Starting phenix.real_space_refine on Sat Feb 17 12:20:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpk_22414/02_2024/7jpk_22414_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpk_22414/02_2024/7jpk_22414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpk_22414/02_2024/7jpk_22414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpk_22414/02_2024/7jpk_22414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpk_22414/02_2024/7jpk_22414_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpk_22414/02_2024/7jpk_22414_neut_updated.pdb" } resolution = 3.0 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 10 5.49 5 S 109 5.16 5 C 12134 2.51 5 N 2985 2.21 5 O 3349 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 500": "OD1" <-> "OD2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 598": "OD1" <-> "OD2" Residue "A TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 662": "OD1" <-> "OD2" Residue "A PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A PHE 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1022": "NH1" <-> "NH2" Residue "A ASP 1030": "OD1" <-> "OD2" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1070": "OE1" <-> "OE2" Residue "A TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1099": "NH1" <-> "NH2" Residue "A TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1151": "OD1" <-> "OD2" Residue "A GLU 1164": "OE1" <-> "OE2" Residue "A PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1180": "OD1" <-> "OD2" Residue "A ASP 1203": "OD1" <-> "OD2" Residue "A PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1236": "NH1" <-> "NH2" Residue "A PHE 1238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1242": "NH1" <-> "NH2" Residue "A PHE 1260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1339": "OD1" <-> "OD2" Residue "A GLU 1349": "OE1" <-> "OE2" Residue "A TYR 1350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1382": "OD1" <-> "OD2" Residue "A ARG 1389": "NH1" <-> "NH2" Residue "A ASP 1390": "OD1" <-> "OD2" Residue "A GLU 1408": "OE1" <-> "OE2" Residue "A GLU 1412": "OE1" <-> "OE2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1428": "NH1" <-> "NH2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "E GLU 219": "OE1" <-> "OE2" Residue "F ASP 38": "OD1" <-> "OD2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ASP 116": "OD1" <-> "OD2" Residue "F ASP 132": "OD1" <-> "OD2" Residue "F ASP 139": "OD1" <-> "OD2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F ARG 230": "NH1" <-> "NH2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F ASP 302": "OD1" <-> "OD2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 373": "OE1" <-> "OE2" Residue "F GLU 457": "OE1" <-> "OE2" Residue "F GLU 497": "OE1" <-> "OE2" Residue "F ASP 498": "OD1" <-> "OD2" Residue "F ARG 544": "NH1" <-> "NH2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F GLU 567": "OE1" <-> "OE2" Residue "F ASP 571": "OD1" <-> "OD2" Residue "F ARG 591": "NH1" <-> "NH2" Residue "F ARG 607": "NH1" <-> "NH2" Residue "F GLU 658": "OE1" <-> "OE2" Residue "F PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 668": "OD1" <-> "OD2" Residue "F PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 692": "NH1" <-> "NH2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 745": "NH1" <-> "NH2" Residue "F TYR 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 826": "OE1" <-> "OE2" Residue "F ASP 843": "OD1" <-> "OD2" Residue "F ARG 846": "NH1" <-> "NH2" Residue "F ASP 868": "OD1" <-> "OD2" Residue "F GLU 880": "OE1" <-> "OE2" Residue "F ASP 882": "OD1" <-> "OD2" Residue "F PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 908": "OE1" <-> "OE2" Residue "F TYR 984": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1004": "NH1" <-> "NH2" Residue "F ASP 1030": "OD1" <-> "OD2" Residue "F GLU 1069": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18591 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 9009 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 1078} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "A" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 419 Unusual residues: {' CA': 1, '3PE': 8, 'C8U': 1, 'PC1': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Time building chain proxies: 13.16, per 1000 atoms: 0.71 Number of scatterers: 18591 At special positions: 0 Unit cell: (143.706, 138.136, 157.074, 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) Ca 1 19.99 S 109 16.00 P 10 15.00 F 3 9.00 O 3349 8.00 N 2985 7.00 C 12134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.03 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.03 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.03 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=2.03 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.98 Conformation dependent library (CDL) restraints added in 4.3 seconds 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 14 sheets defined 47.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'A' and resid 54 through 69 removed outlier: 4.959A pdb=" N LEU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 93 through 105 removed outlier: 3.846A pdb=" N PHE A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 140 removed outlier: 3.834A pdb=" N VAL A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.768A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 178 removed outlier: 3.508A pdb=" N LEU A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.592A pdb=" N SER A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 218 removed outlier: 3.613A pdb=" N LEU A 202 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 294 through 305 Processing helix chain 'A' and resid 310 through 321 removed outlier: 4.157A pdb=" N VAL A 315 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR A 316 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 318 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 319 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 320 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY A 321 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 345 removed outlier: 3.819A pdb=" N SER A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 451 removed outlier: 4.355A pdb=" N ILE A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 removed outlier: 3.583A pdb=" N ASP A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 479 removed outlier: 3.694A pdb=" N GLU A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 500 through 514 Processing helix chain 'A' and resid 521 through 528 removed outlier: 4.041A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 541 removed outlier: 3.852A pdb=" N ARG A 534 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A 536 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 