Starting phenix.real_space_refine on Sat Jan 20 06:18:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpe_23479/01_2024/7lpe_23479_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpe_23479/01_2024/7lpe_23479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpe_23479/01_2024/7lpe_23479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpe_23479/01_2024/7lpe_23479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpe_23479/01_2024/7lpe_23479_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpe_23479/01_2024/7lpe_23479_updated.pdb" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 76 5.16 5 C 9072 2.51 5 N 2216 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 474": "NH1" <-> "NH2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "C ARG 579": "NH1" <-> "NH2" Residue "C PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B ARG 575": "NH1" <-> "NH2" Residue "B ARG 579": "NH1" <-> "NH2" Residue "B PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 474": "NH1" <-> "NH2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "D ARG 575": "NH1" <-> "NH2" Residue "D ARG 579": "NH1" <-> "NH2" Residue "D PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13844 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3376 Classifications: {'peptide': 486} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 162} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 473} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 616 Unresolved non-hydrogen angles: 780 Unresolved non-hydrogen dihedrals: 502 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 20, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 334 Chain: "B" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3376 Classifications: {'peptide': 486} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 162} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 473} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 616 Unresolved non-hydrogen angles: 780 Unresolved non-hydrogen dihedrals: 502 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 20, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 334 Chain: "A" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3376 Classifications: {'peptide': 486} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 162} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 473} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 616 Unresolved non-hydrogen angles: 780 Unresolved non-hydrogen dihedrals: 502 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 20, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 334 Chain: "D" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3376 Classifications: {'peptide': 486} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 162} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 473} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 616 Unresolved non-hydrogen angles: 780 Unresolved non-hydrogen dihedrals: 502 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 20, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 334 Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'4DY': 1, '6OU': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'4DY': 1, '6OU': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'4DY': 1, '6OU': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'4DY': 1, '6OU': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 8.78, per 1000 atoms: 0.63 Number of scatterers: 13844 At special positions: 0 Unit cell: (117.549, 118.608, 104.841, 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 76 16.00 P 8 15.00 O 2472 8.00 N 2216 7.00 C 9072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.03 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: 6.07 Conformation dependent library (CDL) restraints added in 2.9 seconds 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 4 sheets defined 64.6% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'C' and resid 207 through 210 No H-bonds generated for 'chain 'C' and resid 207 through 210' Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 361 through 364 removed outlier: 3.972A pdb=" N HIS C 364 " --> pdb=" O GLU C 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 