Starting phenix.real_space_refine on Fri Dec 15 06:32:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkr_21707/12_2023/6wkr_21707_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkr_21707/12_2023/6wkr_21707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkr_21707/12_2023/6wkr_21707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkr_21707/12_2023/6wkr_21707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkr_21707/12_2023/6wkr_21707_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkr_21707/12_2023/6wkr_21707_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1328 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 314 5.49 5 Mg 1 5.21 5 S 116 5.16 5 C 17488 2.51 5 N 5363 2.21 5 O 6013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "T GLU 34": "OE1" <-> "OE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "L GLU 131": "OE1" <-> "OE2" Residue "L ARG 414": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 456": "NH1" <-> "NH2" Residue "C ARG 497": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C ARG 685": "NH1" <-> "NH2" Residue "C PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 727": "NH1" <-> "NH2" Residue "C GLU 742": "OE1" <-> "OE2" Residue "P ARG 181": "NH1" <-> "NH2" Residue "P ARG 230": "NH1" <-> "NH2" Residue "P ARG 259": "NH1" <-> "NH2" Residue "P ARG 295": "NH1" <-> "NH2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "K GLU 41": "OE1" <-> "OE2" Residue "O ARG 129": "NH1" <-> "NH2" Residue "S GLU 102": "OE1" <-> "OE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "E ARG 27": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 29296 Number of models: 1 Model: "" Number of chains: 21 Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 604 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3340 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 7 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 9, 'ASN:plan1': 9, 'HIS:plan': 1, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 184 Chain: "L" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2874 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 349} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "N" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3080 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4278 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 33, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 604 Unresolved non-hydrogen angles: 753 Unresolved non-hydrogen dihedrals: 486 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 15, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 372 Chain: "B" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 290 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'M3L:plan-1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "P" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1346 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 1 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 5, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 154 Chain: "H" Number of atoms: 6439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 6439 Classifications: {'DNA': 314} Link IDs: {'rna3p': 313} Chain breaks: 1 Chain: "I" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 935 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Q" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 667 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 203 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 34} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N LEU T 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU T 73 " occ=0.45 residue: pdb=" N ARG T 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG T 74 " occ=0.45 residue: pdb=" N GLY T 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY T 75 " occ=0.25 Time building chain proxies: 15.35, per 1000 atoms: 0.52 Number of scatterers: 29296 At special positions: 0 Unit cell: (167.783, 203.408, 171.231, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 116 16.00 P 314 15.00 Mg 1 11.99 O 6013 8.00 N 5363 7.00 C 17488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 429 " distance=2.04 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 294 " distance=2.02 Simple disulfide: pdb=" SG CYS C 523 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 549 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 549 " - pdb=" SG CYS C 553 " distance=2.87 Simple disulfide: pdb=" SG CYS C 560 " - pdb=" SG CYS C 573 " distance=2.01 Simple disulfide: pdb=" SG CYS C 560 " - pdb=" SG CYS C 580 " distance=2.03 Simple disulfide: pdb=" SG CYS C 562 " - pdb=" SG CYS C 571 " distance=2.02 Simple disulfide: pdb=" SG CYS C 566 " - pdb=" SG CYS C 585 " distance=3.00 Simple disulfide: pdb=" SG CYS C 566 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 573 " - pdb=" SG CYS C 580 " distance=2.84 Simple disulfide: pdb=" SG CYS C 585 " - pdb=" SG CYS C 588 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.40 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN P 301 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS P 110 " 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5726 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 27 sheets defined 32.7% alpha, 11.7% beta 147 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 