Starting phenix.real_space_refine on Sun Feb 18 05:44:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvy_8920/02_2024/6dvy_8920_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvy_8920/02_2024/6dvy_8920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvy_8920/02_2024/6dvy_8920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvy_8920/02_2024/6dvy_8920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvy_8920/02_2024/6dvy_8920_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dvy_8920/02_2024/6dvy_8920_updated.pdb" } resolution = 4.0 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 124 5.16 5 B 8 2.79 5 C 13684 2.51 5 N 3452 2.21 5 O 3740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 714": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 714": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" 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: 21008 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5218 Classifications: {'peptide': 641} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 623} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5218 Classifications: {'peptide': 641} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 623} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5218 Classifications: {'peptide': 641} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 623} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5218 Classifications: {'peptide': 641} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 623} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'FZ4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'FZ4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'FZ4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'FZ4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.40, per 1000 atoms: 0.50 Number of scatterers: 21008 At special positions: 0 Unit cell: (132.98, 132.98, 124.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 O 3740 8.00 N 3452 7.00 C 13684 6.00 B 8 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.69 Conformation dependent library (CDL) restraints added in 3.8 seconds 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 4 sheets defined 52.6% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.38 Creating SS restraints... Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.526A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 removed outlier: 4.093A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 183 through 197 removed outlier: 4.407A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 228 through 236 removed outlier: 3.627A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 3.565A pdb=" N ALA A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 removed outlier: 3.878A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 316 through 327 removed outlier: 3.788A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.599A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 417 through 420 No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.515A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 459 removed outlier: 3.586A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 507 removed outlier: 3.558A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 514 No H-bonds generated for 'chain 'A' and resid 511 through 514' Processing helix chain 'A' and resid 522 through 542 removed outlier: 3.518A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 566 removed outlier: 3.587A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 605 removed outlier: 4.050A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 587 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 633 removed outlier: 3.562A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 676 removed outlier: 3.500A pdb=" N LEU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 669 " --> pdb=" O THR A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 706 removed outlier: 3.706A pdb=" N SER A 688 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 129 Processing helix chain 'B' and resid 133 through 148 removed outlier: 3.526A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 removed outlier: 4.092A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 183 through 197 removed outlier: 4.407A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 228 through 236 removed outlier: 3.627A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 3.565A pdb=" N ALA B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 removed outlier: 3.879A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 316 through 327 removed outlier: 3.790A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.600A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 417 through 420 No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 423 through 435 removed outlier: 3.515A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 459 removed outlier: 3.586A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 507 removed outlier: 3.558A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 514 No H-bonds generated for 'chain 'B' and resid 511 through 514' Processing helix chain 'B' and resid 522 through 542 removed outlier: 3.517A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 566 removed outlier: 3.586A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 605 removed outlier: 4.050A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL B 587 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 633 removed outlier: 3.563A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 676 removed outlier: 3.562A pdb=" N THR B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 669 " --> pdb=" O THR B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 706 removed outlier: 3.706A pdb=" N SER B 688 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 129 Processing helix chain 'C' and resid 133 through 148 removed outlier: 3.526A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 161 removed outlier: 4.093A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 183 through 197 removed outlier: 4.408A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.627A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 3.566A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 removed outlier: 3.880A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 316 through 327 removed outlier: 3.789A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.600A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 423 through 435 removed outlier: 3.515A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 459 removed outlier: 3.587A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 507 removed outlier: 3.557A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 514 No H-bonds generated for 'chain 'C' and resid 511 through 514' Processing helix chain 'C' and resid 522 through 542 removed outlier: 3.517A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 566 removed outlier: 3.587A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 605 removed outlier: 4.049A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL C 587 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 633 removed outlier: 3.564A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 676 removed outlier: 3.561A pdb=" N THR C 660 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 669 " --> pdb=" O THR C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 706 removed outlier: 3.706A pdb=" N SER C 688 " --> pdb=" O VAL C 684 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 129 Processing helix chain 'D' and resid 133 through 148 removed outlier: 3.526A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 removed outlier: 4.094A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 183 through 197 removed outlier: 4.408A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 228 through 236 removed outlier: 3.627A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.566A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 283 removed outlier: 3.879A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 316 through 327 removed outlier: 3.789A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 350 Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.600A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 403 through 407 Processing helix chain 'D' and resid 417 through 420 No H-bonds generated for 'chain 'D' and resid 417 through 420' Processing helix chain 'D' and resid 423 through 435 removed outlier: 3.514A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 459 removed outlier: 3.586A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 507 removed outlier: 3.558A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 514 No H-bonds generated for 'chain 'D' and resid 511 through 514' Processing helix chain 'D' and resid 522 through 542 removed outlier: 3.517A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 566 removed outlier: 3.587A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 605 removed outlier: 4.050A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL D 587 " --> pdb=" O ILE D 583 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 633 removed outlier: 3.563A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 676 removed outlier: 3.562A pdb=" N THR D 660 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU D 669 " --> pdb=" O THR D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 706 removed outlier: 3.706A pdb=" N SER D 688 " --> pdb=" O VAL D 684 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.791A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.792A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.792A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.792A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) 767 hydrogen bonds defined for protein. 