361 through 364' Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.308A pdb=" N THR C 389 " --> pdb=" O SER C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 389' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 416 through 428 Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 removed outlier: 3.783A pdb=" N GLY C 492 " --> pdb=" O PHE C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 509 removed outlier: 4.498A pdb=" N PHE C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 531 removed outlier: 4.074A pdb=" N SER C 520 " --> pdb=" O PHE C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 557 removed outlier: 4.102A pdb=" N VAL C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 553 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 554 " --> pdb=" O ASN C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 574 removed outlier: 4.283A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 598 removed outlier: 3.962A pdb=" N MET C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 4.041A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 removed outlier: 3.702A pdb=" N LEU C 662 " --> pdb=" O VAL C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 711 removed outlier: 3.618A pdb=" N LYS C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU C 699 " --> pdb=" O ASN C 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 709 " --> pdb=" O ILE C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 717 Processing helix chain 'B' and resid 207 through 210 No H-bonds generated for 'chain 'B' and resid 207 through 210' Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 268 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 361 through 364 removed outlier: 3.972A pdb=" N HIS B 364 " --> pdb=" O GLU B 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 361 through 364' Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.307A pdb=" N THR B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 389' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 removed outlier: 3.783A pdb=" N GLY B 492 " --> pdb=" O PHE B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 509 removed outlier: 4.499A pdb=" N PHE B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 531 removed outlier: 4.074A pdb=" N SER B 520 " --> pdb=" O PHE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 557 removed outlier: 4.102A pdb=" N VAL B 538 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 553 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B 554 " --> pdb=" O ASN B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 574 removed outlier: 4.283A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 598 removed outlier: 3.962A pdb=" N MET B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 4.042A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 removed outlier: 3.702A pdb=" N LEU B 662 " --> pdb=" O VAL B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 711 removed outlier: 3.617A pdb=" N LYS B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 699 " --> pdb=" O ASN B 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'A' and resid 207 through 210 No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.972A pdb=" N HIS A 364 " --> pdb=" O GLU A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.308A pdb=" N THR A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 416 through 428 Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 removed outlier: 3.783A pdb=" N GLY A 492 " --> pdb=" O PHE A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 509 removed outlier: 4.498A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 531 removed outlier: 4.074A pdb=" N SER A 520 " --> pdb=" O PHE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 557 removed outlier: 4.101A pdb=" N VAL A 538 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 553 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 554 " --> pdb=" O ASN A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 574 removed outlier: 4.284A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 598 removed outlier: 3.963A pdb=" N MET A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 