538 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 539 " --> pdb=" O PHE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 549 through 580 removed outlier: 5.088A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 635 through 669 removed outlier: 3.558A pdb=" N TYR A 640 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE A 645 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL A 646 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N CYS A 647 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR A 650 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A 651 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 666 " --> pdb=" O ASN A 663 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER A 669 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 817 removed outlier: 3.661A pdb=" N LEU A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 841 removed outlier: 3.665A pdb=" N ILE A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 846 No H-bonds generated for 'chain 'A' and resid 843 through 846' Processing helix chain 'A' and resid 869 through 881 Processing helix chain 'A' and resid 893 through 898 removed outlier: 3.576A pdb=" N ARG A 897 " --> pdb=" O LYS A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.768A pdb=" N ILE A 908 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 910 " --> pdb=" O ALA A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 927 removed outlier: 3.510A pdb=" N HIS A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 950 removed outlier: 3.876A pdb=" N VAL A 934 " --> pdb=" O ASN A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 978 No H-bonds generated for 'chain 'A' and resid 976 through 978' Processing helix chain 'A' and resid 1000 through 1011 Processing helix chain 'A' and resid 1016 through 1023 removed outlier: 3.516A pdb=" N ARG A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1052 removed outlier: 3.578A pdb=" N ALA A1042 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A1047 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR A1048 " --> pdb=" O PHE A1045 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A1049 " --> pdb=" O ILE A1046 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE A1052 " --> pdb=" O ILE A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1071 removed outlier: 3.918A pdb=" N GLU A1070 " --> pdb=" O VAL A1066 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN A1071 " --> pdb=" O THR A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1094 removed outlier: 3.877A pdb=" N LEU A1093 " --> pdb=" O VAL A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 4.564A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1135 Processing helix chain 'A' and resid 1152 through 1172 Processing helix chain 'A' and resid 1177 through 1179 No H-bonds generated for 'chain 'A' and resid 1177 through 1179' Processing helix chain 'A' and resid 1181 through 1204 Processing helix chain 'A' and resid 1235 through 1237 No H-bonds generated for 'chain 'A' and resid 1235 through 1237' Processing helix chain 'A' and resid 1241 through 1248 removed outlier: 3.539A pdb=" N LEU A1246 " --> pdb=" O LEU A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1266 removed outlier: 3.652A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1288 Processing helix chain 'A' and resid 1309 through 1320 Processing helix chain 'A' and resid 1325 through 1331 removed outlier: 3.644A pdb=" N LEU A1330 " --> pdb=" O GLN A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1387 removed outlier: 3.598A pdb=" N TYR A1358 " --> pdb=" O ASN A1355 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE A1361 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE A1362 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A1363 " --> pdb=" O TYR A1360 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR A1365 " --> pdb=" O ILE A1362 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A1371 " --> pdb=" O CYS A1368 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A1372 " --> pdb=" O ALA A1369 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA A1378 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A1379 " --> pdb=" O PHE A1376 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP A1382 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP A1385 " --> pdb=" O ASP A1382 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A1387 " --> pdb=" O PHE A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1409 removed outlier: 3.715A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1428 Processing helix chain 'E' and resid 7 through 26 removed outlier: 4.167A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 18 " --> pdb=" O PHE E 14 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY E 19 " --> pdb=" O CYS E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 129 removed outlier: 3.526A pdb=" N ILE E 123 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 164 Proline residue: E 139 - end of helix Processing helix chain 'E' and resid 181 through 203 removed outlier: 3.884A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 52 Processing helix chain 'F' and resid 54 through 62 Processing helix chain 'F' and resid 77 through 95 Processing helix chain 'F' and resid 97 through 109 removed outlier: 3.625A pdb=" N LEU F 102 " --> pdb=" O VAL F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 182 No H-bonds generated for 'chain 'F' and resid 179 through 182' Processing helix chain 'F' and resid 184 through 190 removed outlier: 3.904A pdb=" N SER F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 201 Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 269 through 284 removed outlier: 3.876A pdb=" N THR F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.920A pdb=" N ASN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 347 removed outlier: 3.698A pdb=" N LEU F 347 " --> pdb=" O PHE F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 378 Processing helix chain 'F' and resid 399 through 407 Processing helix chain 'F' and resid 418 through 425 removed outlier: 4.609A pdb=" N ARG F 422 " --> pdb=" O GLY F 419 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE F 423 " --> pdb=" O ALA F 420 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR F 425 " --> pdb=" O ARG F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 431 No H-bonds generated for 'chain 'F' and resid 428 through 431' Processing helix chain 'F' and resid 434 through 443 removed outlier: 3.511A pdb=" N ALA F 439 " --> pdb=" O PRO F 435 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY F 440 " --> pdb=" O MET F 436 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP F 441 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LYS