2301 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: 5.42 Time building geometry restraints manager: 8.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6393 1.34 - 1.46: 4040 1.46 - 1.57: 10831 1.57 - 1.69: 4 1.69 - 1.81: 204 Bond restraints: 21472 Sorted by residual: bond pdb=" C ASP C 752 " pdb=" N PRO C 753 " ideal model delta sigma weight residual 1.335 1.397 -0.062 1.28e-02 6.10e+03 2.38e+01 bond pdb=" C ASP A 752 " pdb=" N PRO A 753 " ideal model delta sigma weight residual 1.335 1.397 -0.062 1.28e-02 6.10e+03 2.35e+01 bond pdb=" C ASP D 752 " pdb=" N PRO D 753 " ideal model delta sigma weight residual 1.335 1.397 -0.062 1.28e-02 6.10e+03 2.34e+01 bond pdb=" C ASP B 752 " pdb=" N PRO B 753 " ideal model delta sigma weight residual 1.335 1.396 -0.062 1.28e-02 6.10e+03 2.31e+01 bond pdb=" C TYR C 650 " pdb=" N PRO C 651 " ideal model delta sigma weight residual 1.335 1.378 -0.043 1.19e-02 7.06e+03 1.32e+01 ... (remaining 21467 not shown) Histogram of bond angle deviations from ideal: 98.59 - 105.71: 332 105.71 - 112.83: 11163 112.83 - 119.96: 8039 119.96 - 127.08: 9252 127.08 - 134.20: 250 Bond angle restraints: 29036 Sorted by residual: angle pdb=" C CYS D 619 " pdb=" N SER D 620 " pdb=" CA SER D 620 " ideal model delta sigma weight residual 122.44 115.72 6.72 1.19e+00 7.06e-01 3.19e+01 angle pdb=" C CYS C 619 " pdb=" N SER C 620 " pdb=" CA SER C 620 " ideal model delta sigma weight residual 122.44 115.74 6.70 1.19e+00 7.06e-01 3.17e+01 angle pdb=" C CYS B 619 " pdb=" N SER B 620 " pdb=" CA SER B 620 " ideal model delta sigma weight residual 122.44 115.79 6.65 1.19e+00 7.06e-01 3.12e+01 angle pdb=" C TRP A 739 " pdb=" N THR A 740 " pdb=" CA THR A 740 " ideal model delta sigma weight residual 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 angle pdb=" C TRP C 739 " pdb=" N THR C 740 " pdb=" CA THR C 740 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.11e+01 ... (remaining 29031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.22: 12272 22.22 - 44.45: 480 44.45 - 66.67: 24 66.67 - 88.90: 28 88.90 - 111.12: 8 Dihedral angle restraints: 12812 sinusoidal: 5244 harmonic: 7568 Sorted by residual: dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N ASP B 153 " pdb=" CA ASP B 153 " ideal model delta harmonic sigma weight residual -180.00 -139.63 -40.37 0 5.00e+00 4.00e-02 6.52e+01 dihedral pdb=" CA LEU D 152 " pdb=" C LEU D 152 " pdb=" N ASP D 153 " pdb=" CA ASP D 153 " ideal model delta harmonic sigma weight residual -180.00 -139.66 -40.34 0 5.00e+00 4.00e-02 6.51e+01 dihedral pdb=" CA LEU A 152 " pdb=" C LEU A 152 " pdb=" N ASP A 153 " pdb=" CA ASP A 153 " ideal model delta harmonic sigma weight residual -180.00 -139.66 -40.34 0 5.00e+00 4.00e-02 6.51e+01 ... (remaining 12809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2372 0.059 - 0.117: 776 0.117 - 0.176: 97 0.176 - 0.234: 34 0.234 - 0.293: 13 Chirality restraints: 3292 Sorted by residual: chirality pdb=" CG LEU C 730 " pdb=" CB LEU C 730 " pdb=" CD1 LEU C 730 " pdb=" CD2 LEU C 730 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CG LEU B 730 " pdb=" CB LEU B 730 " pdb=" CD1 LEU B 730 " pdb=" CD2 LEU B 730 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU A 730 " pdb=" CB LEU A 730 " pdb=" CD1 LEU A 730 " pdb=" CD2 LEU A 730 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 3289 not shown) Planarity restraints: 3616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 368 " 0.062 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO D 369 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 369 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 369 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 368 " 0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO A 369 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 369 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 369 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 368 " 0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO C 369 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO C 369 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 369 " 0.052 5.00e-02 4.00e+02 ... (remaining 3613 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 72 2.39 - 3.02: 10678 3.02 - 3.64: 32505 3.64 - 4.27: 47570 4.27 - 4.90: 74630 Nonbonded interactions: 165455 Sorted by model distance: nonbonded pdb=" CZ ARG D 696 " pdb=" C05 FZ4 D 801 " model vdw 1.762 2.856 nonbonded pdb=" CZ ARG C 696 " pdb=" C05 FZ4 C 801 " model vdw 1.774 2.856 nonbonded pdb=" CZ ARG A 696 " pdb=" C05 FZ4 A 801 " model vdw 1.781 2.856 nonbonded pdb=" CZ ARG B 696 " pdb=" C05 FZ4 B 801 " model vdw 1.797 2.856 nonbonded pdb=" CD2 HIS C 426 " pdb=" C12 FZ4 C 801 " model vdw 2.249 3.560 ... (remaining 165450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 3.110 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 52.820 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.008 0.083 21472 Z= 0.520 Angle : 1.252 10.671 29036 Z= 0.711 Chirality : 0.059 0.293 3292 Planarity : 0.007 0.094 3616 Dihedral : 12.657 111.121 7900 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.78 % Allowed : 12.99 % Favored : 86.23 % Rotamer: Outliers : 0.88 % Allowed : 4.03 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.80 % 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: -5.79 (0.11), residues: 2556 helix: -3.93 (0.07), residues: 1396 sheet: -1.69 (0.65), residues: 76 loop : -3.76 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D 481 HIS 0.011 0.002 HIS B 417 PHE 0.043 0.004 PHE B 633 TYR 0.017 0.003 TYR C 650 ARG 0.012 0.001 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 831 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8430 (mmt) cc_final: 0.7903 (mmt) REVERT: A 171 CYS cc_start: 0.8480 (t) cc_final: 0.8192 (t) REVERT: A 191 LEU cc_start: 0.9165 (mt) cc_final: 0.8829 (mt) REVERT: A 195 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7887 (mm-30) REVERT: A 200 LEU cc_start: 0.9303 (pp) cc_final: 0.9041 (pp) REVERT: A 209 THR cc_start: 0.8958 (p) cc_final: 0.8727 (t) REVERT: A 235 ILE cc_start: 0.8935 (mt) cc_final: 0.8598 (tt) REVERT: A 288 ASP cc_start: 0.8452 (t0) cc_final: 0.7525 (p0) REVERT: A 291 SER cc_start: 0.8611 (t) cc_final: 0.8347 (p) REVERT: A 293 ASP cc_start: 0.8418 (t0) cc_final: 0.7910 (t0) REVERT: A 336 MET cc_start: 0.8831 (ttm) cc_final: 0.8613 (ttm) REVERT: A 373 LEU cc_start: 0.8829 (mt) cc_final: 0.8114 (mt) REVERT: A 444 SER cc_start: 0.9139 (p) cc_final: 0.8672 (t) REVERT: A 479 MET cc_start: 0.7759 (mmm) cc_final: 0.7411 (mtp) REVERT: A 562 MET cc_start: 0.8481 (mmp) cc_final: 0.8277 (mmm) REVERT: A 572 MET cc_start: 0.8977 (tpt) cc_final: 0.8772 (tpp) REVERT: A 639 LEU cc_start: 0.7615 (tt) cc_final: 0.7333 (tt) REVERT: A 683 ASN cc_start: 0.8360 (m-40) cc_final: 0.7871 (m-40) REVERT: A 688 SER cc_start: 0.9428 (m) cc_final: 0.8846 (p) REVERT: B 159 MET cc_start: 0.8369 (mmt) cc_final: 0.7948 (mmt) REVERT: B 171 CYS cc_start: 0.8503 (t) cc_final: 0.8203 (t) REVERT: B 195 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7941 (mm-30) REVERT: B 200 LEU cc_start: 0.9303 (pp) cc_final: 0.8620 (pp) REVERT: B 209 THR cc_start: 0.8971 (p) cc_final: 0.8716 (t) REVERT: B 235 ILE cc_start: 0.8985 (mt) cc_final: 0.8679 (tt) REVERT: B 265 PRO cc_start: 0.9350 (Cg_exo) cc_final: 0.9125 (Cg_endo) REVERT: B 288 ASP cc_start: 0.8460 (t0) cc_final: 0.7668 (p0) REVERT: B 291 SER cc_start: 0.8681 (t) cc_final: 0.8451 (p) REVERT: B 305 THR cc_start: 0.9186 (p) cc_final: 0.8957 (t) REVERT: B 373 LEU cc_start: 0.8813 (mt) cc_final: 0.8127 (mt) REVERT: B 444 SER cc_start: 0.9149 (p) cc_final: 0.8668 (t) REVERT: B 631 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7401 (mm-30) REVERT: B 683 ASN cc_start: 0.8325 (m-40) cc_final: 0.7925 (m-40) REVERT: B 688 SER cc_start: 0.9359 (m) cc_final: 0.8748 (p) REVERT: C 159 MET cc_start: 0.8437 (mmt) cc_final: 0.8126 (mmt) REVERT: C 167 THR cc_start: 0.8921 (p) cc_final: 0.8719 (t) REVERT: C 171 CYS cc_start: 0.8505 (t) cc_final: 0.8228 (t) REVERT: C 191 LEU cc_start: 0.9156 (mt) cc_final: 0.8825 (mt) REVERT: C 195 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7871 (mm-30) REVERT: C 200 LEU cc_start: 0.9295 (pp) cc_final: 0.9018 (pp) REVERT: C 209 THR cc_start: 0.8912 (p) cc_final: 0.8681 (t) REVERT: C 235 ILE cc_start: 0.9014 (mt) cc_final: 0.8701 (tt) REVERT: C 265 PRO cc_start: 0.9360 (Cg_exo) cc_final: 0.9153 (Cg_endo) REVERT: C 288 ASP cc_start: 0.8519 (t0) cc_final: 0.7454 (p0) REVERT: C 291 SER cc_start: 0.8701 (t) cc_final: 0.8420 (p) REVERT: C 373 LEU cc_start: 0.8806 (mt) cc_final: 0.8046 (mt) REVERT: C 444 SER cc_start: 0.9154 (p) cc_final: 0.8675 (t) REVERT: C 631 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7520 (mm-30) REVERT: C 683 ASN cc_start: 0.8358 (m-40) cc_final: 0.7866 (m-40) REVERT: C 688 SER cc_start: 0.9369 (m) cc_final: 0.8834 (p) REVERT: D 159 MET cc_start: 0.8479 (mmt) cc_final: 0.8100 (mmt) REVERT: D 171 CYS cc_start: 0.8478 (t) cc_final: 0.8155 (t) REVERT: D 191 LEU cc_start: 0.9157 (mt) cc_final: 0.8810 (mt) REVERT: D 195 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7910 (mm-30) REVERT: D 200 LEU cc_start: 0.9272 (pp) cc_final: 0.9016 (pp) REVERT: D 209 THR cc_start: 0.8885 (p) cc_final: 0.8673 (t) REVERT: D 235 ILE cc_start: 0.9017 (mt) cc_final: 0.8573 (tt) REVERT: D 265 PRO cc_start: 0.9392 (Cg_exo) cc_final: 0.9153 (Cg_endo) REVERT: D 288 ASP cc_start: 0.8448 (t0) cc_final: 0.8108 (t0) REVERT: D 291 SER cc_start: 0.8651 (t) cc_final: 0.8285 (p) REVERT: D 293 ASP cc_start: 0.8378 (t0) cc_final: 0.7455 (t0) REVERT: D 373 LEU cc_start: 0.8836 (mt) cc_final: 0.8074 (mt) REVERT: D 444 SER cc_start: 0.9165 (p) cc_final: 0.8722 (t) REVERT: D 479 MET cc_start: 0.7733 (mmm) cc_final: 0.7333 (mtp) REVERT: D 562 MET cc_start: 0.8497 (mmp) cc_final: 0.8193 (mmm) REVERT: D 572 MET cc_start: 0.9026 (tpt) cc_final: 0.8761 (tpp) REVERT: D 683 ASN cc_start: 0.8387 (m-40) cc_final: 0.7856 (m-40) REVERT: D 688 SER cc_start: 0.9418 (m) cc_final: 0.8947 (p) outliers start: 20 outliers final: 4 residues processed: 851 average time/residue: 0.3176 time to fit residues: 413.0979 Evaluate side-chains 494 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 490 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain D residue 539 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN A 483 GLN A 529 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN B 297 ASN B 483 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN C 529 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN ** C 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 483 GLN D 529 GLN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21472 Z= 0.336 Angle : 0.887 15.098 29036 Z= 0.447 Chirality : 0.045 0.215 3292 Planarity : 0.006 0.069 3616 Dihedral : 9.536 92.052 2844 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.32 % Favored : 87.21 % Rotamer: Outliers : 6.30 % Allowed : 12.48 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.76 (0.14), residues: 2556 helix: -1.79 (0.11), residues: 1444 sheet: -1.77 (0.64), residues: 76 loop : -3.55 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 710 HIS 0.010 0.002 HIS D 160 PHE 0.029 0.002 PHE D 666 TYR 0.025 0.002 TYR A 451 ARG 0.007 0.001 ARG D 696 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 539 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8938 (pm20) REVERT: A 209 THR cc_start: 0.8986 (p) cc_final: 0.8739 (t) REVERT: A 235 ILE cc_start: 0.8848 (mt) cc_final: 0.8643 (tt) REVERT: A 282 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8079 (mmm) REVERT: A 288 ASP cc_start: 0.8586 (t0) cc_final: 0.8134 (t0) REVERT: A 291 SER cc_start: 0.8700 (t) cc_final: 0.8332 (p) REVERT: A 391 ASP cc_start: 0.7535 (t70) cc_final: 0.7156 (t0) REVERT: A 529 GLN cc_start: 0.8736 (tm130) cc_final: 0.8531 (tm130) REVERT: A 562 MET cc_start: 0.8675 (mmp) cc_final: 0.8453 (mmm) REVERT: A 631 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7280 (tp30) REVERT: A 702 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7726 (mm-30) REVERT: A 710 TRP cc_start: 0.7690 (p-90) cc_final: 0.7365 (p-90) REVERT: B 137 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8872 (pm20) REVERT: B 209 THR cc_start: 0.8993 (p) cc_final: 0.8712 (t) REVERT: B 288 ASP cc_start: 0.8376 (t0) cc_final: 0.7711 (p0) REVERT: B 291 SER cc_start: 0.8808 (t) cc_final: 0.8344 (p) REVERT: B 346 GLN cc_start: 0.8871 (mt0) cc_final: 0.8177 (mt0) REVERT: B 391 ASP cc_start: 0.7505 (t70) cc_final: 0.7084 (t0) REVERT: B 430 HIS cc_start: 0.8733 (t-90) cc_final: 0.8363 (t70) REVERT: B 529 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8617 (tm-30) REVERT: B 587 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.9075 (p) REVERT: B 616 LYS cc_start: 0.7785 (mptt) cc_final: 0.7417 (mptt) REVERT: B 631 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7335 (tp30) REVERT: B 683 ASN cc_start: 0.8203 (m-40) cc_final: 0.7968 (m-40) REVERT: B 702 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7799 (mm-30) REVERT: B 710 TRP cc_start: 0.7711 (p-90) cc_final: 0.7291 (p-90) REVERT: C 137 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8899 (mp0) REVERT: C 209 THR cc_start: 0.8945 (p) cc_final: 0.8706 (t) REVERT: C 288 ASP cc_start: 0.8513 (t0) cc_final: 0.8228 (t0) REVERT: C 291 SER cc_start: 0.8846 (t) cc_final: 0.8437 (p) REVERT: C 391 ASP cc_start: 0.7560 (t70) cc_final: 0.7304 (t0) REVERT: C 631 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7491 (tp30) REVERT: C 683 ASN cc_start: 0.8163 (m-40) cc_final: 0.7904 (m-40) REVERT: C 702 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7867 (mm-30) REVERT: C 707 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8566 (tm) REVERT: C 710 TRP cc_start: 0.7750 (p-90) cc_final: 0.7327 (p-90) REVERT: C 742 TRP cc_start: 0.7642 (m-90) cc_final: 0.7386 (m-90) REVERT: D 137 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8947 (pm20) REVERT: D 209 THR cc_start: 0.8966 (p) cc_final: 0.8745 (t) REVERT: D 282 MET cc_start: 0.8174 (mtp) cc_final: 0.7760 (mmm) REVERT: D 288 ASP cc_start: 0.8393 (t0) cc_final: 0.8084 (t0) REVERT: D 289 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8819 (tp) REVERT: D 291 SER cc_start: 0.8831 (t) cc_final: 0.8430 (p) REVERT: D 430 HIS cc_start: 0.8803 (t-90) cc_final: 0.8425 (t70) REVERT: D 483 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7068 (pp30) REVERT: D 562 MET cc_start: 0.8681 (mmp) cc_final: 0.8440 (mmm) REVERT: D 631 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7273 (tp30) REVERT: D 710 TRP cc_start: 0.7690 (p-90) cc_final: 0.7288 (p-90) outliers start: 144 outliers final: 60 residues processed: 634 average time/residue: 0.2993 time to fit residues: 298.4028 Evaluate side-chains 489 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 420 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 731 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 232 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 230 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 529 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 HIS A 750 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 HIS C 645 GLN C 750 ASN ** D 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN D 645 GLN D 750 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21472 Z= 0.249 Angle : 0.799 11.459 29036 Z= 0.397 Chirality : 0.043 0.282 3292 Planarity : 0.005 0.064 3616 Dihedral : 8.617 69.727 2844 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.82 % Favored : 87.72 % Rotamer: Outliers : 5.78 % Allowed : 17.60 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.73 (0.16), residues: 2556 helix: -0.79 (0.13), residues: 1468 sheet: -2.00 (0.62), residues: 76 loop : -3.37 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 493 HIS 0.006 0.001 HIS D 160 PHE 0.029 0.002 PHE D 666 TYR 0.023 0.002 TYR B 451 ARG 0.006 0.001 ARG C 696 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 488 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: A 137 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: A 141 ASP cc_start: 0.8502 (m-30) cc_final: 