Starting phenix.real_space_refine on Sat Mar 16 06:04:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpe_23479/03_2024/7lpe_23479_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpe_23479/03_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_23479/03_2024/7lpe_23479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpe_23479/03_2024/7lpe_23479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpe_23479/03_2024/7lpe_23479_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpe_23479/03_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-dev-5265/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: 8.21, per 1000 atoms: 0.59 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: 6.11 Conformation dependent library (CDL) restraints added in 3.1 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: 3.06 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: 4.26 Time building geometry restraints manager: 6.59 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: 1.130 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: 4.340 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 41.530 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.500 ------------------------------------------------------------------------------- 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 : 1.642 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: 0.2158 time to fit residues: 116.8049 Evaluate side-chains 236 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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 : 1.583 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: 0.2200 time to fit residues: 96.2890 Evaluate side-chains 254 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 236 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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 : 1.753 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: 0.2255 time to fit residues: 87.7543 Evaluate side-chains 249 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 : 1.766 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: 95.6197 Evaluate side-chains 269 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 : 1.558 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: 0.2214 time to fit residues: 88.6791 Evaluate side-chains 249 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 208 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 : 1.557 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: 0.2161 time to fit residues: 85.0393 Evaluate side-chains 252 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 203 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14124 Z= 0.193 Angle : 0.572 11.295 19280 Z= 0.298 Chirality : 0.037 0.162 2276 Planarity : 0.003 0.029 2420 Dihedral : 15.902 170.885 2316 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.98 % Allowed : 21.13 % Favored : 73.89 % 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: 0.72 (0.20), residues: 1912 helix: 1.09 (0.15), residues: 1276 sheet: -1.97 (0.52), residues: 100 loop : -0.30 (0.30), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 697 HIS 0.010 0.004 HIS A 410 PHE 0.027 0.001 PHE C 496 TYR 0.019 0.001 TYR A 565 ARG 0.002 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 7 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 292 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 238 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 382 TYR cc_start: 0.8055 (m-80) cc_final: 0.7834 (m-80) REVERT: C 399 ILE cc_start: 0.9401 (mm) cc_final: 0.9106 (tt) REVERT: C 460 LEU cc_start: 0.9345 (tp) cc_final: 0.9062 (tt) REVERT: C 523 MET cc_start: 0.8860 (tpt) cc_final: 0.8431 (tpt) REVERT: C 562 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6667 (mmm) REVERT: C 568 MET cc_start: 0.7825 (mtt) cc_final: 0.7433 (mtm) REVERT: C 636 GLU cc_start: 0.8255 (tp30) cc_final: 0.7768 (tp30) REVERT: C 646 ASP cc_start: 0.8131 (t0) cc_final: 0.7666 (t0) REVERT: C 678 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7374 (tm) REVERT: B 399 ILE cc_start: 0.9375 (mm) cc_final: 0.9062 (tt) REVERT: B 439 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.7106 (t80) REVERT: B 552 MET cc_start: 0.8260 (ttm) cc_final: 0.7854 (ttm) REVERT: B 562 MET cc_start: 0.7210 (mmm) cc_final: 0.6869 (mmt) REVERT: B 599 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8210 (tt) REVERT: B 646 ASP cc_start: 0.8073 (t0) cc_final: 0.7779 (t0) REVERT: A 399 ILE cc_start: 0.9474 (mm) cc_final: 0.9120 (tt) REVERT: A 552 MET cc_start: 0.8226 (ttm) cc_final: 0.7760 (ttm) REVERT: A 562 MET cc_start: 0.7320 (mmm) cc_final: 0.6968 (mmt) REVERT: A 599 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8506 (tt) REVERT: A 646 ASP cc_start: 0.8176 (t0) cc_final: 0.7891 (t0) REVERT: D 399 ILE cc_start: 