F 442 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 499 No H-bonds generated for 'chain 'F' and resid 496 through 499' Processing helix chain 'F' and resid 563 through 566 No H-bonds generated for 'chain 'F' and resid 563 through 566' Processing helix chain 'F' and resid 572 through 581 Processing helix chain 'F' and resid 641 through 650 Processing helix chain 'F' and resid 653 through 659 removed outlier: 4.294A pdb=" N GLU F 657 " --> pdb=" O ASP F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 692 Processing helix chain 'F' and resid 702 through 721 Processing helix chain 'F' and resid 749 through 754 removed outlier: 3.743A pdb=" N GLU F 753 " --> pdb=" O LYS F 749 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASN F 754 " --> pdb=" O GLU F 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 749 through 754' Processing helix chain 'F' and resid 765 through 772 removed outlier: 3.556A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) Processing helix chain 'F' and resid 821 through 829 Processing helix chain 'F' and resid 878 through 880 No H-bonds generated for 'chain 'F' and resid 878 through 880' Processing helix chain 'F' and resid 883 through 891 Processing helix chain 'F' and resid 1024 through 1026 No H-bonds generated for 'chain 'F' and resid 1024 through 1026' Processing helix chain 'F' and resid 1046 through 1049 No H-bonds generated for 'chain 'F' and resid 1046 through 1049' Processing sheet with id= A, first strand: chain 'A' and resid 225 through 228 Processing sheet with id= B, first strand: chain 'A' and resid 955 through 957 Processing sheet with id= C, first strand: chain 'A' and resid 971 through 975 Processing sheet with id= D, first strand: chain 'E' and resid 34 through 36 removed outlier: 3.559A pdb=" N TYR E 177 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 48 through 50 removed outlier: 4.034A pdb=" N ASN E 79 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 68 through 72 Processing sheet with id= G, first strand: chain 'F' and resid 124 through 126 Processing sheet with id= H, first strand: chain 'F' and resid 167 through 169 removed outlier: 6.884A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 411 through 415 removed outlier: 6.229A pdb=" N ASP F 255 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N MET F 361 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU F 257 " --> pdb=" O MET F 361 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE F 363 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU F 259 " --> pdb=" O PHE F 363 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE F 290 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE F 258 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN F 292 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL F 260 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA F 294 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 513 through 517 Processing sheet with id= K, first strand: chain 'F' and resid 661 through 664 removed outlier: 3.926A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE F 736 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 851 through 857 removed outlier: 4.413A pdb=" N LEU F1016 " --> pdb=" O LEU F1011 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 895 through 902 removed outlier: 4.463A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 905 through 907 759 hydrogen bonds defined for protein. 1910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 7.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2941 1.30 - 1.43: 5125 1.43 - 1.56: 10751 1.56 - 1.69: 20 1.69 - 1.82: 168 Bond restraints: 19005 Sorted by residual: bond pdb=" N09 C8U A1911 " pdb=" O10 C8U A1911 " ideal model delta sigma weight residual 1.220 1.400 -0.180 2.00e-02 2.50e+03 8.08e+01 bond pdb=" C05 C8U A1911 " pdb=" C06 C8U A1911 " ideal model delta sigma weight residual 1.364 1.530 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C02 C8U A1911 " pdb=" C03 C8U A1911 " ideal model delta sigma weight residual 1.351 1.514 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" C21 3PE A1905 " pdb=" O21 3PE A1905 " ideal model delta sigma weight residual 1.316 1.455 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C21 3PE A1906 " pdb=" O21 3PE A1906 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.78e+01 ... (remaining 19000 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.29: 444 106.29 - 113.23: 10315 113.23 - 120.17: 7200 120.17 - 127.10: 7550 127.10 - 134.04: 178 Bond angle restraints: 25687 Sorted by residual: angle pdb=" N ASN A 649 " pdb=" CA ASN A 649 " pdb=" C ASN A 649 " ideal model delta sigma weight residual 111.03 103.57 7.46 1.11e+00 8.12e-01 4.51e+01 angle pdb=" N ALA A 665 " pdb=" CA ALA A 665 " pdb=" C ALA A 665 " ideal model delta sigma weight residual 111.07 105.36 5.71 1.07e+00 8.73e-01 2.85e+01 angle pdb=" N ILE A 466 " pdb=" CA ILE A 466 " pdb=" C ILE A 466 " ideal model delta sigma weight residual 112.98 108.02 4.96 1.25e+00 6.40e-01 1.58e+01 angle pdb=" C PHE A 112 " pdb=" N HIS A 113 " pdb=" CA HIS A 113 " ideal model delta sigma weight residual 121.54 128.50 -6.96 1.91e+00 2.74e-01 1.33e+01 angle pdb=" O ASN A 649 " pdb=" C ASN A 649 " pdb=" N TYR A 650 " ideal model delta sigma weight residual 122.03 125.92 -3.89 1.08e+00 8.57e-01 1.29e+01 ... (remaining 25682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.51: 9980 22.51 - 45.01: 1114 45.01 - 67.52: 318 67.52 - 90.02: 40 90.02 - 112.53: 1 Dihedral angle restraints: 11453 sinusoidal: 4837 harmonic: 6616 Sorted by residual: dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual -86.00 -142.82 56.82 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" CA THR F 628 " pdb=" C THR F 628 " pdb=" N TYR F 629 " pdb=" CA TYR F 629 " ideal model delta harmonic sigma weight residual -180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CB CYS F 999 " pdb=" SG CYS F 999 " pdb=" SG CYS F1029 " pdb=" CB CYS F1029 " ideal model delta sinusoidal sigma weight residual 93.00 46.72 46.28 1 1.00e+01 1.00e-02 2.97e+01 ... (remaining 11450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2514 0.068 - 0.137: 317 0.137 - 0.205: 15 0.205 - 0.273: 1 0.273 - 0.342: 1 Chirality restraints: 2848 Sorted by residual: chirality pdb=" CA VAL A 661 " pdb=" N VAL A 661 " pdb=" C VAL A 661 " pdb=" CB VAL A 661 " both_signs ideal model delta sigma weight residual False 2.44 2.10 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA PHE A 656 " pdb=" N PHE A 656 " pdb=" C PHE A 656 " pdb=" CB PHE A 656 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CG LEU F 257 " pdb=" CB LEU F 257 " pdb=" CD1 LEU F 257 " pdb=" CD2 LEU F 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 