0.8277 (m-30) REVERT: A 209 THR cc_start: 0.8909 (p) cc_final: 0.8629 (t) REVERT: A 282 MET cc_start: 0.8286 (mtp) cc_final: 0.7957 (mmm) REVERT: A 288 ASP cc_start: 0.8524 (t0) cc_final: 0.8231 (t0) REVERT: A 290 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8653 (p) REVERT: A 291 SER cc_start: 0.8846 (t) cc_final: 0.8397 (p) REVERT: A 293 ASP cc_start: 0.7953 (t0) cc_final: 0.7659 (t0) REVERT: A 333 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8946 (tt) REVERT: A 391 ASP cc_start: 0.7385 (t70) cc_final: 0.6987 (t0) REVERT: A 419 MET cc_start: 0.9208 (mmm) cc_final: 0.8654 (mmm) REVERT: A 446 CYS cc_start: 0.8658 (m) cc_final: 0.8242 (m) REVERT: A 529 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 555 MET cc_start: 0.8072 (mtp) cc_final: 0.7782 (mtm) REVERT: A 598 LEU cc_start: 0.9440 (tp) cc_final: 0.9180 (tp) REVERT: A 739 TRP cc_start: 0.8196 (OUTLIER) cc_final: 0.7348 (t-100) REVERT: B 133 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7895 (mp0) REVERT: B 137 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8720 (pm20) REVERT: B 209 THR cc_start: 0.8929 (p) cc_final: 0.8639 (t) REVERT: B 282 MET cc_start: 0.8036 (mmm) cc_final: 0.7731 (mmm) REVERT: B 290 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8767 (p) REVERT: B 333 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8992 (tt) REVERT: B 389 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8421 (mt) REVERT: B 391 ASP cc_start: 0.7372 (t70) cc_final: 0.6876 (t0) REVERT: B 419 MET cc_start: 0.9190 (mmm) cc_final: 0.8537 (mmm) REVERT: B 446 CYS cc_start: 0.8591 (m) cc_final: 0.8163 (m) REVERT: B 611 LYS cc_start: 0.3860 (tmtt) cc_final: 0.3638 (tmtt) REVERT: B 739 TRP cc_start: 0.8257 (OUTLIER) cc_final: 0.7228 (t-100) REVERT: C 133 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: C 137 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8543 (pm20) REVERT: C 141 ASP cc_start: 0.8520 (m-30) cc_final: 0.8290 (m-30) REVERT: C 148 ARG cc_start: 0.7546 (tpt170) cc_final: 0.7129 (tpt90) REVERT: C 209 THR cc_start: 0.8872 (p) cc_final: 0.8623 (t) REVERT: C 282 MET cc_start: 0.7961 (mmm) cc_final: 0.7632 (mmm) REVERT: C 290 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8738 (p) REVERT: C 360 ILE cc_start: 0.9385 (mt) cc_final: 0.9120 (tt) REVERT: C 419 MET cc_start: 0.9260 (mmm) cc_final: 0.8674 (mmm) REVERT: C 446 CYS cc_start: 0.8612 (m) cc_final: 0.8185 (m) REVERT: C 555 MET cc_start: 0.8182 (mtp) cc_final: 0.7945 (mtm) REVERT: C 610 GLU cc_start: 0.6906 (tp30) cc_final: 0.6698 (tp30) REVERT: C 631 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7574 (tp30) REVERT: C 707 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8566 (tm) REVERT: C 732 LEU cc_start: 0.8571 (mt) cc_final: 0.8309 (mt) REVERT: C 739 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.7262 (t-100) REVERT: D 137 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8455 (pm20) REVERT: D 141 ASP cc_start: 0.8501 (m-30) cc_final: 0.8251 (m-30) REVERT: D 159 MET cc_start: 0.8409 (mmm) cc_final: 0.8177 (mpp) REVERT: D 209 THR cc_start: 0.8890 (p) cc_final: 0.8620 (t) REVERT: D 290 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8729 (p) REVERT: D 293 ASP cc_start: 0.7916 (t0) cc_final: 0.7600 (t0) REVERT: D 419 MET cc_start: 0.9263 (mmm) cc_final: 0.8737 (mmm) REVERT: D 555 MET cc_start: 0.8172 (mtp) cc_final: 0.7834 (mtm) REVERT: D 631 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7516 (tp30) REVERT: D 722 LYS cc_start: 0.6923 (mttt) cc_final: 0.6719 (mttt) REVERT: D 739 TRP cc_start: 0.8177 (OUTLIER) cc_final: 0.7357 (t-100) outliers start: 132 outliers final: 72 residues processed: 581 average time/residue: 0.2973 time to fit residues: 273.7134 Evaluate side-chains 501 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 410 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 739 TRP Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 739 TRP Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 739 TRP Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 LYS Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 710 TRP Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 739 TRP Chi-restraints excluded: chain D residue 748 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 120 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 247 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 221 optimal weight: 0.0980 chunk 66 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 645 GLN ** C 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN D 314 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21472 Z= 0.178 Angle : 0.755 11.448 29036 Z= 0.371 Chirality : 0.041 0.181 3292 Planarity : 0.004 0.060 3616 Dihedral : 7.696 56.545 2842 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.09 % Favored : 87.44 % Rotamer: Outliers : 5.25 % Allowed : 19.22 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.09 (0.16), residues: 2556 helix: -0.20 (0.13), residues: 1504 sheet: -1.88 (0.63), residues: 76 loop : -3.32 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 481 HIS 0.004 0.001 HIS D 160 PHE 0.027 0.001 PHE C 193 TYR 0.023 0.001 TYR D 451 ARG 0.004 0.000 ARG D 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 479 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: A 137 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8560 (pm20) REVERT: A 141 ASP cc_start: 0.8516 (m-30) cc_final: 0.8310 (m-30) REVERT: A 209 THR cc_start: 0.8829 (p) cc_final: 0.8524 (t) REVERT: A 276 GLU cc_start: 0.8563 (pm20) cc_final: 0.8233 (pm20) REVERT: A 288 ASP cc_start: 0.8529 (t0) cc_final: 0.8324 (t0) REVERT: A 290 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8621 (p) REVERT: A 293 ASP cc_start: 0.8046 (t0) cc_final: 0.7779 (t0) REVERT: A 333 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8900 (tt) REVERT: A 346 GLN cc_start: 0.8854 (mt0) cc_final: 0.8048 (mt0) REVERT: A 360 ILE cc_start: 0.9340 (mt) cc_final: 0.9057 (tt) REVERT: A 419 MET cc_start: 0.8975 (mmm) cc_final: 0.8569 (mmt) REVERT: A 446 CYS cc_start: 0.8596 (m) cc_final: 0.8116 (m) REVERT: A 479 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6889 (mtm) REVERT: A 529 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8555 (tm-30) REVERT: A 555 MET cc_start: 0.8028 (mtp) cc_final: 0.7652 (mtm) REVERT: A 562 MET cc_start: 0.9093 (mmm) cc_final: 0.8462 (mmm) REVERT: A 739 TRP cc_start: 0.8168 (OUTLIER) cc_final: 0.7637 (t-100) REVERT: B 133 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: B 137 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: B 141 ASP cc_start: 0.8474 (m-30) cc_final: 0.8204 (m-30) REVERT: B 171 CYS cc_start: 0.8836 (t) cc_final: 0.8206 (t) REVERT: B 209 THR cc_start: 0.8784 (p) cc_final: 0.8465 (t) REVERT: B 282 MET cc_start: 0.8003 (mmm) cc_final: 0.7803 (mmm) REVERT: B 288 ASP cc_start: 0.8348 (t0) cc_final: 0.7740 (p0) REVERT: B 290 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8645 (p) REVERT: B 346 GLN cc_start: 0.8856 (mt0) cc_final: 0.8040 (mt0) REVERT: B 360 ILE cc_start: 0.9358 (mt) cc_final: 0.9063 (tt) REVERT: B 389 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8381 (mt) REVERT: B 419 MET cc_start: 0.8985 (mmm) cc_final: 0.8569 (mmt) REVERT: B 446 CYS cc_start: 0.8515 (m) cc_final: 0.8045 (m) REVERT: B 555 MET cc_start: 0.8039 (mtp) cc_final: 0.7759 (mtm) REVERT: B 574 MET cc_start: 0.8799 (tpp) cc_final: 0.8475 (mmt) REVERT: B 611 LYS cc_start: 0.3448 (tmtt) cc_final: 0.3185 (tmtt) REVERT: B 631 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7891 (tm-30) REVERT: B 739 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.7662 (t-100) REVERT: C 133 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: C 137 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8612 (pm20) REVERT: C 209 THR cc_start: 0.8720 (p) cc_final: 0.8433 (t) REVERT: C 282 MET cc_start: 0.8053 (mmm) cc_final: 0.7739 (mmm) REVERT: C 288 ASP cc_start: 0.8420 (t0) cc_final: 0.7747 (p0) REVERT: C 290 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8686 (p) REVERT: C 346 GLN cc_start: 0.8763 (mt0) cc_final: 0.8089 (mt0) REVERT: C 360 ILE cc_start: 0.9371 (mt) cc_final: 0.9079 (tt) REVERT: C 419 MET cc_start: 0.9004 (mmm) cc_final: 0.8546 (mmt) REVERT: C 446 CYS cc_start: 0.8507 (m) cc_final: 0.8035 (m) REVERT: C 481 TRP cc_start: 0.5954 (p-90) cc_final: 0.5717 (p-90) REVERT: C 555 MET cc_start: 0.8121 (mtp) cc_final: 0.7831 (mtm) REVERT: C 561 ASN cc_start: 0.8761 (m-40) cc_final: 0.8005 (t0) REVERT: C 739 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7727 (t-100) REVERT: D 137 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8447 (pm20) REVERT: D 138 LEU cc_start: 0.8942 (mt) cc_final: 0.8698 (mt) REVERT: D 141 ASP cc_start: 0.8522 (m-30) cc_final: 0.8286 (m-30) REVERT: D 209 THR cc_start: 0.8728 (p) cc_final: 0.8438 (t) REVERT: D 282 MET cc_start: 0.7950 (mmm) cc_final: 0.7639 (mmm) REVERT: D 288 ASP cc_start: 0.8355 (t0) cc_final: 0.7635 (p0) REVERT: D 290 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8776 (p) REVERT: D 293 ASP cc_start: 0.8037 (t0) cc_final: 0.7812 (t0) REVERT: D 346 GLN cc_start: 0.8889 (mt0) cc_final: 0.8098 (mt0) REVERT: D 360 ILE cc_start: 0.9310 (mt) cc_final: 0.8918 (tt) REVERT: D 419 MET cc_start: 0.9059 (mmm) cc_final: 0.8636 (mmt) REVERT: D 446 CYS cc_start: 0.8597 (m) cc_final: 0.8155 (m) REVERT: D 555 MET cc_start: 0.8021 (mtp) cc_final: 0.7705 (mtm) REVERT: D 587 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8985 (t) REVERT: D 610 GLU cc_start: 0.6892 (tp30) cc_final: 0.6607 (tp30) REVERT: D 616 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.6964 (tmtt) REVERT: D 631 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7755 (tm-30) REVERT: D 702 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7888 (mm-30) REVERT: D 739 TRP cc_start: 0.8131 (OUTLIER) cc_final: 0.7601 (t-100) outliers start: 120 outliers final: 57 residues processed: 564 average time/residue: 0.2823 time to fit residues: 254.5472 Evaluate side-chains 505 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 428 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 739 TRP Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 739 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 739 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 LYS Chi-restraints excluded: chain D residue 710 TRP Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 739 TRP Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 0.1980 chunk 222 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 750 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21472 Z= 0.190 Angle : 0.746 12.200 29036 Z= 0.366 Chirality : 0.041 0.244 3292 Planarity : 0.004 0.056 3616 Dihedral : 7.248 56.424 2836 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.09 % Favored : 87.56 % Rotamer: Outliers : 4.77 % Allowed : 21.19 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.80 (0.17), residues: 2556 helix: 0.07 (0.13), residues: 1496 sheet: -2.02 (0.60), residues: 76 loop : -3.22 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 742 HIS 0.003 0.001 HIS B 160 PHE 0.024 0.001 PHE D 666 TYR 0.020 0.001 TYR A 451 ARG 0.004 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 446 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: A 137 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8481 (pm20) REVERT: A 141 ASP cc_start: 0.8494 (m-30) cc_final: 0.8249 (m-30) REVERT: A 171 CYS cc_start: 0.8864 (t) cc_final: 0.8241 (t) REVERT: A 209 THR cc_start: 0.8727 (p) cc_final: 0.8439 (t) REVERT: A 288 ASP cc_start: 0.8544 (t0) cc_final: 0.8326 (t0) REVERT: A 290 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8612 (p) REVERT: A 333 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8964 (tt) REVERT: A 419 MET cc_start: 0.8954 (mmm) cc_final: 0.8576 (mmt) REVERT: A 446 CYS cc_start: 0.8481 (m) cc_final: 0.8013 (m) REVERT: A 529 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8660 (tm-30) REVERT: A 555 MET cc_start: 0.7947 (mtp) cc_final: 0.7589 (mtm) REVERT: A 561 ASN cc_start: 0.8902 (m-40) cc_final: 0.7813 (t0) REVERT: A 562 MET cc_start: 0.8850 (mmm) cc_final: 0.8598 (mmm) REVERT: A 616 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6936 (pttm) REVERT: A 682 GLU cc_start: 0.7165 (tt0) cc_final: 0.6900 (tt0) REVERT: A 710 TRP cc_start: 0.7529 (OUTLIER) cc_final: 0.7209 (p-90) REVERT: A 739 TRP cc_start: 0.8334 (OUTLIER) cc_final: 0.7645 (t-100) REVERT: B 133 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: B 209 THR cc_start: 0.8669 (p) cc_final: 0.8348 (t) REVERT: B 282 MET cc_start: 0.8011 (mmm) cc_final: 0.7694 (mmm) REVERT: B 288 ASP cc_start: 0.8297 (t0) cc_final: 0.7591 (p0) REVERT: B 290 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8655 (p) REVERT: B 346 GLN cc_start: 0.8835 (mt0) cc_final: 0.7933 (mt0) REVERT: B 419 MET cc_start: 0.8949 (mmm) cc_final: 0.8569 (mmt) REVERT: B 446 CYS cc_start: 0.8422 (m) cc_final: 0.7894 (m) REVERT: B 555 MET cc_start: 0.8016 (mtp) cc_final: 0.7605 (mtm) REVERT: B 561 ASN cc_start: 0.8838 (m-40) cc_final: 0.7758 (t0) REVERT: B 562 MET cc_start: 0.8994 (mmm) cc_final: 0.8635 (mmm) REVERT: B 611 LYS cc_start: 0.2964 (tmtt) cc_final: 0.2726 (tmtt) REVERT: B 739 TRP cc_start: 0.8325 (OUTLIER) cc_final: 0.7689 (t-100) REVERT: C 133 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: C 137 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8476 (pm20) REVERT: C 171 CYS cc_start: 0.8821 (t) cc_final: 0.8318 (t) REVERT: C 209 THR cc_start: 0.8586 (p) cc_final: 0.8317 (t) REVERT: C 282 MET cc_start: 0.8037 (mmm) cc_final: 0.7735 (mmm) REVERT: C 288 ASP cc_start: 0.8453 (t0) cc_final: 0.7579 (p0) REVERT: C 290 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8678 (p) REVERT: C 419 MET cc_start: 0.8976 (mmm) cc_final: 0.8494 (mmt) REVERT: C 446 CYS cc_start: 0.8469 (m) cc_final: 0.7921 (m) REVERT: C 479 MET cc_start: 0.7747 (mtp) cc_final: 0.7440 (mpp) REVERT: C 481 TRP cc_start: 0.6238 (p-90) cc_final: 0.6036 (p-90) REVERT: C 555 MET cc_start: 0.8083 (mtp) cc_final: 0.7755 (mtm) REVERT: C 598 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9188 (tp) REVERT: C 739 TRP cc_start: 0.8348 (OUTLIER) cc_final: 0.7677 (t-100) REVERT: D 141 ASP cc_start: 0.8432 (m-30) cc_final: 0.8217 (m-30) REVERT: D 171 CYS cc_start: 0.8833 (t) cc_final: 0.8263 (t) REVERT: D 209 THR cc_start: 0.8705 (p) cc_final: 0.8433 (t) REVERT: D 282 MET cc_start: 0.7824 (mmm) cc_final: 0.7545 (mmm) REVERT: D 288 ASP cc_start: 0.8411 (t0) cc_final: 0.8169 (t0) REVERT: D 290 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8631 (p) REVERT: D 293 ASP cc_start: 0.8143 (t0) cc_final: 0.7907 (t0) REVERT: D 297 ASN cc_start: 0.8951 (m-40) cc_final: 0.8694 (m-40) REVERT: D 346 GLN cc_start: 0.8816 (mt0) cc_final: 0.7959 (mt0) REVERT: D 360 ILE cc_start: 0.9244 (mt) cc_final: 0.9003 (tt) REVERT: D 419 MET cc_start: 0.9016 (mmm) cc_final: 0.8549 (mmt) REVERT: D 446 CYS cc_start: 0.8543 (m) cc_final: 0.8084 (m) REVERT: D 555 MET cc_start: 0.8029 (mtp) cc_final: 0.7689 (mtm) REVERT: D 561 ASN cc_start: 0.8859 (m-40) cc_final: 0.7861 (t0) REVERT: D 610 GLU cc_start: 0.6817 (tp30) cc_final: 0.6533 (tp30) REVERT: D 616 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7215 (pttm) REVERT: D 631 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7844 (tm-30) REVERT: D 702 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7891 (mm-30) REVERT: D 722 LYS cc_start: 0.6681 (mttt) cc_final: 0.6445 (mttp) REVERT: D 739 TRP cc_start: 0.8295 (OUTLIER) cc_final: 0.7636 (t-100) outliers start: 109 outliers final: 61 residues processed: 523 average time/residue: 0.2948 time to fit residues: 246.2098 Evaluate side-chains 489 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 410 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 739 TRP Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 739 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 739 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 LYS Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 TRP Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 739 TRP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 742 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.8980 chunk 222 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 chunk 114 optimal weight: 0.0070 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21472 Z= 0.178 Angle : 0.750 13.830 29036 Z= 0.363 Chirality : 0.041 0.266 3292 Planarity : 0.004 0.053 3616 Dihedral : 6.994 56.627 2836 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.40 % Favored : 87.28 % Rotamer: Outliers : 4.64 % Allowed : 21.85 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.60 (0.17), residues: 2556 helix: 0.34 (0.14), residues: 1456 sheet: -2.27 (0.57), residues: 76 loop : -3.15 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 710 HIS 0.002 0.001 HIS B 160 PHE 0.032 0.001 PHE D 666 TYR 0.020 0.001 TYR A 661 ARG 0.005 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 445 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8231 (t) REVERT: A 209 THR cc_start: 0.8614 (p) cc_final: 0.8362 (t) REVERT: A 288 ASP cc_start: 0.8622 (t0) cc_final: 0.8121 (t0) REVERT: A 291 SER cc_start: 0.8616 (t) cc_final: 0.8119 (p) REVERT: A 346 GLN cc_start: 0.8797 (mt0) cc_final: 0.7949 (mt0) REVERT: A 370 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8173 (pp) REVERT: A 419 MET cc_start: 0.8925 (mmm) cc_final: 0.8522 (mmt) REVERT: A 481 TRP cc_start: 0.6078 (p-90) cc_final: 0.5869 (p-90) REVERT: A 529 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8560 (tm-30) REVERT: A 555 MET cc_start: 0.7825 (mtp) cc_final: 0.7458 (mtm) REVERT: A 561 ASN cc_start: 0.8885 (m-40) cc_final: 0.7921 (t0) REVERT: A 616 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7027 (pttm) REVERT: A 710 TRP cc_start: 0.7445 (OUTLIER) cc_final: 0.7137 (p-90) REVERT: A 739 TRP cc_start: 0.8283 (OUTLIER) cc_final: 0.7694 (t-100) REVERT: B 133 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: B 171 CYS cc_start: 0.8808 (t) cc_final: 0.8254 (t) REVERT: B 209 THR cc_start: 0.8564 (p) cc_final: 0.8290 (t) REVERT: B 288 ASP cc_start: 0.8304 (t0) cc_final: 0.7576 (p0) REVERT: B 290 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 346 GLN cc_start: 0.8742 (mt0) cc_final: 0.7864 (mt0) REVERT: B 419 MET cc_start: 0.8924 (mmm) cc_final: 0.8515 (mmt) REVERT: B 555 MET cc_start: 0.7995 (mtp) cc_final: 0.7597 (mtm) REVERT: B 561 ASN cc_start: 0.8823 (m-40) cc_final: 0.7834 (t0) REVERT: B 562 MET cc_start: 0.9091 (mmm) cc_final: 0.8635 (mmm) REVERT: B 574 MET cc_start: 0.8866 (mmp) cc_final: 0.8629 (mmt) REVERT: B 611 LYS cc_start: 0.2642 (tmtt) cc_final: 0.2363 (tmtt) REVERT: B 629 VAL cc_start: 0.9510 (t) cc_final: 0.9275 (p) REVERT: B 739 TRP cc_start: 0.8375 (OUTLIER) cc_final: 0.7843 (t-100) REVERT: C 133 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: C 137 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: C 171 CYS cc_start: 0.8782 (t) cc_final: 0.8296 (t) REVERT: C 209 THR cc_start: 0.8589 (p) cc_final: 0.8323 (t) REVERT: C 282 MET cc_start: 0.8024 (mmm) cc_final: 0.7634 (mmm) REVERT: C 288 ASP cc_start: 0.8427 (t0) cc_final: 0.8033 (t0) REVERT: C 290 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8538 (p) REVERT: C 297 ASN cc_start: 0.8957 (m-40) cc_final: 0.8675 (m-40) REVERT: C 346 GLN cc_start: 0.8774 (mt0) cc_final: 0.7890 (mt0) REVERT: C 370 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8173 (pp) REVERT: C 479 MET cc_start: 0.7682 (mtp) cc_final: 0.7353 (mpp) REVERT: C 555 MET cc_start: 0.8045 (mtp) cc_final: 0.7691 (mtm) REVERT: C 561 ASN cc_start: 0.8902 (m-40) cc_final: 0.7859 (t0) REVERT: C 611 LYS cc_start: 0.3738 (tmtt) cc_final: 0.3527 (tmtt) REVERT: C 616 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7007 (pttm) REVERT: C 739 TRP cc_start: 0.8309 (OUTLIER) cc_final: 0.7738 (t-100) REVERT: D 137 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8364 (pm20) REVERT: D 141 ASP cc_start: 0.8490 (m-30) cc_final: 0.8225 (m-30) REVERT: D 148 ARG cc_start: 0.7394 (tpt170) cc_final: 0.7097 (tpt90) REVERT: D 171 CYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8188 (t) REVERT: D 209 THR cc_start: 0.8603 (p) cc_final: 0.8360 (t) REVERT: D 282 MET cc_start: 0.7908 (mmm) cc_final: 0.7610 (mmm) REVERT: D 290 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8588 (p) REVERT: D 346 GLN cc_start: 0.8795 (mt0) cc_final: 0.8074 (mt0) REVERT: D 446 CYS cc_start: 0.8512 (m) cc_final: 0.8029 (m) REVERT: D 481 TRP cc_start: 0.5840 (p-90) cc_final: 0.5479 (p-90) REVERT: D 532 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9217 (tp) REVERT: D 555 MET cc_start: 0.7990 (mtp) cc_final: 0.7637 (mtm) REVERT: D 561 ASN cc_start: 0.8821 (m-40) cc_final: 0.7792 (t0) REVERT: D 598 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9127 (tp) REVERT: D 610 GLU cc_start: 0.6799 (tp30) cc_final: 0.6494 (tp30) REVERT: D 616 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7238 (pttm) REVERT: D 631 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7859 (tm-30) REVERT: D 739 TRP cc_start: 0.8288 (OUTLIER) cc_final: 0.7732 (t-100) outliers start: 106 outliers final: 60 residues processed: 516 average time/residue: 0.2895 time to fit residues: 238.6729 Evaluate side-chains 489 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 408 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 TRP Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 739 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 739 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 616 LYS Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 TRP Chi-restraints excluded: chain D residue 739 TRP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 742 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 154 optimal weight: 0.0970 chunk 150 optimal weight: 1.9990 chunk 113 optimal weight: 0.0010 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.6130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21472 Z= 0.184 Angle : 0.750 13.041 29036 Z= 0.362 Chirality : 0.041 0.172 3292 Planarity : 0.004 0.050 3616 Dihedral : 6.810 57.204 2836 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.97 % Favored : 87.72 % Rotamer: Outliers : 4.38 % Allowed : 22.55 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2556 helix: 0.49 (0.14), residues: 1452 sheet: -2.41 (0.55), residues: 76 loop : -3.07 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 710 HIS 0.002 0.001 HIS C 256 PHE 0.027 0.001 PHE D 666 TYR 0.018 0.001 TYR A 575 ARG 0.003 0.000 ARG A 714 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 420 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8602 (pm20) REVERT: A 148 ARG cc_start: 0.7436 (tpt170) cc_final: 0.7232 (tmt-80) REVERT: A 171 CYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8220 (t) REVERT: A 209 THR cc_start: 0.8570 (p) cc_final: 0.8291 (t) REVERT: A 282 MET cc_start: 0.7978 (mmm) cc_final: 0.7481 (mmm) REVERT: A 346 GLN cc_start: 0.8862 (mt0) cc_final: 0.7961 (mt0) REVERT: A 370 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8203 (pp) REVERT: A 529 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8556 (tm-30) REVERT: A 555 MET cc_start: 0.7793 (mtp) cc_final: 0.7362 (mtm) REVERT: A 561 ASN cc_start: 0.8872 (m-40) cc_final: 0.7955 (t0) REVERT: A 562 MET cc_start: 0.9039 (mmm) cc_final: 0.8682 (mmm) REVERT: A 616 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7230 (tptp) REVERT: A 656 PHE cc_start: 0.8521 (m-10) cc_final: 0.8226 (m-80) REVERT: A 702 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7731 (mm-30) REVERT: A 710 TRP cc_start: 0.7158 (OUTLIER) cc_final: 0.6807 (t-100) REVERT: A 722 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.6023 (mttm) REVERT: A 739 TRP cc_start: 0.8433 (OUTLIER) cc_final: 0.7882 (t-100) REVERT: B 171 CYS cc_start: 0.8794 (t) cc_final: 0.8261 (t) REVERT: B 209 THR cc_start: 0.8522 (p) cc_final: 0.8223 (t) REVERT: B 276 GLU cc_start: 0.8510 (pm20) cc_final: 0.8243 (pm20) REVERT: B 288 ASP cc_start: 0.8242 (t0) cc_final: 0.7937 (t0) REVERT: B 290 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8320 (p) REVERT: B 293 ASP cc_start: 0.7957 (t0) cc_final: 0.7672 (t0) REVERT: B 297 ASN cc_start: 0.8904 (m-40) cc_final: 0.8626 (m-40) REVERT: B 346 GLN cc_start: 0.8799 (mt0) cc_final: 0.7892 (mt0) REVERT: B 370 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8176 (pp) REVERT: B 479 MET cc_start: 0.6007 (mpp) cc_final: 0.5470 (mpp) REVERT: B 555 MET cc_start: 0.7856 (mtp) cc_final: 0.7468 (mtm) REVERT: B 562 MET cc_start: 0.9078 (mmm) cc_final: 0.8666 (mmm) REVERT: B 702 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7801 (mm-30) REVERT: B 739 TRP cc_start: 0.8424 (OUTLIER) cc_final: 0.7930 (t-100) REVERT: C 171 CYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8182 (t) REVERT: C 288 ASP cc_start: 0.8472 (t0) cc_final: 0.8137 (t0) REVERT: C 290 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8601 (p) REVERT: C 370 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8191 (pp) REVERT: C 419 MET cc_start: 0.9171 (mmm) cc_final: 0.8420 (mmt) REVERT: C 479 MET cc_start: 0.7599 (mtp) cc_final: 0.7358 (mpp) REVERT: C 481 TRP cc_start: 0.5948 (p-90) cc_final: 0.5504 (p-90) REVERT: C 555 MET cc_start: 0.7999 (mtp) cc_final: 0.7639 (mtm) REVERT: C 561 ASN cc_start: 0.8889 (m-40) cc_final: 0.7880 (t0) REVERT: C 611 LYS cc_start: 0.3752 (tmtt) cc_final: 0.3521 (tmtt) REVERT: C 616 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7128 (pttm) REVERT: C 739 TRP cc_start: 0.8301 (OUTLIER) cc_final: 0.7722 (t-100) REVERT: D 137 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: D 141 ASP cc_start: 0.8421 (m-30) cc_final: 0.8128 (m-30) REVERT: D 171 CYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8194 (t) REVERT: D 209 THR cc_start: 0.8579 (p) cc_final: 0.8306 (t) REVERT: D 282 MET cc_start: 0.7892 (mmm) cc_final: 0.7605 (mmm) REVERT: D 290 