0.9417 (mm) cc_final: 0.9104 (tt) REVERT: D 523 MET cc_start: 0.8865 (tpt) cc_final: 0.8402 (tpt) REVERT: D 552 MET cc_start: 0.8316 (ttm) cc_final: 0.7845 (ttm) REVERT: D 636 GLU cc_start: 0.8278 (tp30) cc_final: 0.7783 (tp30) REVERT: D 646 ASP cc_start: 0.8118 (t0) cc_final: 0.7675 (t0) REVERT: D 682 MET cc_start: 0.6159 (mtp) cc_final: 0.5828 (mtp) REVERT: D 695 ASN cc_start: 0.9126 (t0) cc_final: 0.8680 (t0) REVERT: D 698 LYS cc_start: 0.9161 (pttt) cc_final: 0.8939 (pptt) outliers start: 54 outliers final: 35 residues processed: 280 average time/residue: 0.2160 time to fit residues: 92.7804 Evaluate side-chains 263 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 223 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 482 VAL 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 583 VAL Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 439 PHE Chi-restraints excluded: chain B residue 469 VAL 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 583 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 469 VAL 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 599 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain D residue 469 VAL 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 516 PHE Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 663 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 126 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 145 optimal weight: 0.2980 chunk 168 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** A 560 GLN ** 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 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14124 Z= 0.183 Angle : 0.592 11.107 19280 Z= 0.300 Chirality : 0.038 0.182 2276 Planarity : 0.003 0.021 2420 Dihedral : 15.479 166.514 2316 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.34 % Allowed : 21.86 % Favored : 73.80 % 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: 0.84 (0.20), residues: 1912 helix: 1.20 (0.15), residues: 1268 sheet: -2.88 (0.51), residues: 76 loop : -0.21 (0.29), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 697 HIS 0.008 0.003 HIS A 410 PHE 0.011 0.001 PHE A 559 TYR 0.017 0.001 TYR D 565 ARG 0.003 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 8 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 284 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 237 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 382 TYR cc_start: 0.8091 (m-80) cc_final: 0.7754 (m-80) REVERT: C 399 ILE cc_start: 0.9391 (mm) cc_final: 0.9102 (tt) REVERT: C 460 LEU cc_start: 0.9320 (tp) cc_final: 0.9033 (tt) REVERT: C 515 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6851 (mm) REVERT: C 562 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6754 (mmm) REVERT: C 568 MET cc_start: 0.7818 (mtt) cc_final: 0.7591 (mtm) REVERT: C 636 GLU cc_start: 0.8185 (tp30) cc_final: 0.7681 (tp30) REVERT: C 646 ASP cc_start: 0.7905 (t0) cc_final: 0.7486 (t0) REVERT: B 399 ILE cc_start: 0.9380 (mm) cc_final: 0.9065 (tt) REVERT: B 552 MET cc_start: 0.8202 (ttm) cc_final: 0.7729 (ttm) REVERT: B 599 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8205 (tt) REVERT: B 646 ASP cc_start: 0.7948 (t0) cc_final: 0.7722 (t0) REVERT: A 399 ILE cc_start: 0.9467 (mm) cc_final: 0.9086 (tt) REVERT: A 552 MET cc_start: 0.8195 (ttm) cc_final: 0.7679 (ttm) REVERT: A 562 MET cc_start: 0.7237 (mmm) cc_final: 0.6875 (mmt) REVERT: A 599 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8472 (tt) REVERT: A 646 ASP cc_start: 0.7997 (t0) cc_final: 0.7745 (t0) REVERT: D 399 ILE cc_start: 0.9413 (mm) cc_final: 0.9110 (tt) REVERT: D 412 MET cc_start: 0.7458 (mmt) cc_final: 0.7143 (mmt) REVERT: D 552 MET cc_start: 0.8313 (ttm) cc_final: 0.7766 (ttm) REVERT: D 568 MET cc_start: 0.7661 (mtm) cc_final: 0.7416 (mtm) REVERT: D 636 GLU cc_start: 0.8205 (tp30) cc_final: 0.7702 (tp30) REVERT: D 646 ASP cc_start: 0.7935 (t0) cc_final: 0.7519 (t0) REVERT: D 682 MET cc_start: 0.6364 (mtp) cc_final: 0.6061 (mtp) outliers start: 47 outliers final: 38 residues processed: 273 average time/residue: 0.2088 time to fit residues: 87.2515 Evaluate side-chains 269 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 227 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 482 VAL 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 562 MET Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 469 VAL 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 583 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 469 VAL 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 588 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain D residue 469 VAL 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 583 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 663 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.0370 