2845 not shown) Planarity restraints: 3203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 648 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLY A 648 " -0.056 2.00e-02 2.50e+03 pdb=" O GLY A 648 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 649 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 656 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C PHE A 656 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE A 656 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 657 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 654 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C ASN A 654 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN A 654 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 655 " 0.016 2.00e-02 2.50e+03 ... (remaining 3200 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 211 2.62 - 3.19: 16192 3.19 - 3.76: 27482 3.76 - 4.33: 40975 4.33 - 4.90: 66325 Nonbonded interactions: 151185 Sorted by model distance: nonbonded pdb=" OD2 ASP F 711 " pdb=" OG1 THR F 739 " model vdw 2.047 2.440 nonbonded pdb=" O ILE A 931 " pdb=" CG2 THR A 935 " model vdw 2.113 3.460 nonbonded pdb=" OD2 ASP F 154 " pdb=" OH TYR F 163 " model vdw 2.125 2.440 nonbonded pdb=" O TYR F 647 " pdb=" OG1 THR F 650 " model vdw 2.142 2.440 nonbonded pdb=" O GLU F 184 " pdb=" OG1 THR F 188 " model vdw 2.150 2.440 ... (remaining 151180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.860 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 53.420 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.007 0.180 19005 Z= 0.465 Angle : 0.856 9.987 25687 Z= 0.446 Chirality : 0.046 0.342 2848 Planarity : 0.005 0.059 3203 Dihedral : 19.601 112.530 7142 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.84 % Favored : 93.02 % Rotamer: Outliers : 8.84 % Allowed : 24.15 % Favored : 67.02 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % 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: -3.85 (0.15), residues: 2222 helix: -2.22 (0.13), residues: 1076 sheet: -1.61 (0.30), residues: 244 loop : -3.14 (0.17), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1016 HIS 0.006 0.001 HIS A 113 PHE 0.022 0.002 PHE F 157 TYR 0.023 0.002 TYR F 629 ARG 0.004 0.000 ARG A 489 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 255 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6774 (pt0) REVERT: A 524 ILE cc_start: 0.8138 (mt) cc_final: 0.7923 (mp) REVERT: A 538 ILE cc_start: 0.6281 (OUTLIER) cc_final: 0.5762 (tt) REVERT: A 905 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6860 (mp) REVERT: A 926 ARG cc_start: 0.6467 (mtt90) cc_final: 0.5917 (mtp85) REVERT: A 967 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7914 (mt-10) REVERT: A 1004 MET cc_start: 0.8651 (mtm) cc_final: 0.8263 (mtp) REVERT: A 1091 TYR cc_start: 0.7744 (t80) cc_final: 0.7430 (t80) REVERT: A 1125 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.7072 (t80) REVERT: A 1129 MET cc_start: 0.8091 (mtp) cc_final: 0.7762 (mtt) REVERT: A 1199 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7364 (mt) REVERT: A 1234 PHE cc_start: 0.8714 (p90) cc_final: 0.8385 (p90) REVERT: A 1239 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8388 (ptt180) REVERT: A 1385 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7392 (p0) REVERT: F 404 MET cc_start: 0.9011 (mtt) cc_final: 0.8610 (mtt) REVERT: F 501 ARG cc_start: 0.7773 (mtm110) cc_final: 0.7570 (mtm110) REVERT: F 505 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7693 (ppt-90) REVERT: F 717 GLU cc_start: 0.7943 (tt0) cc_final: 0.7685 (tt0) REVERT: F 1020 MET cc_start: 0.8295 (ttp) cc_final: 0.8076 (ttm) outliers start: 176 outliers final: 100 residues processed: 402 average time/residue: 0.9318 time to fit residues: 435.9851 Evaluate side-chains 322 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 214 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1067 THR Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1125 PHE Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1263 SER Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 659 SER Chi-restraints excluded: chain F residue 707 ARG Chi-restraints excluded: chain F residue 711 ASP Chi-restraints excluded: chain F residue 715 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 753 GLU Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 907 CYS Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 183 GLN A 453 HIS A 464 GLN A 490 GLN A 554 ASN A 599 ASN A 829 ASN ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 ASN A1071 GLN A1087 GLN A1108 GLN A1138 GLN A1307 GLN E 31 HIS E 38 HIS E 209 GLN F 56 GLN F 145 GLN F 156 ASN F 165 HIS F 169 HIS F 186 ASN F 233 ASN F 308 HIS ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 ASN F 484 GLN F 511 ASN F 542 ASN F 644 GLN F 655 ASN F 679 ASN F 685 ASN F 696 ASN F 728 ASN F 806 GLN F 847 ASN F 872 ASN F 888 HIS F 891 ASN F1007 HIS F1065 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19005 Z= 0.206 Angle : 0.590 8.937 25687 Z= 0.301 Chirality : 0.043 0.254 2848 Planarity : 0.005 0.059 3203 Dihedral : 15.465 102.716 3058 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 6.93 % Allowed : 27.01 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.58 (0.16), residues: 2222 helix: -1.10 (0.15), residues: 1084 sheet: -1.16 (0.32), residues: 238 loop : -2.57 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1016 HIS 0.004 0.001 HIS E 31 PHE 0.014 0.001 PHE A 801 TYR 0.023 0.001 TYR F 629 ARG 0.004 0.000 ARG A1099 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 232 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.3069 (OUTLIER) cc_final: 0.2835 (m90) REVERT: A 187 ASN cc_start: 0.6712 (t0) cc_final: 0.6244 (p0) REVERT: A 190 PHE cc_start: 0.7588 (t80) cc_final: 0.6588 (m-80) REVERT: A 479 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.4795 (ppp) REVERT: A 491 TYR cc_start: 0.5505 (OUTLIER) cc_final: 0.5112 (t80) REVERT: A 524 ILE cc_start: 0.7990 (mt) cc_final: 0.7783 (mp) REVERT: A 538 ILE cc_start: 0.6222 (OUTLIER) cc_final: 0.5511 (tt) REVERT: A 926 ARG cc_start: 0.6443 (mtt90) cc_final: 0.5646 (mtp85) REVERT: A 1091 TYR cc_start: 0.7749 (t80) cc_final: 0.7488 (t80) REVERT: A 1125 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6939 (t80) REVERT: A 1165 MET cc_start: 0.7365 (tmm) cc_final: 0.6792 (tmm) REVERT: A 1199 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7602 (mt) REVERT: A 1384 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.6840 (t80) REVERT: F 205 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8457 (tt) REVERT: F 404 MET cc_start: 0.8935 (mtt) cc_final: 0.8461 (mtt) REVERT: F 717 GLU cc_start: 0.7873 (tt0) cc_final: 0.7639 (tt0) REVERT: F 851 MET cc_start: 0.7300 (ptp) cc_final: 0.7096 (ptp) REVERT: F 1051 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8355 (mttt) outliers start: 138 outliers final: 64 residues processed: 335 average time/residue: 1.0701 time to fit residues: 416.7887 Evaluate side-chains 286 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 213 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1125 PHE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 545 LYS Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 753 GLU Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1012 MET Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1048 ASP Chi-restraints excluded: chain F residue 1051 LYS Chi-restraints excluded: chain F residue 1061 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 169 optimal weight: 0.5980 chunk 138 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 599 ASN A 829 ASN ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 GLN E 209 GLN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN F 484 GLN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 806 GLN F1065 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 19005 Z= 0.423 Angle : 0.683 12.245 25687 Z= 0.347 Chirality : 0.047 0.292 2848 Planarity : 0.005 0.059 3203 Dihedral : 14.947 87.417 2949 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 8.08 % Allowed : 26.81 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.35 (0.17), residues: 2222 helix: -0.93 (0.15), residues: 1094 sheet: -0.95 (0.32), residues: 242 loop : -2.47 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1016 HIS 0.011 0.001 HIS A 113 PHE 0.019 0.002 PHE A 573 TYR 0.019 0.002 TYR F 629 ARG 0.009 0.001 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 218 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.2948 (OUTLIER) cc_final: 0.2655 (m90) REVERT: A 187 ASN cc_start: 0.6688 (t0) cc_final: 0.6201 (p0) REVERT: A 190 PHE cc_start: 0.7618 (t80) cc_final: 0.6551 (m-80) REVERT: A 479 MET cc_start: 0.5836 (OUTLIER) cc_final: 0.5140 (ppp) REVERT: A 491 TYR cc_start: 0.5401 (OUTLIER) cc_final: 0.5027 (t80) REVERT: A 495 ILE cc_start: 0.4881 (OUTLIER) cc_final: 0.4592 (pp) REVERT: A 538 ILE cc_start: 0.6117 (OUTLIER) cc_final: 0.5533 (tt) REVERT: A 894 LYS cc_start: 0.6895 (mmtm) cc_final: 0.6648 (mmtp) REVERT: A 926 ARG cc_start: 0.6453 (mtt90) cc_final: 0.5652 (mtp85) REVERT: A 1124 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.6588 (mpm) REVERT: A 1199 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7661 (mt) REVERT: A 1384 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6955 (t80) REVERT: A 1385 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7403 (p0) REVERT: A 1401 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6404 (mm-30) REVERT: F 404 MET cc_start: 0.8980 (mtt) cc_final: 0.8535 (mtt) REVERT: F 552 ASN cc_start: 0.2465 (OUTLIER) cc_final: 0.1948 (t0) REVERT: F 673 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8272 (pt) REVERT: F 717 GLU cc_start: 0.7958 (tt0) cc_final: 0.7735 (tt0) outliers start: 161 outliers final: 91 residues processed: 344 average time/residue: 0.9702 time to fit residues: 390.2072 Evaluate side-chains 315 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 212 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1124 MET Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1300 ILE Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1401 GLU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 673 LEU Chi-restraints excluded: chain F residue 728 ASN Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 753 GLU Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 823 SER Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1012 MET Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1048 ASP Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.3980 chunk 153 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 193 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 829 ASN ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 GLN E 209 GLN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 806 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19005 Z= 0.163 Angle : 0.570 11.264 25687 Z= 0.287 Chirality : 0.042 0.301 2848 Planarity : 0.005 0.058 3203 Dihedral : 13.904 85.962 2944 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.62 % Allowed : 29.27 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.82 (0.17), residues: 2222 helix: -0.48 (0.15), residues: 1086 sheet: -0.84 (0.32), residues: 242 loop : -2.18 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1112 HIS 0.021 0.001 HIS A 113 PHE 0.011 0.001 PHE A 801 TYR 0.023 0.001 TYR F 629 ARG 0.006 0.000 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 229 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.6547 (t0) cc_final: 0.6240 (p0) REVERT: A 190 PHE cc_start: 0.7555 (t80) cc_final: 0.6498 (m-80) REVERT: A 449 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8292 (tt) REVERT: A 479 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.4786 (ppp) REVERT: A 491 TYR cc_start: 0.5374 (OUTLIER) cc_final: 0.4921 (t80) REVERT: A 666 GLU cc_start: 0.7381 (mm-30) cc_final: 0.6854 (mp0) REVERT: A 897 ARG cc_start: 0.7139 (mpt-90) cc_final: 0.6781 (mpt-90) REVERT: A 926 ARG cc_start: 0.6429 (mtt90) cc_final: 0.5620 (mtp85) REVERT: A 984 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: A 1091 TYR cc_start: 0.7397 (t80) cc_final: 0.7190 (t80) REVERT: A 1199 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7654 (mt) REVERT: A 1384 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6843 (t80) REVERT: E 131 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.5689 (ttpt) REVERT: F 404 MET cc_start: 0.8908 (mtt) cc_final: 0.8402 (mtt) REVERT: F 717 GLU cc_start: 0.7865 (tt0) cc_final: 0.7665 (tt0) outliers start: 112 outliers final: 66 residues processed: 307 average time/residue: 1.0058 time to fit residues: 358.5670 Evaluate side-chains 288 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 215 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 390 SER Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 545 LYS Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 715 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 753 GLU Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 907 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1012 MET Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1048 ASP Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.4980 chunk 122 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 161 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 464 GLN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN F 325 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 806 