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8633 (p) REVERT: D 346 GLN cc_start: 0.8844 (mt0) cc_final: 0.8377 (mt0) REVERT: D 419 MET cc_start: 0.9206 (mmm) cc_final: 0.8515 (mmt) REVERT: D 532 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9205 (tp) REVERT: D 555 MET cc_start: 0.7893 (mtp) cc_final: 0.7615 (mtm) REVERT: D 598 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9116 (tp) REVERT: D 610 GLU cc_start: 0.6791 (tp30) cc_final: 0.6486 (tp30) REVERT: D 616 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7224 (pttm) REVERT: D 632 LEU cc_start: 0.9238 (tt) cc_final: 0.9015 (tt) REVERT: D 656 PHE cc_start: 0.8411 (m-80) cc_final: 0.8124 (m-80) REVERT: D 702 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7811 (mm-30) REVERT: D 739 TRP cc_start: 0.8397 (OUTLIER) cc_final: 0.7961 (t-100) outliers start: 100 outliers final: 56 residues processed: 488 average time/residue: 0.3018 time to fit residues: 234.0355 Evaluate side-chains 461 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 383 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 TRP Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 739 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 739 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 616 LYS Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 TRP Chi-restraints excluded: chain D residue 739 TRP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 742 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.6283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21472 Z= 0.202 Angle : 0.763 13.051 29036 Z= 0.368 Chirality : 0.042 0.342 3292 Planarity : 0.004 0.050 3616 Dihedral : 6.743 59.871 2836 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.32 % Favored : 87.36 % Rotamer: Outliers : 4.29 % Allowed : 23.07 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.33 (0.17), residues: 2556 helix: 0.60 (0.14), residues: 1444 sheet: -2.48 (0.56), residues: 76 loop : -3.03 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 742 HIS 0.003 0.001 HIS C 417 PHE 0.031 0.001 PHE A 666 TYR 0.024 0.001 TYR C 661 ARG 0.003 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 394 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8608 (pm20) REVERT: A 171 CYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8267 (t) REVERT: A 209 THR cc_start: 0.8612 (p) cc_final: 0.8310 (t) REVERT: A 276 GLU cc_start: 0.8547 (pm20) cc_final: 0.8167 (pm20) REVERT: A 290 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8054 (p) REVERT: A 293 ASP cc_start: 0.7891 (t70) cc_final: 0.7187 (t0) REVERT: A 370 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8245 (pp) REVERT: A 479 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6342 (mpp) REVERT: A 561 ASN cc_start: 0.8888 (m-40) cc_final: 0.8019 (t0) REVERT: A 616 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7310 (tptt) REVERT: A 656 PHE cc_start: 0.8529 (m-10) cc_final: 0.8192 (m-80) REVERT: A 710 TRP cc_start: 0.7193 (OUTLIER) cc_final: 0.6884 (t-100) REVERT: A 722 LYS cc_start: 0.6235 (OUTLIER) cc_final: 0.6025 (mttm) REVERT: A 739 TRP cc_start: 0.8435 (OUTLIER) cc_final: 0.7882 (t-100) REVERT: B 171 CYS cc_start: 0.8827 (t) cc_final: 0.8263 (t) REVERT: B 288 ASP cc_start: 0.8374 (t0) cc_final: 0.8040 (t0) REVERT: B 290 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8675 (p) REVERT: B 370 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8190 (pp) REVERT: B 479 MET cc_start: 0.6214 (mpp) cc_final: 0.5675 (mpp) REVERT: B 538 PHE cc_start: 0.8116 (m-80) cc_final: 0.7847 (m-10) REVERT: B 562 MET cc_start: 0.9112 (mmm) cc_final: 0.8705 (mmm) REVERT: B 574 MET cc_start: 0.8487 (mmt) cc_final: 0.8171 (mmm) REVERT: B 732 LEU cc_start: 0.8031 (mt) cc_final: 0.7798 (mt) REVERT: B 739 TRP cc_start: 0.8439 (OUTLIER) cc_final: 0.7948 (t-100) REVERT: B 748 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.5989 (m-80) REVERT: C 276 GLU cc_start: 0.8548 (pm20) cc_final: 0.8155 (pm20) REVERT: C 288 ASP cc_start: 0.8442 (t0) cc_final: 0.8125 (t0) REVERT: C 290 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8559 (p) REVERT: C 370 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8254 (pp) REVERT: C 555 MET cc_start: 0.8092 (mtp) cc_final: 0.7731 (mtm) REVERT: C 561 ASN cc_start: 0.8883 (m-40) cc_final: 0.7920 (t0) REVERT: C 616 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7202 (tptt) REVERT: C 702 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7773 (mm-30) REVERT: C 739 TRP cc_start: 0.8420 (OUTLIER) cc_final: 0.7847 (t-100) REVERT: D 137 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8621 (pm20) REVERT: D 148 ARG cc_start: 0.7468 (tpt170) cc_final: 0.7089 (tpt90) REVERT: D 288 ASP cc_start: 0.8562 (t0) cc_final: 0.8198 (t0) REVERT: D 290 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8619 (p) REVERT: D 346 GLN cc_start: 0.8818 (mt0) cc_final: 0.8430 (mt0) REVERT: D 419 MET cc_start: 0.9215 (mmm) cc_final: 0.8544 (mmt) REVERT: D 555 MET cc_start: 0.7873 (mtp) cc_final: 0.7662 (mtp) REVERT: D 561 ASN cc_start: 0.8735 (t0) cc_final: 0.7839 (t0) REVERT: D 574 MET cc_start: 0.8852 (mmp) cc_final: 0.8607 (mmt) REVERT: D 610 GLU cc_start: 0.6776 (tp30) cc_final: 0.6491 (tp30) REVERT: D 656 PHE cc_start: 0.8410 (m-80) cc_final: 0.8150 (m-80) REVERT: D 739 TRP cc_start: 0.8390 (OUTLIER) cc_final: 0.7923 (t-100) outliers start: 98 outliers final: 60 residues processed: 459 average time/residue: 0.2847 time to fit residues: 208.6281 Evaluate side-chains 463 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 383 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 739 TRP Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 739 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 739 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 TRP Chi-restraints excluded: chain D residue 739 TRP Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 742 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 chunk 215 optimal weight: 0.0570 chunk 229 optimal weight: 5.9990 chunk 138 optimal weight: 0.2980 chunk 100 optimal weight: 20.0000 chunk 180 optimal weight: 0.0020 chunk 70 optimal weight: 0.1980 chunk 207 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.2906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21472 Z= 0.178 Angle : 0.773 14.623 29036 Z= 0.369 Chirality : 0.041 0.352 3292 Planarity : 0.004 0.048 3616 Dihedral : 6.607 60.553 2836 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.42 % Favored : 88.26 % Rotamer: Outliers : 3.55 % Allowed : 24.34 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.17), residues: 2556 helix: 0.65 (0.14), residues: 1456 sheet: -2.48 (0.55), residues: 76 loop : -2.97 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 710 HIS 0.002 0.000 HIS A 745 PHE 0.025 0.001 PHE A 666 TYR 0.021 0.001 TYR A 575 ARG 0.002 0.000 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 424 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8823 (pp) cc_final: 0.8555 (pt) REVERT: A 159 MET cc_start: 0.8375 (mpp) cc_final: 0.8113 (mmt) REVERT: A 209 THR cc_start: 0.8582 (p) cc_final: 0.8280 (t) REVERT: A 293 ASP cc_start: 0.7873 (t70) cc_final: 0.7147 (t0) REVERT: A 370 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8079 (pp) REVERT: A 419 MET cc_start: 0.9062 (mmm) cc_final: 0.8368 (mmt) REVERT: A 479 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6227 (mpp) REVERT: A 529 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8541 (tm-30) REVERT: A 561 ASN cc_start: 0.8831 (m-40) cc_final: 0.8035 (t0) REVERT: A 562 MET cc_start: 0.8995 (mmm) cc_final: 0.8572 (mmm) REVERT: A 571 SER cc_start: 0.7993 (p) cc_final: 0.7678 (t) REVERT: A 574 MET cc_start: 0.6943 (mmp) cc_final: 0.6265 (tpp) REVERT: A 656 PHE cc_start: 0.8301 (m-10) cc_final: 0.7938 (m-80) REVERT: A 702 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7783 (mm-30) REVERT: A 710 TRP cc_start: 0.7223 (OUTLIER) cc_final: 0.6977 (t-100) REVERT: A 739 TRP cc_start: 0.8394 (OUTLIER) cc_final: 0.8016 (t-100) REVERT: B 171 CYS cc_start: 0.8720 (t) cc_final: 0.8210 (t) REVERT: B 176 LEU cc_start: 0.9153 (mm) cc_final: 0.8913 (mt) REVERT: B 288 ASP cc_start: 0.8375 (t0) cc_final: 0.8032 (t0) REVERT: B 290 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8416 (p) REVERT: B 360 ILE cc_start: 0.9226 (mt) cc_final: 0.8979 (tt) REVERT: B 370 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8170 (pp) REVERT: B 419 MET cc_start: 0.9061 (mmm) cc_final: 0.8357 (mmt) REVERT: B 479 MET cc_start: 0.6043 (mpp) cc_final: 0.5394 (mpp) REVERT: B 538 PHE cc_start: 0.8137 (m-80) cc_final: 0.7926 (m-10) REVERT: B 555 MET cc_start: 0.8013 (mtp) cc_final: 