14.07 Creating SS restraints... Processing helix chain 'T' and resid 23 through 34 Processing helix chain 'T' and resid 38 through 40 No H-bonds generated for 'chain 'T' and resid 38 through 40' Processing helix chain 'T' and resid 56 through 59 No H-bonds generated for 'chain 'T' and resid 56 through 59' Processing helix chain 'A' and resid 84 through 106 Proline residue: A 93 - end of helix removed outlier: 4.107A pdb=" N ILE A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.997A pdb=" N MET A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 460 through 469 Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'A' and resid 608 through 624 removed outlier: 4.891A pdb=" N VAL A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 650 removed outlier: 4.648A pdb=" N ASN A 633 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLY A 644 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLN A 645 " --> pdb=" O ASN A 642 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 646 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 648 " --> pdb=" O GLN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 671 through 681 removed outlier: 4.286A pdb=" N ASP A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS A 676 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 277 Processing helix chain 'N' and resid 6 through 30 Proline residue: N 29 - end of helix Processing helix chain 'N' and resid 154 through 156 No H-bonds generated for 'chain 'N' and resid 154 through 156' Processing helix chain 'N' and resid 207 through 209 No H-bonds generated for 'chain 'N' and resid 207 through 209' Processing helix chain 'N' and resid 356 through 361 Processing helix chain 'C' and resid 19 through 62 removed outlier: 4.266A pdb=" N LEU C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 152 Processing helix chain 'C' and resid 169 through 177 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 274 through 284 removed outlier: 4.757A pdb=" N SER C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N PHE C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 337 removed outlier: 4.541A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 445 removed outlier: 4.197A pdb=" N GLY C 445 " --> pdb=" O ARG C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 457 removed outlier: 3.581A pdb=" N ARG C 456 " --> pdb=" O CYS C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 474 through 476 No H-bonds generated for 'chain 'C' and resid 474 through 476' Processing helix chain 'C' and resid 492 through 513 removed outlier: 4.130A pdb=" N ARG C 497 " --> pdb=" O LYS C 493 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU C 498 " --> pdb=" O ARG C 494 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP C 499 " --> pdb=" O LYS C 495 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 510 " --> pdb=" O ILE C 506 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLY C 512 " --> pdb=" O LEU C 508 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N SER C 513 " --> pdb=" O LYS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 538 No H-bonds generated for 'chain 'C' and resid 535 through 538' Processing helix chain 'C' and resid 572 through 575 No H-bonds generated for 'chain 'C' and resid 572 through 575' Processing helix chain 'C' and resid 605 through 608 No H-bonds generated for 'chain 'C' and resid 605 through 608' Processing helix chain 'C' and resid 648 through 661 removed outlier: 3.507A pdb=" N ARG C 653 " --> pdb=" O ASP C 649 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 656 " --> pdb=" O ASP C 652 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 686 Processing helix chain 'C' and resid 730 through 736 Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 144 through 151 removed outlier: 4.428A pdb=" N LYS B 151 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 165 Processing helix chain 'P' and resid 67 through 77 Processing helix chain 'P' and resid 80 through 82 No H-bonds generated for 'chain 'P' and resid 80 through 82' Processing helix chain 'P' and resid 104 through 115 Processing helix chain 'P' and resid 192 through 209 removed outlier: 4.422A pdb=" N ALA P 197 " --> pdb=" O GLN P 193 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE P 198 " --> pdb=" O THR P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 256 through 258 No H-bonds generated for 'chain 'P' and resid 256 through 258' Processing helix chain 'P' and resid 269 through 271 No H-bonds generated for 'chain 'P' and resid 269 through 271' Processing helix chain 'P' and resid 275 through 280 removed outlier: 3.819A pdb=" N LEU P 278 " --> pdb=" O ASP P 275 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU P 279 " --> pdb=" O THR P 276 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 284 No H-bonds generated for 'chain 'P' and resid 282 through 284' Processing helix chain 'I' and resid 45 through 54 Processing helix chain 'I' and resid 64 through 78 removed outlier: 3.527A pdb=" N GLN I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE I 78 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 114 removed outlier: 3.662A pdb=" N MET I 90 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU I 100 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA I 