460 ASN ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 32516 Z= 0.194 Angle : 0.786 12.541 43942 Z= 0.385 Chirality : 0.050 0.301 4978 Planarity : 0.005 0.081 5767 Dihedral : 6.853 121.798 4446 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.13), residues: 4015 helix: -1.13 (0.12), residues: 1680 sheet: -1.16 (0.23), residues: 476 loop : -1.32 (0.15), residues: 1859 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8030 Ramachandran restraints generated. 4015 Oldfield, 0 Emsley, 4015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 674 time to evaluate : 4.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 674 average time/residue: 0.4951 time to fit residues: 523.2723 Evaluate side-chains 505 residues out of total 3470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 4.225 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 253 optimal weight: 4.9990 chunk 340 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 320 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 328 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS F 533 ASN ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.091191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067901 restraints weight = 138325.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.070296 restraints weight = 95618.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.072194 restraints weight = 72796.520| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 32516 Z= 0.274 Angle : 0.811 11.226 43942 Z= 0.409 Chirality : 0.050 0.296 4978 Planarity : 0.006 0.092 5767 Dihedral : 7.044 121.913 4446 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 32.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 4015 helix: -1.19 (0.12), residues: 1659 sheet: -1.40 (0.22), residues: 499 loop : -1.37 (0.15), residues: 1857 =============================================================================== Job complete usr+sys time: 8768.77 seconds wall clock time: 160 minutes 21.86 seconds (9621.86 seconds total)