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19005 Z= 0.226 Angle : 0.601 12.103 25687 Z= 0.299 Chirality : 0.043 0.265 2848 Planarity : 0.005 0.058 3203 Dihedral : 13.477 84.440 2935 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.97 % Allowed : 29.67 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.63 (0.17), residues: 2222 helix: -0.33 (0.15), residues: 1086 sheet: -0.72 (0.32), residues: 248 loop : -2.07 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1112 HIS 0.002 0.001 HIS A 113 PHE 0.019 0.001 PHE F 689 TYR 0.021 0.001 TYR F 629 ARG 0.007 0.000 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 223 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7277 (mp) REVERT: A 76 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: A 187 ASN cc_start: 0.6567 (t0) cc_final: 0.6234 (p0) REVERT: A 190 PHE cc_start: 0.7589 (t80) cc_final: 0.6498 (m-80) REVERT: A 449 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8298 (tt) REVERT: A 479 MET cc_start: 0.6151 (pp-130) cc_final: 0.5383 (ppp) REVERT: A 481 LEU cc_start: 0.4021 (OUTLIER) cc_final: 0.3718 (pp) REVERT: A 491 TYR cc_start: 0.5310 (OUTLIER) cc_final: 0.4846 (t80) REVERT: A 897 ARG cc_start: 0.7211 (mpt-90) cc_final: 0.6804 (mpt-90) REVERT: A 926 ARG cc_start: 0.6418 (mtt90) cc_final: 0.5600 (mtp85) REVERT: A 1199 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7646 (mt) REVERT: A 1384 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6756 (m-80) REVERT: E 118 LEU cc_start: 0.7464 (mm) cc_final: 0.7254 (mm) REVERT: E 131 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.5705 (ttpt) REVERT: E 216 MET cc_start: 0.7154 (ttp) cc_final: 0.6910 (ttp) REVERT: F 404 MET cc_start: 0.8960 (mtt) cc_final: 0.8472 (mtt) REVERT: F 552 ASN cc_start: 0.3154 (OUTLIER) cc_final: 0.2906 (t0) outliers start: 119 outliers final: 72 residues processed: 314 average time/residue: 0.9925 time to fit residues: 361.7643 Evaluate side-chains 303 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 222 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 545 LYS Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 715 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 753 GLU Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 823 SER Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 907 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1009 GLU Chi-restraints excluded: chain F residue 1012 MET Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1048 ASP Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 18 optimal weight: 0.0370 chunk 71 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 930 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN F 551 GLN F 806 GLN F 872 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19005 Z= 0.168 Angle : 0.568 12.941 25687 Z= 0.282 Chirality : 0.041 0.226 2848 Planarity : 0.004 0.057 3203 Dihedral : 12.675 82.813 2933 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.97 % Allowed : 29.42 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.31 (0.18), residues: 2222 helix: -0.09 (0.16), residues: 1082 sheet: -0.62 (0.33), residues: 243 loop : -1.86 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1112 HIS 0.002 0.001 HIS A 113 PHE 0.021 0.001 PHE F 689 TYR 0.021 0.001 TYR F 629 ARG 0.011 0.000 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 235 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7246 (mp) REVERT: A 120 SER cc_start: 0.7722 (OUTLIER) cc_final: 0.7106 (m) REVERT: A 187 ASN cc_start: 0.6506 (t0) cc_final: 0.6266 (p0) REVERT: A 190 PHE cc_start: 0.7479 (t80) cc_final: 0.6406 (m-80) REVERT: A 479 MET cc_start: 0.6368 (pp-130) cc_final: 0.5037 (ppp) REVERT: A 480 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.5041 (mp) REVERT: A 481 LEU cc_start: 0.3854 (OUTLIER) cc_final: 0.3525 (pp) REVERT: A 491 TYR cc_start: 0.5211 (OUTLIER) cc_final: 0.4857 (t80) REVERT: A 493 MET cc_start: 0.5483 (mpt) cc_final: 0.5181 (mpt) REVERT: A 926 ARG cc_start: 0.6467 (mtt90) cc_final: 0.5610 (mtp85) REVERT: A 1164 GLU cc_start: 0.7358 (tt0) cc_final: 0.7079 (tp30) REVERT: A 1199 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7637 (mt) REVERT: A 1295 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8391 (t) REVERT: A 1384 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.7047 (m-80) REVERT: E 59 LYS cc_start: 0.3812 (OUTLIER) cc_final: 0.2645 (ptmm) REVERT: E 131 LYS cc_start: 0.6295 (OUTLIER) cc_final: 0.5721 (ttpt) REVERT: E 213 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6738 (pt0) REVERT: E 216 MET cc_start: 0.6883 (ttp) cc_final: 0.6682 (ttp) REVERT: F 404 MET cc_start: 0.8901 (mtt) cc_final: 0.8406 (mtt) REVERT: F 681 GLU cc_start: 0.5010 (mp0) cc_final: 0.4485 (mp0) outliers start: 119 outliers final: 71 residues processed: 326 average time/residue: 0.9608 time to fit residues: 365.2838 Evaluate side-chains 308 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 227 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 390 SER Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 715 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 753 GLU Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 823 SER Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 907 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1048 ASP Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN F 186 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN F 678 ASN F 806 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19005 Z= 0.199 Angle : 0.583 14.913 25687 Z= 0.291 Chirality : 0.042 0.349 2848 Planarity : 0.005 0.057 3203 Dihedral : 12.425 80.910 2927 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.32 % Allowed : 30.72 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.20 (0.18), residues: 2222 helix: 0.02 (0.16), residues: 1076 sheet: -0.57 (0.33), residues: 243 loop : -1.82 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1112 HIS 0.002 0.001 HIS F 394 PHE 0.019 0.001 PHE F 689 TYR 0.020 0.001 TYR F 629 ARG 0.013 0.000 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 229 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7315 (mp) REVERT: A 113 HIS cc_start: 0.2837 (OUTLIER) cc_final: 0.2436 (m170) REVERT: A 120 SER cc_start: 0.7733 (OUTLIER) cc_final: 0.7111 (m) REVERT: A 187 ASN cc_start: 0.6539 (t0) cc_final: 0.6274 (p0) REVERT: A 190 PHE cc_start: 0.7519 (t80) cc_final: 0.6419 (m-80) REVERT: A 479 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5662 (pp-130) REVERT: A 480 LEU cc_start: 0.5513 (OUTLIER) cc_final: 0.5274 (mp) REVERT: A 481 LEU cc_start: 0.3909 (OUTLIER) cc_final: 0.3512 (pp) REVERT: A 483 MET cc_start: 0.4278 (ptm) cc_final: 0.4052 (ptm) REVERT: A 491 TYR cc_start: 0.5101 (OUTLIER) cc_final: 0.4800 (t80) REVERT: A 493 MET