114 " --> pdb=" O CYS I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 131 Processing helix chain 'J' and resid 25 through 28 Processing helix chain 'J' and resid 31 through 41 Processing helix chain 'J' and resid 50 through 75 removed outlier: 4.338A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS J 59 " --> pdb=" O ARG J 55 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL J 65 " --> pdb=" O PHE J 61 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 92 Processing helix chain 'K' and resid 17 through 21 Processing helix chain 'K' and resid 27 through 37 removed outlier: 3.604A pdb=" N ARG K 35 " --> pdb=" O HIS K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 73 removed outlier: 3.526A pdb=" N ASN K 73 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 89 removed outlier: 4.298A pdb=" N ASN K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 97 removed outlier: 3.880A pdb=" N LEU K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 44 Processing helix chain 'M' and resid 54 through 81 removed outlier: 3.951A pdb=" N MET M 59 " --> pdb=" O ALA M 55 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL M 63 " --> pdb=" O MET M 59 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU M 68 " --> pdb=" O ASN M 64 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 98 Processing helix chain 'M' and resid 101 through 120 removed outlier: 4.047A pdb=" N VAL M 108 " --> pdb=" O LYS M 105 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS M 117 " --> pdb=" O ALA M 114 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR M 119 " --> pdb=" O THR M 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 54 removed outlier: 3.547A pdb=" N ARG O 49 " --> pdb=" O THR O 45 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG O 52 " --> pdb=" O LEU O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 77 removed outlier: 3.672A pdb=" N GLN O 76 " --> pdb=" O ARG O 72 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 114 removed outlier: 3.591A pdb=" N ASP O 106 " --> pdb=" O GLY O 102 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA O 114 " --> pdb=" O CYS O 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 130 removed outlier: 3.638A pdb=" N ARG O 129 " --> pdb=" O GLN O 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 28 No H-bonds generated for 'chain 'Q' and resid 26 through 28' Processing helix chain 'Q' and resid 31 through 41 Processing helix chain 'Q' and resid 50 through 76 removed outlier: 4.248A pdb=" N ARG Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS Q 59 " --> pdb=" O ARG Q 55 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 92 Processing helix chain 'R' and resid 17 through 21 Processing helix chain 'R' and resid 27 through 37 Processing helix chain 'R' and resid 46 through 73 removed outlier: 3.972A pdb=" N ALA R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN R 73 " --> pdb=" O ALA R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 89 removed outlier: 3.869A pdb=" N ASN R 89 " --> pdb=" O LEU R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 96 Processing helix chain 'S' and resid 35 through 43 Processing helix chain 'S' and resid 53 through 81 removed outlier: 3.758A pdb=" N ASN S 81 " --> pdb=" O LEU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 97 Processing helix chain 'S' and resid 102 through 120 removed outlier: 3.577A pdb=" N TYR S 118 " --> pdb=" O ALA S 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 34 Processing helix chain 'E' and resid 25 through 35 Processing helix chain 'E' and resid 47 through 50 No H-bonds generated for 'chain 'E' and resid 47 through 50' Processing helix chain 'E' and resid 52 through 55 No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing sheet with id= A, first strand: chain 'T' and resid 12 through 16 removed outlier: 3.645A pdb=" N LEU T 15 " --> pdb=" O ILE T 3 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE T 3 " --> pdb=" O LEU T 15 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 157 through 161 removed outlier: 4.605A pdb=" N SER A 229 " --> pdb=" O PHE A 161 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 209 through 211 removed outlier: 4.353A pdb=" N GLY A 209 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 186 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS A 211 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 188 through 191 Processing sheet with id= E, first strand: chain 'A' and resid 315 through 318 Processing sheet with id= F, first strand: chain 'A' and resid 484 through 489 removed outlier: 6.095A pdb=" N ARG A 427 " --> pdb=" O ALA A 485 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ILE A 487 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 429 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL A 489 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN A 431 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE A 428 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 111 through 116 removed outlier: 4.509A pdb=" N LEU L 111 " --> pdb=" O CYS L 126 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU L 125 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU L 134 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS L 127 " --> pdb=" O ILE L 132 