chunk 161 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 chunk 52 optimal weight: 50.0000 chunk 155 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 519 GLN ** C 551 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 560 GLN ** 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 628 ASN ** 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: 0.6658 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14124 Z= 0.188 Angle : 0.616 14.062 19280 Z= 0.310 Chirality : 0.038 0.190 2276 Planarity : 0.003 0.021 2420 Dihedral : 15.189 164.059 2316 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.43 % Allowed : 21.96 % 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: 0.97 (0.20), residues: 1912 helix: 1.25 (0.15), residues: 1268 sheet: -2.91 (0.52), residues: 76 loop : -0.02 (0.30), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 697 HIS 0.006 0.002 HIS B 410 PHE 0.026 0.001 PHE B 496 TYR 0.015 0.001 TYR A 565 ARG 0.004 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 9 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 284 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 236 time to evaluate : 1.708 Fit side-chains revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9385 (mm) cc_final: 0.9098 (tt) REVERT: C 460 LEU cc_start: 0.9335 (tp) cc_final: 0.9023 (tt) REVERT: C 515 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6830 (mm) REVERT: C 562 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6776 (mmm) REVERT: C 568 MET cc_start: 0.7829 (mtt) cc_final: 0.7616 (mtm) REVERT: C 636 GLU cc_start: 0.8143 (tp30) cc_final: 0.7645 (tp30) REVERT: C 646 ASP cc_start: 0.7955 (t0) cc_final: 0.7526 (t0) REVERT: B 399 ILE cc_start: 0.9379 (mm) cc_final: 0.9048 (tt) REVERT: B 412 MET cc_start: 0.6931 (mmt) cc_final: 0.6698 (mmt) REVERT: B 496 PHE cc_start: 0.8287 (m-80) cc_final: 0.8037 (m-80) REVERT: B 515 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6980 (mm) REVERT: B 552 MET cc_start: 0.8216 (ttm) cc_final: 0.7734 (ttm) REVERT: B 562 MET cc_start: 0.7181 (mmm) cc_final: 0.6710 (mmt) REVERT: B 599 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8191 (tt) REVERT: A 399 ILE cc_start: 0.9454 (mm) cc_final: 0.9086 (tt) REVERT: A 523 MET cc_start: 0.8887 (tpt) cc_final: 0.8375 (tpt) REVERT: A 552 MET cc_start: 0.8158 (ttm) cc_final: 0.7635 (ttm) REVERT: A 599 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8378 (tt) REVERT: A 646 ASP cc_start: 0.8000 (t0) cc_final: 0.7758 (t0) REVERT: D 399 ILE cc_start: 0.9413 (mm) cc_final: 0.9109 (tt) REVERT: D 412 MET cc_start: 0.7569 (mmt) cc_final: 0.7269 (mmt) REVERT: D 552 MET cc_start: 0.8309 (ttm) cc_final: 0.7738 (ttm) REVERT: D 568 MET cc_start: 0.7520 (mtm) cc_final: 0.7310 (mtm) REVERT: D 636 GLU cc_start: 0.8167 (tp30) cc_final: 0.7563 (tp30) REVERT: D 646 ASP cc_start: 0.7922 (t0) cc_final: 0.7511 (t0) REVERT: D 682 MET cc_start: 0.6354 (mtp) cc_final: 0.6067 (mtp) REVERT: D 695 ASN cc_start: 0.9127 (t0) cc_final: 0.8853 (t0) outliers start: 48 outliers final: 37 residues processed: 272 average time/residue: 0.2247 time to fit residues: 94.5338 Evaluate side-chains 271 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 229 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 482 VAL 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 562 MET Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain B residue 469 VAL 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 551 ASN Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 647 LEU 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 469 VAL 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 588 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain D residue 469 VAL 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 583 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 663 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.0770 chunk 111 optimal weight: 0.0870 chunk 86 optimal weight: 0.2980 chunk 126 optimal weight: 1.9990 chunk 191 optimal weight: 20.0000 chunk 176 optimal weight: 1.9990 chunk 152 optimal weight: 50.0000 chunk 15 optimal weight: 9.9990 chunk 117 optimal weight: 0.4980 chunk 93 optimal weight: 50.0000 chunk 120 optimal weight: 0.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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** ** 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** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14124 Z= 0.173 Angle : 0.623 14.506 19280 Z= 0.311 Chirality : 0.038 0.200 2276 Planarity : 0.003 0.022 2420 Dihedral : 14.707 160.025 2316 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.61 % Allowed : 22.60 % Favored : 72.79 % 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: 1.03 (0.20), residues: 1912 helix: 1.31 (0.15), residues: 1268 sheet: -2.99 (0.52), residues: 76 loop : -0.04 (0.29), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 697 HIS 0.009 0.004 HIS A 410 PHE 0.025 0.001 PHE B 496 TYR 0.018 0.001 TYR D 565 ARG 0.004 0.000 ARG D 701 ********************** REFINEMENT MACRO_CYCLE 10 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 304 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 254 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9365 (mm) cc_final: 0.9108 (tt) REVERT: C 412 MET cc_start: 0.7210 (mmt) cc_final: 0.6909 (mmt) REVERT: C 460 LEU cc_start: 0.9312 (tp) cc_final: 0.8996 (tt) REVERT: C 515 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6632 (mm) REVERT: C 551 ASN cc_start: 0.7019 (t0) cc_final: 0.6297 (t0) REVERT: C 562 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6670 (mmm) REVERT: C 568 MET cc_start: 0.7885 (mtt) cc_final: 0.7653 (mtm) REVERT: C 636 GLU cc_start: 0.8044 (tp30) cc_final: 0.7552 (tp30) REVERT: C 646 ASP cc_start: 0.7818 (t0) cc_final: 0.7433 (t0) REVERT: B 399 ILE cc_start: 0.9390 (mm) cc_final: 0.9043 (tt) REVERT: B 412 MET cc_start: 0.7139 (mmt) cc_final: 0.6847 (mmt) REVERT: B 496 PHE cc_start: 0.8300 (m-80) cc_final: 0.8072 (m-80) REVERT: B 523 MET cc_start: 0.8902 (tpt) cc_final: 0.8439 (tpt) REVERT: B 552 MET cc_start: 0.8110 (ttm) cc_final: 0.7589 (ttm) REVERT: B 568 MET cc_start: 0.7516 (mtm) cc_final: 0.6862 (mtp) REVERT: B 599 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8184 (tt) REVERT: B 674 LEU cc_start: 0.7774 (tp) cc_final: 0.7515 (mt) REVERT: A 399 ILE cc_start: 0.9410 (mm) cc_final: 0.8999 (tt) REVERT: A 523 MET cc_start: 0.8897 (tpt) cc_final: 0.8401 (tpt) REVERT: A 552 MET cc_start: 0.7897 (ttm) cc_final: 0.7414 (ttm) REVERT: A 553 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7384 (mt) REVERT: A 599 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8424 (tt) REVERT: A 677 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6994 (ttp) REVERT: D 399 ILE cc_start: 0.9407 (mm) cc_final: 0.9095 (tt) REVERT: D 412 MET cc_start: 0.7576 (mmt) cc_final: 0.7144 (mmt) REVERT: D 552 MET cc_start: 0.8238 (ttm) cc_final: 0.7795 (ttm) REVERT: D 568 MET cc_start: 0.7522 (mtm) cc_final: 0.7258 (mtm) REVERT: D 599 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8329 (tt) REVERT: D 646 ASP cc_start: 0.7741 (t0) cc_final: 0.7534 (t0) REVERT: D 682 MET cc_start: 0.6227 (mtp) cc_final: 0.6013 (mtp) REVERT: D 695 ASN cc_start: 0.9075 (t0) cc_final: 0.8819 (t0) outliers start: 50 outliers final: 35 residues processed: 281 average time/residue: 0.2134 time to fit residues: 93.5674 Evaluate side-chains 276 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 482 VAL 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 562 MET Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 VAL 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 583 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 469 VAL 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 553 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain D residue 469 VAL 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 583 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 663 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 9.9990 chunk 46 optimal weight: 0.4980 chunk 140 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 156 optimal weight: 0.0270 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.8842 ------------------------------------------------------------------------------- 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 695 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.189586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.130532 restraints weight = 21955.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.136335 restraints weight = 10756.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.140061 restraints weight = 7039.136| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4089 r_free = 0.4089 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4088 r_free = 0.4088 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14124 Z= 0.202 Angle : 0.634 14.518 19280 Z= 0.321 Chirality : 0.038 0.207 2276 Planarity : 0.003 0.022 2420 Dihedral : 14.503 160.321 2316 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.97 % Allowed : 23.52 % Favored : 72.51 % 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: 1.04 (0.20), residues: 1912 helix: 1.35 (0.15), residues: 1264 sheet: -3.01 (0.53), residues: 76 loop : -0.11 (0.29), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 697 HIS 0.009 0.003 HIS A 410 PHE 0.031 0.001 PHE A 496 TYR 0.022 0.001 TYR A 627 ARG 0.002 0.000 ARG C 701 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2723.70 seconds wall clock time: 52 minutes 43.54 seconds (3163.54 seconds total)