cc_start: 0.5082 (mpt) cc_final: 0.4830 (mpt) REVERT: A 837 ILE cc_start: 0.6443 (OUTLIER) cc_final: 0.5799 (pp) REVERT: A 926 ARG cc_start: 0.6664 (mtt90) cc_final: 0.5652 (mtp85) REVERT: A 1165 MET cc_start: 0.7038 (tmm) cc_final: 0.6599 (tmm) REVERT: A 1199 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7643 (mt) REVERT: A 1401 GLU cc_start: 0.7246 (tm-30) cc_final: 0.7045 (tm-30) REVERT: E 8 LYS cc_start: 0.6308 (OUTLIER) cc_final: 0.5631 (ttmm) REVERT: E 59 LYS cc_start: 0.3839 (OUTLIER) cc_final: 0.2678 (ptmm) REVERT: E 131 LYS cc_start: 0.6302 (OUTLIER) cc_final: 0.5801 (ttpt) REVERT: F 205 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8391 (tt) REVERT: F 311 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: F 404 MET cc_start: 0.8919 (mtt) cc_final: 0.8366 (mtt) REVERT: F 517 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8656 (tt) REVERT: F 552 ASN cc_start: 0.3266 (OUTLIER) cc_final: 0.3060 (t0) outliers start: 106 outliers final: 69 residues processed: 311 average time/residue: 0.9498 time to fit residues: 345.1100 Evaluate side-chains 304 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 219 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 390 SER Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 711 ASP Chi-restraints excluded: chain F residue 715 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 823 SER Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 907 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1048 ASP Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 147 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 169 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN F 186 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN F 644 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19005 Z= 0.172 Angle : 0.579 16.505 25687 Z= 0.287 Chirality : 0.042 0.236 2848 Planarity : 0.004 0.056 3203 Dihedral : 12.004 79.967 2924 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.32 % Allowed : 30.77 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2222 helix: 0.13 (0.16), residues: 1076 sheet: -0.56 (0.33), residues: 243 loop : -1.69 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1112 HIS 0.002 0.001 HIS A 274 PHE 0.021 0.001 PHE F 689 TYR 0.020 0.001 TYR F 629 ARG 0.012 0.000 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 230 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7319 (mp) REVERT: A 113 HIS cc_start: 0.2749 (OUTLIER) cc_final: 0.2357 (m170) REVERT: A 120 SER cc_start: 0.7718 (OUTLIER) cc_final: 0.7082 (m) REVERT: A 187 ASN cc_start: 0.6667 (t0) cc_final: 0.6417 (p0) REVERT: A 190 PHE cc_start: 0.7617 (t80) cc_final: 0.6458 (m-80) REVERT: A 479 MET cc_start: 0.6184 (OUTLIER) cc_final: 0.5800 (pp-130) REVERT: A 480 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.5404 (mp) REVERT: A 481 LEU cc_start: 0.4012 (OUTLIER) cc_final: 0.3622 (pp) REVERT: A 483 MET cc_start: 0.4204 (ptt) cc_final: 0.3969 (ptm) REVERT: A 491 TYR cc_start: 0.5111 (OUTLIER) cc_final: 0.4774 (t80) REVERT: A 493 MET cc_start: 0.5162 (OUTLIER) cc_final: 0.4935 (mpt) REVERT: A 547 ASN cc_start: 0.5741 (OUTLIER) cc_final: 0.5305 (p0) REVERT: A 653 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6384 (tt) REVERT: A 837 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.5797 (pp) REVERT: A 894 LYS cc_start: 0.6994 (mmtt) cc_final: 0.6675 (mmmt) REVERT: A 916 HIS cc_start: 0.5852 (t-90) cc_final: 0.5569 (t-90) REVERT: A 926 ARG cc_start: 0.6696 (mtt90) cc_final: 0.5656 (mtp85) REVERT: A 984 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7578 (pm20) REVERT: A 1069 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: A 1125 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.7143 (t80) REVERT: A 1164 GLU cc_start: 0.7766 (tp30) cc_final: 0.7508 (tp30) REVERT: A 1199 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7570 (mt) REVERT: A 1295 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8418 (t) REVERT: A 1384 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.7059 (m-80) REVERT: E 59 LYS cc_start: 0.3766 (OUTLIER) cc_final: 0.2637 (ptmm) REVERT: E 118 LEU cc_start: 0.7366 (mm) cc_final: 0.7135 (mm) REVERT: E 131 LYS cc_start: 0.6302 (OUTLIER) cc_final: 0.5795 (ttpt) REVERT: E 216 MET cc_start: 0.6847 (ttp) cc_final: 0.6598 (tmt) REVERT: F 205 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8388 (tt) REVERT: F 311 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: F 404 MET cc_start: 0.8892 (mtt) cc_final: 0.8402 (mtt) REVERT: F 492 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8913 (m) REVERT: F 517 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8652 (tt) REVERT: F 552 ASN cc_start: 0.3181 (OUTLIER) cc_final: 0.2959 (t0) outliers start: 106 outliers final: 69 residues processed: 315 average time/residue: 0.9691 time to fit residues: 358.5140 Evaluate side-chains 313 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 221 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1069 GLN Chi-restraints excluded: chain A residue 1125 PHE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 390 SER Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 711 ASP Chi-restraints excluded: chain F residue 715 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 823 SER Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 907 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1048 ASP Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 190 optimal weight: 0.6980 chunk 200 optimal weight: 0.2980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 930 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN F 186 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN F 866 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19005 Z= 0.175 Angle : 0.584 16.733 25687 Z= 0.289 Chirality : 0.041 0.257 2848 Planarity : 0.004 0.055 3203 Dihedral : 11.744 79.952 2920 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.77 % Allowed : 31.63 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.18), residues: 2222 helix: 0.24 (0.16), residues: 1075 sheet: -0.52 (0.33), residues: 243 loop : -1.65 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1112 HIS 0.002 0.001 HIS A 274 PHE 0.022 0.001 PHE F 689 TYR 0.021 0.001 TYR F 629 ARG 0.013 0.000 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 221 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.2733 (OUTLIER) cc_final: 0.2349 (m170) REVERT: A 120 SER cc_start: 0.7724 (OUTLIER) cc_final: 0.7085 (m) REVERT: A 187 ASN cc_start: 0.6657 (t0) cc_final: 0.6402 (p0) REVERT: A 190 PHE cc_start: 0.7741 (t80) cc_final: 0.6436 (m-80) REVERT: A 479 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5880 (pp-130) REVERT: A 480 LEU cc_start: 0.5847 (OUTLIER) cc_final: 