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE L 132 " --> pdb=" O HIS L 127 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 149 through 154 removed outlier: 3.522A pdb=" N THR L 149 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA L 166 " --> pdb=" O THR L 149 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU L 163 " --> pdb=" O ILE L 175 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN L 176 " --> pdb=" O CYS L 182 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N CYS L 182 " --> pdb=" O ASN L 176 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 193 through 198 removed outlier: 6.801A pdb=" N VAL L 209 " --> pdb=" O ASN L 194 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU L 196 " --> pdb=" O LEU L 207 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU L 207 " --> pdb=" O LEU L 196 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE L 198 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU L 205 " --> pdb=" O PHE L 198 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU L 217 " --> pdb=" O ALA L 227 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA L 227 " --> pdb=" O LEU L 217 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ASN L 219 " --> pdb=" O LEU L 225 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU L 225 " --> pdb=" O ASN L 219 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN L 292 " --> pdb=" O ILE L 228 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 299 through 301 removed outlier: 3.922A pdb=" N PHE L 299 " --> pdb=" O LEU L 262 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER L 259 " --> pdb=" O GLY L 255 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY L 255 " --> pdb=" O SER L 259 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 309 through 315 removed outlier: 3.713A pdb=" N ASP L 310 " --> pdb=" O LYS L 322 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS L 322 " --> pdb=" O ASP L 310 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL L 312 " --> pdb=" O LEU L 320 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU L 320 " --> pdb=" O VAL L 312 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TRP L 314 " --> pdb=" O LEU L 318 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU L 318 " --> pdb=" O TRP L 314 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER L 323 " --> pdb=" O ALA L 327 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ALA L 327 " --> pdb=" O SER L 323 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LYS L 332 " --> pdb=" O ILE L 352 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE L 352 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 368 through 370 Processing sheet with id= M, first strand: chain 'L' and resid 416 through 418 removed outlier: 3.990A pdb=" N ALA L 427 " --> pdb=" O TRP L 435 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN L 86 " --> pdb=" O ARG L 436 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP L 438 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N CYS L 84 " --> pdb=" O ASP L 438 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'N' and resid 64 through 68 removed outlier: 3.654A pdb=" N ASN N 77 " --> pdb=" O HIS N 123 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER N 83 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE N 117 " --> pdb=" O SER N 83 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'N' and resid 221 through 223 removed outlier: 3.976A pdb=" N ALA N 196 " --> pdb=" O GLY N 182 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'N' and resid 242 through 246 Processing sheet with id= Q, first strand: chain 'N' and resid 368 through 370 removed outlier: 3.659A pdb=" N LEU N 342 " --> pdb=" O HIS N 370 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN N 322 " --> pdb=" O SER N 336 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'N' and resid 32 through 39 removed outlier: 5.253A pdb=" N GLN N 403 " --> pdb=" O ASP N 33 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL N 35 " --> pdb=" O VAL N 401 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL N 401 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR N 37 " --> pdb=" O MET N 399 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET N 399 " --> pdb=" O THR N 37 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE N 398 " --> pdb=" O SER N 394 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP N 402 " --> pdb=" O ILE N 390 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE N 390 " --> pdb=" O TRP N 402 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'N' and resid 276 through 281 removed outlier: 6.544A pdb=" N GLY N 292 " --> pdb=" O ASN N 277 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU N 279 " --> pdb=" O ALA N 290 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA N 290 " --> pdb=" O LEU N 279 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 82 through 85 removed outlier: 3.567A pdb=" N VAL C 85 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN C 94 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 614 through 618 removed outlier: 3.760A pdb=" N ALA C 617 " --> pdb=" O GLY C 625 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 644 through 647 Processing sheet with id= W, first strand: chain 'C' and resid 