0.7671 (mtm) REVERT: B 561 ASN cc_start: 0.8769 (m-40) cc_final: 0.7708 (t0) REVERT: B 562 MET cc_start: 0.9089 (mmm) cc_final: 0.8627 (mmm) REVERT: B 571 SER cc_start: 0.8294 (p) cc_final: 0.7973 (t) REVERT: B 739 TRP cc_start: 0.8401 (OUTLIER) cc_final: 0.8018 (t-100) REVERT: B 748 PHE cc_start: 0.6014 (OUTLIER) cc_final: 0.5609 (m-80) REVERT: C 137 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8300 (pm20) REVERT: C 159 MET cc_start: 0.8300 (mpp) cc_final: 0.8093 (mmt) REVERT: C 288 ASP cc_start: 0.8403 (t0) cc_final: 0.8044 (t0) REVERT: C 290 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8320 (p) REVERT: C 370 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8215 (pp) REVERT: C 419 MET cc_start: 0.9203 (mmm) cc_final: 0.8441 (mmt) REVERT: C 479 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6516 (mpp) REVERT: C 538 PHE cc_start: 0.7942 (m-80) cc_final: 0.7725 (m-10) REVERT: C 555 MET cc_start: 0.7912 (mtp) cc_final: 0.7548 (mtm) REVERT: C 561 ASN cc_start: 0.8805 (m-40) cc_final: 0.7897 (t0) REVERT: C 562 MET cc_start: 0.9105 (mmm) cc_final: 0.8621 (mmm) REVERT: C 571 SER cc_start: 0.8194 (p) cc_final: 0.7838 (t) REVERT: C 702 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7748 (mm-30) REVERT: C 739 TRP cc_start: 0.8341 (OUTLIER) cc_final: 0.7993 (t-100) REVERT: D 131 CYS cc_start: 0.8208 (p) cc_final: 0.7989 (p) REVERT: D 137 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8583 (pm20) REVERT: D 282 MET cc_start: 0.7940 (mmm) cc_final: 0.7630 (mmm) REVERT: D 288 ASP cc_start: 0.8179 (t0) cc_final: 0.7852 (t0) REVERT: D 290 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8053 (p) REVERT: D 419 MET cc_start: 0.9202 (mmm) cc_final: 0.8458 (mmt) REVERT: D 532 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9202 (tp) REVERT: D 561 ASN cc_start: 0.8802 (t0) cc_final: 0.7638 (t0) REVERT: D 610 GLU cc_start: 0.6669 (tp30) cc_final: 0.6396 (tp30) REVERT: D 656 PHE cc_start: 0.8309 (m-80) cc_final: 0.8085 (m-80) REVERT: D 702 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7726 (mm-30) REVERT: D 739 TRP cc_start: 0.8391 (OUTLIER) cc_final: 0.8031 (t-100) outliers start: 81 outliers final: 47 residues processed: 474 average time/residue: 0.3112 time to fit residues: 236.8335 Evaluate side-chains 444 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 380 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 739 TRP Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 739 TRP Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 739 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 TRP Chi-restraints excluded: chain D residue 739 TRP Chi-restraints excluded: chain D residue 742 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 chunk 255 optimal weight: 6.9990 chunk 234 optimal weight: 0.8980 chunk 203 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21472 Z= 0.204 Angle : 0.799 14.286 29036 Z= 0.384 Chirality : 0.042 0.337 3292 Planarity : 0.004 0.049 3616 Dihedral : 6.575 62.155 2836 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.17 % Favored : 87.52 % Rotamer: Outliers : 3.06 % Allowed : 25.74 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.17), residues: 2556 helix: 0.65 (0.14), residues: 1460 sheet: -2.42 (0.56), residues: 76 loop : -2.93 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 742 HIS 0.002 0.000 HIS B 417 PHE 0.028 0.001 PHE A 666 TYR 0.024 0.001 TYR D 661 ARG 0.003 0.000 ARG A 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 401 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8353 (mpp) cc_final: 0.8111 (mmt) REVERT: A 288 ASP cc_start: 0.8554 (t0) cc_final: 0.8121 (t0) REVERT: A 293 ASP cc_start: 0.7611 (t70) cc_final: 0.7131 (t0) REVERT: A 370 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8203 (pp) REVERT: A 419 MET cc_start: 0.9144 (mmm) cc_final: 0.8486 (mmt) REVERT: A 479 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6243 (mpp) REVERT: A 555 MET cc_start: 0.7947 (mtp) cc_final: 0.7651 (mtm) REVERT: A 561 ASN cc_start: 0.8829 (m-40) cc_final: 0.8038 (t0) REVERT: A 564 TYR cc_start: 0.8542 (t80) cc_final: 0.8327 (t80) REVERT: A 571 SER cc_start: 0.8047 (p) cc_final: 0.7753 (t) REVERT: A 656 PHE cc_start: 0.8318 (m-10) cc_final: 0.7962 (m-80) REVERT: A 702 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7791 (mm-30) REVERT: A 739 TRP cc_start: 0.8454 (OUTLIER) cc_final: 0.8042 (t-100) REVERT: B 171 CYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8201 (t) REVERT: B 288 ASP cc_start: 0.8447 (t0) cc_final: 0.8106 (t0) REVERT: B 290 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8238 (p) REVERT: B 360 ILE cc_start: 0.9215 (mt) cc_final: 0.8954 (tt) REVERT: B 370 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8193 (pp) REVERT: B 419 MET cc_start: 0.9175 (mmm) cc_final: 0.8458 (mmt) REVERT: B 479 MET cc_start: 0.6014 (mpp) cc_final: 0.5473 (mpp) REVERT: B 538 PHE cc_start: 0.8139 (m-80) cc_final: 0.7933 (m-10) REVERT: B 555 MET cc_start: 0.7975 (mtp) cc_final: 0.7742 (mtm) REVERT: B 562 MET cc_start: 0.9127 (mmm) cc_final: 0.8695 (mmm) REVERT: B 571 SER cc_start: 0.8179 (p) cc_final: 0.7868 (t) REVERT: B 739 TRP cc_start: 0.8394 (OUTLIER) cc_final: 0.8072 (t-100) REVERT: B 748 PHE cc_start: 0.6293 (OUTLIER) cc_final: 0.5851 (m-80) REVERT: C 137 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: C 159 MET cc_start: 0.8303 (mpp) cc_final: 0.8081 (mmt) REVERT: C 288 ASP cc_start: 0.8152 (t0) cc_final: 0.7914 (t0) REVERT: C 290 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8429 (p) REVERT: C 370 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8238 (pp) REVERT: C 419 MET cc_start: 0.9159 (mmm) cc_final: 0.8442 (mmt) REVERT: C 479 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6608 (mpp) REVERT: C 538 PHE cc_start: 0.8019 (m-80) cc_final: 0.7814 (m-10) REVERT: C 555 MET cc_start: 0.7945 (mtp) cc_final: 0.7578 (mtm) REVERT: C 561 ASN cc_start: 0.8832 (m-40) cc_final: 0.7944 (t0) REVERT: C 571 SER cc_start: 0.8135 (p) cc_final: 0.7765 (t) REVERT: C 702 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7785 (mm-30) REVERT: C 739 TRP cc_start: 0.8421 (OUTLIER) cc_final: 0.8081 (t-100) REVERT: D 137 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8578 (pm20) REVERT: D 282 MET cc_start: 0.7872 (mmm) cc_final: 0.7628 (mmm) REVERT: D 288 ASP cc_start: 0.8299 (t0) cc_final: 0.7975 (t0) REVERT: D 290 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7928 (p) REVERT: D 419 MET cc_start: 0.9238 (mmm) cc_final: 0.8531 (mmt) REVERT: D 561 ASN cc_start: 0.8770 (t0) cc_final: 0.7728 (t0) REVERT: D 574 MET cc_start: 0.8835 (mmp) cc_final: 0.8536 (mmt) REVERT: D 610 GLU cc_start: 0.6643 (tp30) cc_final: 0.6316 (tp30) REVERT: D 656 PHE cc_start: 0.8314 (m-80) cc_final: 0.8111 (m-80) REVERT: D 702 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7682 (mm-30) REVERT: D 739 TRP cc_start: 0.8379 (OUTLIER) cc_final: 0.7991 (t-100) outliers start: 70 outliers final: 41 residues processed: 449 average time/residue: 0.2875 time to fit residues: 207.5021 Evaluate side-chains 449 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 392 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 739 TRP Chi-restraints excluded: chain A residue 750 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 739 TRP Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 739 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 TRP Chi-restraints excluded: chain D residue 739 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 178 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.120296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099271 restraints weight = 48809.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101594 restraints weight = 30967.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103219 restraints weight = 22860.386| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.6772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 21472 Z= 0.298 Angle : 0.922 59.163 29036 Z= 0.481 Chirality : 0.042 0.331 3292 Planarity : 0.004 0.049 3616 Dihedral : 6.577 62.163 2836 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.09 % Favored : 87.60 % Rotamer: Outliers : 2.85 % Allowed : 26.14 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.19 (0.17), residues: 2556 helix: 0.66 (0.14), residues: 1460 sheet: -2.42 (0.56), residues: 76 loop : -2.94 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 742 HIS 0.002 0.000 HIS B 417 PHE 0.025 0.001 PHE A 666 TYR 0.022 0.001 TYR D 661 ARG 0.003 0.000 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4794.41 seconds wall clock time: 87 minutes 57.14 seconds (5277.14 seconds total)