4.042A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 removed outlier: 3.701A pdb=" N LEU A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 711 removed outlier: 3.617A pdb=" N LYS A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 709 " --> pdb=" O ILE A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'D' and resid 207 through 210 No H-bonds generated for 'chain 'D' and resid 207 through 210' Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 354 Processing helix chain 'D' and resid 361 through 364 removed outlier: 3.973A pdb=" N HIS D 364 " --> pdb=" O GLU D 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 361 through 364' Processing helix chain 'D' and resid 385 through 389 removed outlier: 4.308A pdb=" N THR D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 385 through 389' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 416 through 428 Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 removed outlier: 3.782A pdb=" N GLY D 492 " --> pdb=" O PHE D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 509 removed outlier: 4.498A pdb=" N PHE D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 508 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 531 removed outlier: 4.074A pdb=" N SER D 520 " --> pdb=" O PHE D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 557 removed outlier: 4.102A pdb=" N VAL D 538 " --> pdb=" O LYS D 535 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 553 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR D 554 " --> pdb=" O ASN D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 574 removed outlier: 4.284A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 598 removed outlier: 3.962A pdb=" N MET D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 4.040A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 removed outlier: 3.702A pdb=" N LEU D 662 " --> pdb=" O VAL D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 711 removed outlier: 3.619A pdb=" N LYS D 688 " --> pdb=" O GLU D 684 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU D 699 " --> pdb=" O ASN D 695 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 709 " --> pdb=" O ILE D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 717 Processing sheet with id= A, first strand: chain 'C' and resid 742 through 747 removed outlier: 6.124A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 742 through 747 removed outlier: 6.124A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 742 through 747 removed outlier: 6.125A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 742 through 747 removed outlier: 6.124A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2304 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: 4.15 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2160 1.30 - 1.43: 3899 1.43 - 1.55: 7867 1.55 - 1.68: 62 1.68 - 1.81: 136 Bond restraints: 14124 Sorted by residual: bond pdb=" C25 LBN C1001 " pdb=" O5 LBN C1001 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C25 LBN B1001 " pdb=" O5 LBN B1001 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C25 LBN D1001 " pdb=" O5 LBN D1001 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C25 LBN A1001 " pdb=" O5 LBN A1001 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C34 LBN C1001 " pdb=" O7 LBN C1001 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.80e+01 ... (remaining 14119 not shown) Histogram of bond angle deviations from ideal: 94.49 - 102.42: 68 102.42 - 110.35: 3339 110.35 - 118.28: 7315 118.28 - 126.21: 8418 126.21 - 134.14: 140 Bond angle restraints: 19280 Sorted by residual: angle pdb=" CB MET D 547 " pdb=" CG MET D 547 " pdb=" SD MET D 547 " ideal model delta sigma weight residual 112.70 100.97 11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CB MET B 547 " pdb=" CG MET B 547 " pdb=" SD MET B 547 " ideal model delta sigma weight residual 112.70 100.99 11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CB MET C 547 " pdb=" CG MET C 547 " pdb=" SD MET C 547 " ideal model delta sigma weight residual 112.70 101.01 11.69 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CB MET A 547 " pdb=" CG MET A 547 " pdb=" SD MET A 547 " ideal