695 through 702 removed outlier: 3.504A pdb=" N GLY C 709 " --> pdb=" O LYS C 698 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER C 639 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA C 712 " --> pdb=" O PHE C 637 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE C 637 " --> pdb=" O ALA C 712 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 219 through 223 Processing sheet with id= Y, first strand: chain 'P' and resid 224 through 226 Processing sheet with id= Z, first strand: chain 'F' and resid 12 through 16 removed outlier: 5.701A pdb=" N SER F 65 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS F 6 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU F 67 " --> pdb=" O LYS F 6 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 41 through 44 removed outlier: 3.880A pdb=" N HIS F 68 " --> pdb=" O ILE F 44 " (cutoff:3.500A) 754 hydrogen bonds defined for protein. 2103 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 12.88 Time building geometry restraints manager: 16.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7790 1.33 - 1.46: 8543 1.46 - 1.58: 13418 1.58 - 1.70: 625 1.70 - 1.83: 165 Bond restraints: 30541 Sorted by residual: bond pdb=" C GLN R 24 " pdb=" N PHE R 25 " ideal model delta sigma weight residual 1.333 1.232 0.101 1.59e-02 3.96e+03 4.03e+01 bond pdb=" CA ARG I 69 " pdb=" C ARG I 69 " ideal model delta sigma weight residual 1.522 1.461 0.061 1.36e-02 5.41e+03 2.03e+01 bond pdb=" CA ALA I 75 " pdb=" C ALA I 75 " ideal model delta sigma weight residual 1.522 1.446 0.076 1.72e-02 3.38e+03 1.96e+01 bond pdb=" C GLN K 24 " pdb=" N PHE K 25 " ideal model delta sigma weight residual 1.333 1.250 0.082 2.74e-02 1.33e+03 9.06e+00 bond pdb=" N VAL E 29 " pdb=" CA VAL E 29 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.52e+00 ... (remaining 30536 not shown) Histogram of bond angle deviations from ideal: 89.99 - 98.81: 27 98.81 - 107.62: 3631 107.62 - 116.44: 19213 116.44 - 125.25: 18526 125.25 - 134.07: 1373 Bond angle restraints: 42770 Sorted by residual: angle pdb=" N VAL L 85 " pdb=" CA VAL L 85 " pdb=" C VAL L 85 " ideal model delta sigma weight residual 112.90 108.04 4.86 9.60e-01 1.09e+00 2.56e+01 angle pdb=" N VAL O 117 " pdb=" CA VAL O 117 " pdb=" C VAL O 117 " ideal model delta sigma weight residual 113.71 109.30 4.41 9.50e-01 1.11e+00 2.16e+01 angle pdb=" N ILE L 265 " pdb=" CA ILE L 265 " pdb=" C ILE L 265 " ideal model delta sigma weight residual 113.71 109.33 4.38 9.50e-01 1.11e+00 2.13e+01 angle pdb=" CB GLU E 25 " pdb=" CG GLU E 25 " pdb=" CD GLU E 25 " ideal model delta sigma weight residual 112.60 119.84 -7.24 1.70e+00 3.46e-01 1.82e+01 angle pdb=" N GLN B 143 " pdb=" CA GLN B 143 " pdb=" C GLN B 143 " ideal model delta sigma weight residual 107.73 113.34 -5.61 1.34e+00 5.57e-01 1.75e+01 ... (remaining 42765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 15796 35.98 - 71.96: 1609 71.96 - 107.94: 62 107.94 - 143.92: 4 143.92 - 179.90: 28 Dihedral angle restraints: 17499 sinusoidal: 8700 harmonic: 8799 Sorted by residual: dihedral pdb=" CB CYS C 560 " pdb=" SG CYS C 560 " pdb=" SG CYS C 573 " pdb=" CB CYS C 573 " ideal model delta sinusoidal sigma weight residual 93.00 172.62 -79.62 1 1.00e+01 1.00e-02 7.87e+01 dihedral pdb=" CB CYS C 530 " pdb=" SG CYS C 530 " pdb=" SG CYS C 549 " pdb=" CB CYS C 549 " ideal model delta sinusoidal sigma weight residual -86.00 -164.28 78.28 1 1.00e+01 1.00e-02 7.65e+01 dihedral pdb=" CB CYS C 549 " pdb=" SG CYS C 549 " pdb=" SG CYS C 553 " pdb=" CB CYS C 553 " ideal model delta sinusoidal sigma weight residual 93.00 31.89 61.11 1 1.00e+01 1.00e-02 4.96e+01 ... (remaining 17496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3613 0.053 - 0.106: 1070 0.106 - 0.159: 154 0.159 - 0.212: 10 0.212 - 0.265: 3 Chirality restraints: 4850 Sorted by residual: chirality pdb=" CA GLU E 25 " pdb=" N GLU E 25 " pdb=" C GLU E 25 " pdb=" CB GLU E 25 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB VAL E 28 " pdb=" CA VAL E 28 " pdb=" CG1 VAL E 28 " pdb=" CG2 VAL E 28 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LYS B 151 " pdb=" N LYS B 151 " pdb=" C LYS B 151 " pdb=" CB LYS B 151 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 4847 not shown) Planarity restraints: 4397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG H 121 " 0.034 2.00e-02 2.50e+03 1.41e-02 5.96e+00 pdb=" N9 DG H 121 " -0.029 2.00e-02 2.50e+03 pdb=" C8 DG H 121 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DG H 121 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG H 121 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DG H 121 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG H 121 " 0.016 2.00e-02 2.50e+03 pdb=" N1 DG H 121 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG H 121 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG H 121 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG H 121 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG H 121 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA H 299 " 0.030 2.00e-02 2.50e+03 1.37e-02 5.17e+00 pdb=" N9 DA H 299 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA H 299 " -0.020 2.00e-02 2.50e+03 pdb=" N7 DA H 299 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DA H 299 