0.5613 (mp) REVERT: A 481 LEU cc_start: 0.3996 (OUTLIER) cc_final: 0.3606 (pp) REVERT: A 483 MET cc_start: 0.4255 (ptt) cc_final: 0.4032 (ptm) REVERT: A 491 TYR cc_start: 0.5146 (OUTLIER) cc_final: 0.4780 (t80) REVERT: A 493 MET cc_start: 0.5003 (mpt) cc_final: 0.4780 (mpt) REVERT: A 547 ASN cc_start: 0.5672 (OUTLIER) cc_final: 0.5256 (p0) REVERT: A 668 GLU cc_start: 0.6048 (OUTLIER) cc_final: 0.5606 (tt0) REVERT: A 916 HIS cc_start: 0.5858 (t-90) cc_final: 0.5572 (t-90) REVERT: A 984 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7621 (pm20) REVERT: A 1125 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6797 (t80) REVERT: A 1164 GLU cc_start: 0.7723 (tp30) cc_final: 0.7450 (tp30) REVERT: A 1165 MET cc_start: 0.7044 (tmm) cc_final: 0.6371 (tmm) REVERT: A 1199 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7563 (mt) REVERT: A 1295 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8424 (t) REVERT: A 1384 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.7069 (m-80) REVERT: E 59 LYS cc_start: 0.3826 (OUTLIER) cc_final: 0.2672 (ptmm) REVERT: E 118 LEU cc_start: 0.7430 (mm) cc_final: 0.7172 (mm) REVERT: E 131 LYS cc_start: 0.6297 (OUTLIER) cc_final: 0.5802 (ttpt) REVERT: E 194 LEU cc_start: 0.8222 (mt) cc_final: 0.7966 (mt) REVERT: E 216 MET cc_start: 0.6878 (ttp) cc_final: 0.6666 (tmm) REVERT: F 205 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8409 (tt) REVERT: F 311 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: F 404 MET cc_start: 0.8902 (mtt) cc_final: 0.8421 (mtt) REVERT: F 492 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8918 (m) REVERT: F 517 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8689 (tt) REVERT: F 552 ASN cc_start: 0.3392 (OUTLIER) cc_final: 0.3127 (t0) outliers start: 95 outliers final: 67 residues processed: 300 average time/residue: 0.9785 time to fit residues: 343.2560 Evaluate side-chains 301 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 215 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1125 PHE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 390 SER Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 711 ASP Chi-restraints excluded: chain F residue 715 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 823 SER Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 907 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1048 ASP Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.2980 chunk 212 optimal weight: 3.9990 chunk 129 optimal weight: 0.0170 chunk 100 optimal weight: 0.1980 chunk 147 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 177 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 overall best weight: 0.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN F 186 ASN F 394 HIS F 484 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19005 Z= 0.136 Angle : 0.571 18.543 25687 Z= 0.280 Chirality : 0.041 0.270 2848 Planarity : 0.004 0.055 3203 Dihedral : 11.155 78.666 2916 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.46 % Allowed : 33.08 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2222 helix: 0.48 (0.16), residues: 1075 sheet: -0.38 (0.33), residues: 242 loop : -1.54 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1112 HIS 0.002 0.000 HIS F 394 PHE 0.026 0.001 PHE F 689 TYR 0.021 0.001 TYR F 629 ARG 0.013 0.000 ARG F 501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 235 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.2885 (OUTLIER) cc_final: 0.2354 (m170) REVERT: A 187 ASN cc_start: 0.6580 (t0) cc_final: 0.6378 (p0) REVERT: A 190 PHE cc_start: 0.7535 (t80) cc_final: 0.6319 (m-80) REVERT: A 447 LEU cc_start: 0.8295 (tt) cc_final: 0.8027 (tp) REVERT: A 479 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.5852 (pp-130) REVERT: A 480 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5625 (mp) REVERT: A 481 LEU cc_start: 0.3943 (OUTLIER) cc_final: 0.3596 (pp) REVERT: A 483 MET cc_start: 0.4499 (ptt) cc_final: 0.4191 (ptm) REVERT: A 493 MET cc_start: 0.5088 (OUTLIER) cc_final: 0.4887 (mpt) REVERT: A 547 ASN cc_start: 0.5679 (OUTLIER) cc_final: 0.5227 (p0) REVERT: A 984 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7559 (pm20) REVERT: A 1125 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6910 (t80) REVERT: A 1164 GLU cc_start: 0.7748 (tp30) cc_final: 0.7548 (tp30) REVERT: A 1165 MET cc_start: 0.6896 (tmm) cc_final: 0.6372 (tmm) REVERT: A 1199 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7562 (mt) REVERT: A 1295 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8409 (t) REVERT: A 1384 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.7016 (m-80) REVERT: E 59 LYS cc_start: 0.3721 (OUTLIER) cc_final: 0.2623 (pttt) REVERT: E 106 SER cc_start: 0.6191 (OUTLIER) cc_final: 0.5896 (p) REVERT: E 118 LEU cc_start: 0.7446 (mm) cc_final: 0.7224 (mm) REVERT: E 131 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5810 (ttpt) REVERT: E 158 MET cc_start: 0.6315 (tpt) cc_final: 0.6068 (tpp) REVERT: E 216 MET cc_start: 0.6693 (ttp) cc_final: 0.6463 (tmm) REVERT: F 141 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5723 (tt0) REVERT: F 404 MET cc_start: 0.8795 (mtt) cc_final: 0.8322 (mtt) REVERT: F 492 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8863 (m) REVERT: F 1068 LEU cc_start: 0.8033 (pp) cc_final: 0.7763 (tp) outliers start: 69 outliers final: 39 residues processed: 290 average time/residue: 0.9765 time to fit residues: 330.5715 Evaluate side-chains 271 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 217 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1125 PHE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 390 SER Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 907 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN F 484 GLN ** F 678 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 = 0.3872 r_free = 0.3872 target = 0.163036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114799 restraints weight = 36759.437| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.35 r_work: 0.3098 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19005 Z= 0.220 Angle : 0.589 15.563 25687 Z= 0.294 Chirality : 0.042 0.265 2848 Planarity : 0.005 0.055 3203 Dihedral : 11.136 79.960 2905 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.31 % Allowed : 33.63 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.69 (0.18), residues: 2222 helix: 0.42 (0.16), residues: 1078 sheet: -0.34 (0.33), residues: 244 loop : -1.54 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1112 HIS 0.003 0.001 HIS F 394 PHE 0.022 0.001 PHE F 689 TYR 0.017 0.001 TYR F 629 ARG 0.013 0.000 ARG F 501 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6691.99 seconds wall clock time: 119 minutes 36.04 seconds (7176.04 seconds total)