model delta sigma weight residual 112.70 101.04 11.66 3.00e+00 1.11e-01 1.51e+01 angle pdb=" N TYR A 653 " pdb=" CA TYR A 653 " pdb=" C TYR A 653 " ideal model delta sigma weight residual 110.28 115.98 -5.70 1.48e+00 4.57e-01 1.48e+01 ... (remaining 19275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.90: 7942 33.90 - 67.80: 202 67.80 - 101.70: 4 101.70 - 135.61: 4 135.61 - 169.51: 16 Dihedral angle restraints: 8168 sinusoidal: 2468 harmonic: 5700 Sorted by residual: dihedral pdb=" CB CYS A 386 " pdb=" SG CYS A 386 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual -86.00 -145.10 59.10 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CB CYS D 386 " pdb=" SG CYS D 386 " pdb=" SG CYS D 390 " pdb=" CB CYS D 390 " ideal model delta sinusoidal sigma weight residual -86.00 -145.10 59.10 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CB CYS C 386 " pdb=" SG CYS C 386 " pdb=" SG CYS C 390 " pdb=" CB CYS C 390 " ideal model delta sinusoidal sigma weight residual -86.00 -145.10 59.10 1 1.00e+01 1.00e-02 4.67e+01 ... (remaining 8165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1780 0.068 - 0.136: 407 0.136 - 0.205: 77 0.205 - 0.273: 8 0.273 - 0.341: 4 Chirality restraints: 2276 Sorted by residual: chirality pdb=" C20 6OU D1002 " pdb=" C19 6OU D1002 " pdb=" C21 6OU D1002 " pdb=" O30 6OU D1002 " both_signs ideal model delta sigma weight residual False 2.35 2.69 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" C20 6OU B1002 " pdb=" C19 6OU B1002 " pdb=" C21 6OU B1002 " pdb=" O30 6OU B1002 " both_signs ideal model delta sigma weight residual False 2.35 2.68 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C20 6OU C1002 " pdb=" C19 6OU C1002 " pdb=" C21 6OU C1002 " pdb=" O30 6OU C1002 " both_signs ideal model delta sigma weight residual False 2.35 2.68 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 2273 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET D 547 " 0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C MET D 547 " -0.078 2.00e-02 2.50e+03 pdb=" O MET D 547 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY D 548 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 547 " 0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C MET A 547 " -0.077 2.00e-02 2.50e+03 pdb=" O MET A 547 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY A 548 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 547 " -0.022 2.00e-02 2.50e+03 4.47e-02 1.99e+01 pdb=" C MET B 547 " 0.077 2.00e-02 2.50e+03 pdb=" O MET B 547 " -0.029 2.00e-02 2.50e+03 pdb=" N GLY B 548 " -0.026 2.00e-02 2.50e+03 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2223 2.75 - 3.29: 14987 3.29 - 3.83: 23388 3.83 - 4.36: 25550 4.36 - 4.90: 42911 Nonbonded interactions: 109059 Sorted by model distance: nonbonded pdb=" O THR A 670 " pdb=" CD2 LEU A 675 " model vdw 2.219 3.460 nonbonded pdb=" O THR C 670 " pdb=" CD2 LEU C 675 " model vdw 2.219 3.460 nonbonded pdb=" O THR D 670 " pdb=" CD2 LEU D 675 " model vdw 2.220 3.460 nonbonded pdb=" O THR B 670 " pdb=" CD2 LEU B 675 " model vdw 2.220 3.460 nonbonded pdb=" O GLY A 485 " pdb=" OG SER A 520 " model vdw 2.275 2.440 ... (remaining 109054 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' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.360 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 43.150 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 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 : 0.011 0.128 14124 Z= 0.719 Angle : 1.290 12.050 19280 Z= 0.688 Chirality : 0.062 0.341 2276 Planarity : 0.007 0.045 2420 Dihedral : 17.198 169.506 4484 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.19), residues: 1912 helix: -0.23 (0.13), residues: 1240 sheet: -2.84 (0.55), residues: 76 loop : -0.63 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP B 697 HIS 0.000 0.000 HIS A 410 PHE 0.047 0.004 PHE D 649 TYR 0.039 0.005 TYR B 511 ARG 0.011 0.003 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 309 TYR cc_start: 0.8233 (t80) cc_final: 0.7948 (t80) REVERT: C 399 ILE cc_start: 0.9433 (mm) cc_final: 0.9201 (tt) REVERT: C 440 VAL cc_start: 0.9198 (t) cc_final: 0.8933 (p) REVERT: C 568 MET cc_start: 0.7922 (mtt) cc_final: 0.7539 (mtp) REVERT: C 571 LYS cc_start: 0.8790 (tppt) cc_final: 0.8296 (mptt) REVERT: C 581 MET cc_start: 0.6998 (tpt) cc_final: 0.6488 (tpt) REVERT: C 678 LEU cc_start: 0.7826 (tm) cc_final: 0.7530 (tm) REVERT: B 399 ILE cc_start: 0.9359 (mm) cc_final: 0.9051 (tt) REVERT: B 541 MET cc_start: 0.8748 (tmm) cc_final: 0.8509 (tmm) REVERT: B 551 ASN cc_start: 0.7472 (t0) cc_final: 0.7226 (t0) REVERT: B 559 PHE cc_start: 0.5946 (m-80) cc_final: 0.5683 (t80) REVERT: B 568 MET cc_start: 0.8018 (mtt) cc_final: 0.7752 (mtm) REVERT: B 703 ILE cc_start: 0.9734 (mm) cc_final: 0.9529 (mm) REVERT: A 309 TYR cc_start: 0.7963 (t80) cc_final: 0.7761 (t80) REVERT: A 399 ILE cc_start: 0.9387 (mm) cc_final: 0.9050 (tt) REVERT: A 440 VAL cc_start: 0.9161 (t) cc_final: 0.8958 (p) REVERT: A 523 MET cc_start: 0.9004 (tpt) cc_final: 0.8718 (tpt) REVERT: A 559 PHE cc_start: 0.5978 (m-80) cc_final: 0.5677 (t80) REVERT: A 568 MET cc_start: 0.8044 (mtt) cc_final: 0.7612 (mtm) REVERT: A 703 ILE cc_start: 0.9683 (mm) cc_final: 0.9482 (mm) REVERT: D 399 ILE cc_start: 0.9367 (mm) cc_final: 0.9122 (tt) REVERT: D 440 VAL cc_start: 0.9210 (t) cc_final: 0.8947 (p) REVERT: D 551 ASN cc_start: 0.7542 (t0) cc_final: 0.7334 (t0) REVERT: D 568 MET cc_start: 0.7946 (mtt) cc_final: 0.7609 (mtp) REVERT: D 581 MET cc_start: 0.6689 (tpt) cc_final: 0.6133 (tpt) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.2213 time to fit residues: 119.7087 Evaluate side-chains 236 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 393 ASN ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14124 Z= 0.216 Angle : 0.651 10.090 19280 Z= 0.334 Chirality : 0.038 0.150 2276 Planarity : 0.005 0.035 2420 Dihedral : 16.861 162.756 2316 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.49 % Allowed : 10.98 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1912 helix: 0.59 (0.14), residues: 1244 sheet: -2.82 (0.52), residues: 76 loop : -0.22 (0.30), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 697 HIS 0.013 0.008 HIS A 410 PHE 0.030 0.002 PHE B 496 TYR 0.016 0.002 TYR C 554 ARG 0.004 0.001 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 274 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9410 (mm) cc_final: 0.9173 (tt) REVERT: C 439 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7199 (t80) REVERT: C 541 MET cc_start: 0.8584 (tmm) cc_final: 0.8352 (tmm) REVERT: C 551 ASN cc_start: 0.7240 (t0) cc_final: 0.6719 (t0) REVERT: C 568 MET cc_start: 0.7702 (mtt) cc_final: 0.7415 (mtm) REVERT: C 581 MET cc_start: 0.6664 (tpt) cc_final: 0.6187 (tpt) REVERT: C 646 ASP cc_start: 0.7790 (t0) cc_final: 0.7562 (t0) REVERT: C 682 MET cc_start: 0.6339 (mtp) cc_final: 0.6054 (mtp) REVERT: B 382 TYR cc_start: 0.8174 (m-80) cc_final: 0.7896 (m-80) REVERT: B 399 ILE cc_start: 0.9342 (mm) cc_final: 0.9043 (tt) REVERT: B 439 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6995 (t80) REVERT: B 541 MET cc_start: 0.8729 (tmm) cc_final: 0.8512 (tmm) REVERT: B 551 ASN cc_start: 0.7195 (t0) cc_final: 0.6968 (t0) REVERT: B 552 MET cc_start: 0.8546 (ttm) cc_final: 0.7888 (ttm) REVERT: B 568 MET cc_start: 0.7902 (mtt) cc_final: 0.7624 (mtm) REVERT: B 646 ASP cc_start: 0.7679 (t0) cc_final: 0.7459 (t0) REVERT: B 682 MET cc_start: 0.6402 (mtp) cc_final: 0.5999 (mtp) REVERT: A 399 ILE cc_start: 0.9426 (mm) cc_final: 0.9085 (tt) REVERT: A 541 MET cc_start: 0.8824 (tmm) cc_final: 0.8535 (tmm) REVERT: A 646 ASP cc_start: 0.7819 (t0) cc_final: 0.7587 (t0) REVERT: A 671 TYR cc_start: 0.7310 (t80) cc_final: 0.7104 (t80) REVERT: A 682 MET cc_start: 0.6259 (mtp) cc_final: 0.5863 (mtp) REVERT: A 700 GLN cc_start: 0.9271 (mp10) cc_final: 0.9030 (mp10) REVERT: A 703 ILE cc_start: 0.9669 (mm) cc_final: 0.9468 (mm) REVERT: D 399 ILE cc_start: 0.9390 (mm) cc_final: 0.9131 (tt) REVERT: D 541 MET cc_start: 0.8871 (tmm) cc_final: 0.8555 (tmm) REVERT: D 581 MET cc_start: 0.6677 (tpt) cc_final: 0.6145 (tpt) REVERT: D 646 ASP cc_start: 0.7815 (t0) cc_final: 0.7608 (t0) outliers start: 27 outliers final: 16 residues processed: 289 average time/residue: 0.2261 time to fit residues: 99.2698 Evaluate side-chains 254 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 236 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 439 PHE Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 110.0000 chunk 54 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 48 optimal weight: 120.0000 chunk 174 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 155 optimal weight: 30.0000 chunk 173 optimal weight: 2.9990 chunk 59 optimal weight: 0.0670 chunk 140 optimal weight: 9.