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA H 299 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA H 299 " 0.017 2.00e-02 2.50e+03 pdb=" N1 DA H 299 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DA H 299 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA H 299 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA H 299 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC H 215 " 0.025 2.00e-02 2.50e+03 1.51e-02 5.11e+00 pdb=" N1 DC H 215 " -0.018 2.00e-02 2.50e+03 pdb=" C2 DC H 215 " -0.018 2.00e-02 2.50e+03 pdb=" O2 DC H 215 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DC H 215 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC H 215 " -0.012 2.00e-02 2.50e+03 pdb=" N4 DC H 215 " 0.023 2.00e-02 2.50e+03 pdb=" C5 DC H 215 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC H 215 " 0.002 2.00e-02 2.50e+03 ... (remaining 4394 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 413 2.52 - 3.11: 25009 3.11 - 3.71: 51659 3.71 - 4.30: 66937 4.30 - 4.90: 100570 Nonbonded interactions: 244588 Sorted by model distance: nonbonded pdb=" O2 DC H 103 " pdb=" N2 DG H 212 " model vdw 1.921 2.520 nonbonded pdb=" O2 DC H 110 " pdb=" N2 DG H 205 " model vdw 1.938 2.496 nonbonded pdb=" O2 DC H 154 " pdb=" N2 DG H 161 " model vdw 1.956 2.496 nonbonded pdb=" O2 DC H 53 " pdb=" N2 DG H 262 " model vdw 1.981 2.496 nonbonded pdb=" N2 DG H 137 " pdb=" O2 DC H 178 " model vdw 2.004 2.496 ... (remaining 244583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'F' selection = (chain 'T' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB or name SG )))) } ncs_group { reference = (chain 'J' and ((resid 20 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'Q' and resid 20 through 102) } ncs_group { reference = chain 'K' selection = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 119)) } ncs_group { reference = chain 'M' selection = (chain 'S' and resid 28 through 122) } 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=0.25 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 12.810 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 96.330 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 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 : 0.010 0.101 30541 Z= 0.619 Angle : 0.929 13.867 42770 Z= 0.539 Chirality : 0.048 0.265 4850 Planarity : 0.004 0.052 4397 Dihedral : 24.154 179.905 11734 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 28.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 0.31 % Allowed : 7.41 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.12), residues: 2956 helix: -3.23 (0.12), residues: 982 sheet: -2.47 (0.21), residues: 436 loop : -3.40 (0.13), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 364 HIS 0.008 0.002 HIS C 516 PHE 0.017 0.002 PHE A 237 TYR 0.021 0.002 TYR M 39 ARG 0.008 0.001 ARG C 685 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 174 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 180 average time/residue: 0.5124 time to fit residues: 137.9430 Evaluate side-chains 122 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 2.957 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2428 time to fit residues: 5.7338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 253 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 293 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 GLN T 68 HIS A 104 ASN A 126 ASN A 235 ASN A 241 ASN A 431 GLN A 440 GLN L 94 GLN L 204 ASN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 221 GLN L 382 GLN ** N 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS N 157 HIS N 188 ASN N 239 HIS N 329 ASN N 397 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 ASN ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 283 ASN I 68 GLN I 85 GLN ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 GLN O 39 HIS O 68 GLN ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN R 31 HIS S 46 HIS F 25 ASN F 40 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30541 Z= 0.204 Angle : 0.667 8.122 42770 Z= 0.369 Chirality : 0.042 0.175 4850 Planarity : 0.004 0.042 4397 Dihedral : 28.493 179.152 6650 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.84 % Allowed : 10.68 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.14), residues: 2956 helix: -0.78 (0.15), residues: 1019 sheet: -1.92 (0.22), residues: 437 loop : -2.67 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP P 106 HIS 0.011 0.001 HIS P 110 PHE 0.013 0.001 PHE A 86 TYR 0.016 0.001 TYR S 37 ARG 0.013 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 179 average time/residue: 0.4450 time to fit residues: 125.7817 Evaluate side-chains 137 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 3.226 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2950 time to fit residues: 7.2029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 293 optimal weight: 2.9990 chunk 317 optimal weight: 50.0000 chunk 261 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 GLN A 481 HIS A 504 GLN A 507 HIS L 176 ASN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 ASN ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30541 Z= 0.319 Angle : 0.667 8.516 42770 Z= 0.367 Chirality : 0.042 0.172 4850 Planarity : 0.004 0.041 4397 Dihedral : 28.224 178.549 6650 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.72 % Allowed : 13.72 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.14), residues: 2956 helix: -0.05 (0.16), residues: 1012 sheet: -1.64 (0.23), residues: 442 loop : -2.43 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 361 HIS 0.004 0.001 HIS Q 75 PHE 0.013 0.001 PHE A 86 TYR 0.019 0.001 TYR R 39 ARG 0.006 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 131 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 163 average time/residue: 0.4332 time to fit residues: 112.6605 Evaluate side-chains 141 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 3.109 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3200 time to fit residues: 14.8594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 152 optimal weight: 40.0000 chunk 32 optimal weight: 20.0000 chunk 140 optimal weight: 40.0000 chunk 197 optimal weight: 8.9990 chunk 294 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 154 optimal weight: 20.0000 chunk 279 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 GLN A 440 GLN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30541 Z= 0.248 Angle : 0.642 11.103 42770 Z= 0.350 Chirality : 0.041 0.172 4850 Planarity : 0.004 0.041 4397 Dihedral : 28.080 179.115 6650 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.24 % Allowed : 15.27 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.15), residues: 2956 helix: 0.50 (0.16), residues: 1011 sheet: -1.45 (0.23), residues: 451 loop : -2.22 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 106 HIS 0.004 0.001 HIS Q 75 PHE 0.012 0.001 PHE A 86 TYR 0.014 0.001 TYR K 39 ARG 0.006 0.000 ARG M 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 159 average time/residue: 0.4171 time to fit residues: 108.8014 Evaluate side-chains 142 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 3.045 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2613 time to fit residues: 12.6271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 4 optimal weight: 40.0000 chunk 232 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 266 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 0 optimal weight: 70.0000 chunk 159 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 GLN A 440 GLN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 210 HIS ** P 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 HIS ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 30541 Z= 0.403 Angle : 0.708 10.904 42770 Z= 0.383 Chirality : 0.042 0.173 4850 Planarity : 0.004 0.041 4397 Dihedral : 28.011 179.834 6650 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 1.46 % Allowed : 16.99 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.15), residues: 2956 helix: 0.31 (0.16), residues: 1008 sheet: -1.44 (0.23), residues: 463 loop : -2.20 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 361 HIS 0.006 0.001 HIS C 516 PHE 0.014 0.001 PHE A 86 TYR 0.019 0.002 TYR K 39 ARG 0.004 0.000 ARG R 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 146 average time/residue: 0.4499 time to fit residues: 104.4667 Evaluate side-chains 132 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 2.927 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2838 time to fit residues: 11.6728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 105 optimal weight: 30.0000 chunk 281 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 312 optimal weight: 0.9990 chunk 259 optimal weight: 4.9990 chunk 144 optimal weight: 50.0000 chunk 25 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 GLN A 440 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30541 Z= 0.251 Angle : 0.647 10.933 42770 Z= 0.350 Chirality : 0.041 0.173 4850 Planarity : 0.004 0.041 4397 Dihedral : 28.008 179.289 6650 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.02 % Allowed : 18.27 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 2956 helix: 0.68 (0.17), residues: 1010 sheet: -1.31 (0.23), residues: 457 loop : -2.07 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 205 HIS 0.006 0.001 HIS P 114 PHE 0.012 0.001 PHE A 86 TYR 0.018 0.001 TYR K 39 ARG 0.005 0.000 ARG I 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 143 average time/residue: 0.4253 time to fit residues: 99.3649 Evaluate side-chains 126 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 3.253 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2740 time to fit residues: 8.7287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 311 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 189 optimal weight: 50.0000 chunk 143 optimal weight: 30.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 GLN A 126 ASN A 440 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 360 GLN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 GLN ** P 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30541 Z= 0.176 Angle : 0.623 11.016 42770 Z= 0.336 Chirality : 0.040 0.174 4850 Planarity : 0.003 0.041 4397 Dihedral : 27.850 179.701 6650 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.62 % Allowed : 18.49 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 2956 helix: 1.08 (0.17), residues: 1002 sheet: -1.16 (0.23), residues: 465 loop : -1.93 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 361 HIS 0.006 0.001 HIS P 114 PHE 0.010 0.001 PHE A 86 TYR 0.015 0.001 TYR K 39 ARG 0.009 0.000 ARG I 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 145 average time/residue: 0.4295 time to fit residues: 101.4189 Evaluate side-chains 128 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 2.880 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2615 time to fit residues: 8.0459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 40.0000 chunk 124 optimal weight: 0.0980 chunk 185 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 GLN A 440 GLN A 562 ASN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30541 Z= 0.309 Angle : 0.667 10.734 42770 Z= 0.358 Chirality : 0.040 0.171 4850 Planarity : 0.004 0.041 4397 Dihedral : 27.771 179.853 6650 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.88 % Allowed : 19.59 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.15), residues: 2956 helix: 0.82 (0.17), residues: 1016 sheet: -1.12 (0.23), residues: 457 loop : -1.92 (0.15), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 361 HIS 0.005 0.001 HIS P 114 PHE 0.013 0.001 PHE Q 61 TYR 0.015 0.001 TYR C 574 ARG 0.008 0.000 ARG I 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 127 average time/residue: 0.4502 time to fit residues: 92.8579 Evaluate side-chains 124 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 2.800 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2746 time to fit residues: 9.7468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 0.7980 chunk 298 optimal weight: 0.7980 chunk 272 optimal weight: 0.9990 chunk 290 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 262 optimal weight: 1.9990 chunk 274 optimal weight: 0.2980 chunk 289 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 GLN A 440 GLN ** L 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 268 HIS ** M 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30541 Z= 0.170 Angle : 0.639 13.778 42770 Z= 0.337 Chirality : 0.040 0.173 4850 Planarity : 0.003 0.041 4397 Dihedral : 27.699 179.506 6650 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.53 % Allowed : 19.51 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 2956 helix: 1.13 (0.17), residues: 1000 sheet: -0.96 (0.23), residues: 468 loop : -1.78 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 361 HIS 0.007 0.001 HIS C 297 PHE 0.008 0.001 PHE A 86 TYR 0.014 0.001 TYR K 39 ARG 0.009 0.000 ARG I 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 142 average time/residue: 0.4180 time to fit residues: 97.0863 Evaluate side-chains 122 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 3.010 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2593 time to fit residues: 4.3081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 190 optimal weight: 40.0000 chunk 306 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 chunk 145 optimal weight: 0.0050 chunk 213 optimal weight: 5.9990 chunk 321 optimal weight: 30.0000 chunk 296 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 26 optimal weight: 30.0000 chunk 197 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 GLN A 440 GLN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 30541 Z= 0.290 Angle : 0.675 12.041 42770 Z= 0.357 Chirality : 0.040 0.172 4850 Planarity : 0.004 0.040 4397 Dihedral : 27.617 179.392 6650 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.31 % Allowed : 20.74 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 2956 helix: 0.99 (0.17), residues: 1008 sheet: -1.01 (0.23), residues: 474 loop : -1.78 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 361 HIS 0.006 0.001 HIS C 297 PHE 0.014 0.001 PHE C 120 TYR 0.015 0.001 TYR J 88 ARG 0.014 0.000 ARG P 230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 121 average time/residue: 0.4262 time to fit residues: 84.4897 Evaluate side-chains 117 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 2.966 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2772 time to fit residues: 6.3614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 203 optimal weight: 0.0870 chunk 272 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 256 optimal weight: 0.5980 chunk 107 optimal weight: 40.0000 chunk 263 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 overall best weight: 2.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 62 GLN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.051826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.030743 restraints weight = 224356.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.031279 restraints weight = 124434.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.031511 restraints weight = 91878.106| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30541 Z= 0.232 Angle : 0.664 12.304 42770 Z= 0.350 Chirality : 0.040 0.172 4850 Planarity : 0.003 0.040 4397 Dihedral : 27.617 179.967 6650 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.22 % Allowed : 20.61 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 2956 helix: 1.03 (0.17), residues: 996 sheet: -0.95 (0.23), residues: 472 loop : -1.70 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 361 HIS 0.006 0.001 HIS C 297 PHE 0.029 0.001 PHE A 99 TYR 0.014 0.001 TYR C 574 ARG 0.008 0.000 ARG P 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4720.11 seconds wall clock time: 92 minutes 3.75 seconds (5523.75 seconds total)