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 ASN ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN A 393 ASN ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14124 Z= 0.393 Angle : 0.704 7.348 19280 Z= 0.363 Chirality : 0.041 0.222 2276 Planarity : 0.004 0.034 2420 Dihedral : 16.664 162.058 2316 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.69 % Allowed : 14.30 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1912 helix: 0.60 (0.14), residues: 1264 sheet: -4.34 (0.55), residues: 40 loop : -0.35 (0.29), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 697 HIS 0.010 0.004 HIS C 410 PHE 0.026 0.002 PHE A 496 TYR 0.037 0.002 TYR B 653 ARG 0.004 0.001 ARG D 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 229 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9411 (mm) cc_final: 0.9143 (tt) REVERT: C 439 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7289 (t80) REVERT: C 460 LEU cc_start: 0.9322 (tp) cc_final: 0.8924 (tt) REVERT: C 515 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6612 (mm) REVERT: C 552 MET cc_start: 0.8883 (tpp) cc_final: 0.8213 (tpp) REVERT: C 568 MET cc_start: 0.7852 (mtt) cc_final: 0.7629 (mtm) REVERT: C 581 MET cc_start: 0.7330 (tpt) cc_final: 0.6682 (tpt) REVERT: C 646 ASP cc_start: 0.7928 (t0) cc_final: 0.7602 (t0) REVERT: B 399 ILE cc_start: 0.9401 (mm) cc_final: 0.9130 (tt) REVERT: B 439 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.7153 (t80) REVERT: B 523 MET cc_start: 0.8834 (tpt) cc_final: 0.8614 (tpt) REVERT: B 552 MET cc_start: 0.8582 (ttm) cc_final: 0.7987 (ttm) REVERT: B 562 MET cc_start: 0.6989 (mmm) cc_final: 0.6666 (mmt) REVERT: B 568 MET cc_start: 0.7888 (mtt) cc_final: 0.7638 (mtm) REVERT: B 646 ASP cc_start: 0.7892 (t0) cc_final: 0.7612 (t0) REVERT: A 399 ILE cc_start: 0.9449 (mm) cc_final: 0.9091 (tt) REVERT: A 552 MET cc_start: 0.8664 (ttm) cc_final: 0.8110 (ttm) REVERT: A 562 MET cc_start: 0.7113 (mmm) cc_final: 0.6703 (mmt) REVERT: A 646 ASP cc_start: 0.7930 (t0) cc_final: 0.7623 (t0) REVERT: D 399 ILE cc_start: 0.9386 (mm) cc_final: 0.9110 (tt) REVERT: D 515 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6588 (mm) REVERT: D 523 MET cc_start: 0.8907 (tpt) cc_final: 0.8480 (tpt) REVERT: D 552 MET cc_start: 0.8692 (ttm) cc_final: 0.8033 (ttm) REVERT: D 646 ASP cc_start: 0.7923 (t0) cc_final: 0.7623 (t0) REVERT: D 682 MET cc_start: 0.6606 (mtp) cc_final: 0.6182 (mtp) outliers start: 40 outliers final: 29 residues processed: 256 average time/residue: 0.2241 time to fit residues: 86.9524 Evaluate side-chains 249 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 439 PHE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.7980 chunk 131 optimal weight: 0.2980 chunk 90 optimal weight: 0.0870 chunk 19 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14124 Z= 0.160 Angle : 0.554 12.655 19280 Z= 0.285 Chirality : 0.037 0.165 2276 Planarity : 0.003 0.022 2420 Dihedral : 16.117 162.699 2316 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.78 % Allowed : 14.85 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1912 helix: 1.17 (0.15), residues: 1240 sheet: -2.62 (0.48), residues: 84 loop : -0.35 (0.29), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 697 HIS 0.014 0.005 HIS B 410 PHE 0.012 0.001 PHE C 439 TYR 0.012 0.001 TYR C 487 ARG 0.001 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 264 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9392 (mm) cc_final: 0.9123 (tt) REVERT: C 439 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.7169 (t80) REVERT: C 460 LEU cc_start: 0.9307 (tp) cc_final: 0.8777 (tt) REVERT: C 551 ASN cc_start: 0.7095 (t0) cc_final: 0.6261 (t0) REVERT: C 552 MET cc_start: 0.8784 (tpp) cc_final: 0.8228 (tpp) REVERT: C 562 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6397 (mmm) REVERT: C 568 MET cc_start: 0.7723 (mtt) cc_final: 0.7498 (mtm) REVERT: C 646 ASP cc_start: 0.7749 (t0) cc_final: 0.7452 (t0) REVERT: B 382 TYR cc_start: 0.8019 (m-80) cc_final: 0.7728 (m-80) REVERT: B 399 ILE cc_start: 0.9395 (mm) cc_final: 0.9117 (tt) REVERT: B 439 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6876 (t80) REVERT: B 552 MET cc_start: 0.8387 (ttm) cc_final: 0.7828 (ttm) REVERT: B 553 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7681 (tt) REVERT: B 646 ASP cc_start: 0.7760 (t0) cc_final: 0.7538 (t0) REVERT: A 399 ILE cc_start: 0.9422 (mm) cc_final: 0.9121 (tt) REVERT: A 523 MET cc_start: 0.8835 (tpt) cc_final: 0.8549 (tpt) REVERT: A 552 MET cc_start: 0.8322 (ttm) cc_final: 0.7903 (ttm) REVERT: A 562 MET cc_start: 0.7047 (mmm) cc_final: 0.6684 (mmt) REVERT: A 646 ASP cc_start: 0.7728 (t0) cc_final: 0.7450 (t0) REVERT: A 648 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7108 (mm-30) REVERT: D 399 ILE cc_start: 0.9393 (mm) cc_final: 0.9099 (tt) REVERT: D 552 MET cc_start: 0.8435 (ttm) cc_final: 0.7941 (ttm) REVERT: D 646 ASP cc_start: 0.7734 (t0) cc_final: 0.7464 (t0) REVERT: D 682 MET cc_start: 0.6614 (mtp) cc_final: 0.6177 (mtp) outliers start: 41 outliers final: 26 residues processed: 284 average time/residue: 0.2233 time to fit residues: 95.7014 Evaluate side-chains 269 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 439 PHE Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 663 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 9.9990 chunk 105 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 158 optimal weight: 30.0000 chunk 128 optimal weight: 0.9980 chunk 0 optimal weight: 70.0000 chunk 94 optimal weight: 20.0000 chunk 166 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN B 676 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 14124 Z= 0.521 Angle : 0.789 10.774 19280 Z= 0.398 Chirality : 0.043 0.166 2276 Planarity : 0.004 0.037 2420 Dihedral : 16.164 165.828 2316 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.35 % Allowed : 17.99 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1912 helix: 0.58 (0.15), residues: 1284 sheet: -2.88 (0.52), residues: 76 loop : -0.33 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 697 HIS 0.007 0.003 HIS A 410 PHE 0.024 0.002 PHE C 439 TYR 0.030 0.003 TYR B 554 ARG 0.003 0.001 ARG B 474 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 222 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: C 382 TYR cc_start: 0.8095 (m-80) cc_final: 0.7842 (m-80) REVERT: C 399 ILE cc_start: 0.9422 (mm) cc_final: 0.9131 (tt) REVERT: C 439 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7377 (t80) REVERT: C 460 LEU cc_start: 0.9356 (tp) cc_final: 0.8969 (tt) REVERT: C 523 MET cc_start: 0.8931 (tpt) cc_final: 0.8555 (tpt) REVERT: C 552 MET cc_start: 0.8969 (tpp) cc_final: 0.8170 (tpp) REVERT: C 562 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6602 (mmt) REVERT: C 568 MET cc_start: 0.7807 (mtt) cc_final: 0.7569 (mtm) REVERT: C 646 ASP cc_start: 0.8036 (t0) cc_final: 0.7758 (t0) REVERT: B 399 ILE cc_start: 0.9402 (mm) cc_final: 0.9105 (tt) REVERT: B 439 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7239 (t80) REVERT: B 552 MET cc_start: 0.8570 (ttm) cc_final: 0.8028 (ttm) REVERT: B 562 MET cc_start: 0.7057 (mmm) cc_final: 0.6530 (mmt) REVERT: B 581 MET cc_start: 0.7273 (tpt) cc_final: 0.6671 (tpt) REVERT: B 599 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8391 (tt) REVERT: B 646 ASP cc_start: 0.8048 (t0) cc_final: 0.7772 (t0) REVERT: A 399 ILE cc_start: 0.9452 (mm) cc_final: 0.9172 (tt) REVERT: A 515 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6771 (mm) REVERT: A 552 MET cc_start: 0.8639 (ttm) cc_final: 0.8117 (ttm) REVERT: A 562 MET cc_start: 0.7211 (mmm) cc_final: 0.6824 (mmt) REVERT: A 581 MET cc_start: 0.7269 (tpt) cc_final: 0.6642 (tpt) REVERT: A 646 ASP cc_start: 0.8119 (t0) cc_final: 0.7852 (t0) REVERT: D 399 ILE cc_start: 0.9411 (mm) cc_final: 0.9101 (tt) REVERT: D 412 MET cc_start: 0.7598 (mmt) cc_final: 0.7263 (mmt) REVERT: D 515 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6940 (mm) REVERT: D 547 MET cc_start: 0.8077 (ttm) cc_final: 0.7872 (ttm) REVERT: D 552 MET cc_start: 0.8616 (ttm) cc_final: 0.8041 (ttm) REVERT: D 562 MET cc_start: 0.7322 (mmt) cc_final: 0.6952 (mmt) REVERT: D 646 ASP cc_start: 0.7994 (t0) cc_final: 0.7717 (t0) REVERT: D 682 MET cc_start: 0.6225 (mtp) cc_final: 0.5841 (mtp) REVERT: D 695 ASN cc_start: 0.9137 (t0) cc_final: 0.8893 (t0) outliers start: 58 outliers final: 35 residues processed: 262 average time/residue: 0.2197 time to fit residues: 88.0889 Evaluate side-chains 249 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 208 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 439 PHE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 30.0000 chunk 167 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 40.0000 chunk 45 optimal weight: 50.0000 chunk 185 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 50.0000 chunk 97 optimal weight: 40.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 14124 Z= 0.515 Angle : 0.762 9.590 19280 Z= 0.390 Chirality : 0.042 0.168 2276 Planarity : 0.004 0.035 2420 Dihedral : 16.213 172.018 2316 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.81 % Allowed : 20.57 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.19), residues: 1912 helix: 0.48 (0.14), residues: 1260 sheet: -2.90 (0.52), residues: 76 loop : -0.45 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 697 HIS 0.017 0.005 HIS A 410 PHE 0.025 0.002 PHE A 496 TYR 0.023 0.003 TYR A 511 ARG 0.002 0.000 ARG B 474 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 210 time to evaluate : 1.592 Fit side-chains REVERT: C 382 TYR cc_start: 0.8023 (m-80) cc_final: 0.7781 (m-80) REVERT: C 399 ILE cc_start: 0.9417 (mm) cc_final: 0.9101 (tt) REVERT: C 439 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7354 (t80) REVERT: C 460 LEU cc_start: 0.9367 (tp) cc_final: 0.9099 (tt) REVERT: C 515 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6715 (mm) REVERT: C 552 MET cc_start: 0.8918 (tpp) cc_final: 0.8254 (tpp) REVERT: C 562 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6779 (mmt) REVERT: C 568 MET cc_start: 0.7783 (mtt) cc_final: 0.7470 (mtm) REVERT: C 581 MET cc_start: 0.7207 (tpt) cc_final: 0.6586 (tpt) REVERT: C 646 ASP cc_start: 0.8160 (t0) cc_final: 0.7861 (t0) REVERT: B 399 ILE cc_start: 0.9392 (mm) cc_final: 0.9080 (tt) REVERT: B 439 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7223 (t80) REVERT: B 552 MET cc_start: 0.8590 (ttm) cc_final: 0.8136 (ttm) REVERT: B 562 MET cc_start: 0.7026 (mmm) cc_final: 0.6608 (mmt) REVERT: B 599 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8301 (tt) REVERT: B 646 ASP cc_start: 0.8247 (t0) cc_final: 0.7951 (t0) REVERT: A 382 TYR cc_start: 0.7928 (m-80) cc_final: 0.7684 (m-80) REVERT: A 399 ILE cc_start: 0.9473 (mm) cc_final: 0.9158 (tt) REVERT: A 515 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6903 (mm) REVERT: A 523 MET cc_start: 0.8932 (tpt) cc_final: 0.8500 (tpt) REVERT: A 552 MET cc_start: 0.8614 (ttm) cc_final: 0.8140 (ttm) REVERT: A 562 MET cc_start: 0.7308 (mmm) cc_final: 0.6788 (mmt) REVERT: A 599 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8633 (tt) REVERT: A 646 ASP cc_start: 0.8188 (t0) cc_final: 0.7895 (t0) REVERT: D 399 ILE cc_start: 0.9434 (mm) cc_final: 0.9113 (tt) REVERT: D 412 MET cc_start: 0.7791 (mmt) cc_final: 0.7400 (mmt) REVERT: D 552 MET cc_start: 0.8632 (ttm) cc_final: 0.8122 (ttm) REVERT: D 562 MET cc_start: 0.7244 (mmt) cc_final: 0.7005 (mmt) REVERT: D 646 ASP cc_start: 0.8151 (t0) cc_final: 0.7864 (t0) REVERT: D 682 MET cc_start: 0.6057 (mtp) cc_final: 0.5600 (mtp) REVERT: D 695 ASN cc_start: 0.9124 (t0) cc_final: 0.8809 (t0) outliers start: 63 outliers final: 42 residues processed: 257 average time/residue: 0.2213 time to fit residues: 87.2119 Evaluate side-chains 252 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 203 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 439 PHE Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 687 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 156 optimal weight: 40.0000 chunk 103 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.3541 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: