Starting phenix.real_space_refine on Sun Feb 18 07:00:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b16_11979/02_2024/7b16_11979_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b16_11979/02_2024/7b16_11979.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b16_11979/02_2024/7b16_11979_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b16_11979/02_2024/7b16_11979_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b16_11979/02_2024/7b16_11979_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b16_11979/02_2024/7b16_11979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b16_11979/02_2024/7b16_11979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b16_11979/02_2024/7b16_11979_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b16_11979/02_2024/7b16_11979_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 Cl 4 4.86 5 C 13844 2.51 5 N 3456 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A ARG 710": "NH1" <-> "NH2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B ARG 710": "NH1" <-> "NH2" Residue "B GLU 737": "OE1" <-> "OE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C GLU 403": "OE1" <-> "OE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 632": "OD1" <-> "OD2" Residue "C GLU 634": "OE1" <-> "OE2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C ARG 710": "NH1" <-> "NH2" Residue "C GLU 737": "OE1" <-> "OE2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "D PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 403": "OE1" <-> "OE2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "D TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 632": "OD1" <-> "OD2" Residue "D GLU 634": "OE1" <-> "OE2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D ARG 710": "NH1" <-> "NH2" Residue "D GLU 737": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21152 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5222 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5222 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5222 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5222 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {' CA': 1, 'LPP': 1, 'SKQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {' CA': 1, 'LPP': 1, 'SKQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {' CA': 1, 'LPP': 1, 'SKQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {' CA': 1, 'LPP': 1, 'SKQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 11.08, per 1000 atoms: 0.52 Number of scatterers: 21152 At special positions: 0 Unit cell: (139.23, 139.23, 139.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 Cl 4 17.00 S 108 16.00 P 4 15.00 O 3732 8.00 N 3456 7.00 C 13844 6.00 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=0, symmetry=0 Time building additional restraints: 7.78 Conformation dependent library (CDL) restraints added in 3.6 seconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 0 sheets defined 65.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'A' and resid 31 through 42 removed outlier: 3.656A pdb=" N TYR A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.826A pdb=" N ILE A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.904A pdb=" N LYS A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 216 through 233 removed outlier: 4.209A pdb=" N LYS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.967A pdb=" N LYS A 238 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA A 239 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 251 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 252 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 removed outlier: 3.772A pdb=" N ILE A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.568A pdb=" N LEU A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.670A pdb=" N CYS A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 362 through 383 Processing helix chain 'A' and resid 403 through 424 Proline residue: A 408 - end of helix removed outlier: 3.546A pdb=" N GLY A 424 " --> pdb=" O GLN A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 457 removed outlier: 3.585A pdb=" N ILE A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 497 removed outlier: 3.659A pdb=" N PHE A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ILE A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N SER A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 514 through 538 removed outlier: 4.127A pdb=" N LYS A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 526 " --> pdb=" O ILE A 522 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 536 " --> pdb=" O ASN A 532 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 572 Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 593 through 609 removed outlier: 3.576A pdb=" N ALA A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 627 removed outlier: 3.835A pdb=" N GLN A 625 " --> pdb=" O ASN A 621 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 646 removed outlier: 4.066A pdb=" N TYR A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 719 removed outlier: 3.836A pdb=" N HIS A 703 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 752 removed outlier: 3.634A pdb=" N ILE A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.656A pdb=" N TYR B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.826A pdb=" N ILE B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 79 Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 99 through 106 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 155 through 164 removed outlier: 3.904A pdb=" N LYS B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 216 through 233 removed outlier: 4.209A pdb=" N LYS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 256 removed outlier: 3.967A pdb=" N LYS B 238 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA B 239 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B 240 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 251 " --> pdb=" O CYS B 248 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 252 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.773A pdb=" N ILE B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 298 through 301 No H-bonds generated for 'chain 'B' and resid 298 through 301' Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.568A pdb=" N LEU B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.669A pdb=" N CYS B 333 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 335 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 337 " --> pdb=" O CYS B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 347 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 362 through 383 Processing helix chain 'B' and resid 403 through 424 Proline residue: B 408 - end of helix removed outlier: 3.587A pdb=" N GLY B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 457 removed outlier: 3.585A pdb=" N ILE B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR B 456 " --> pdb=" O LYS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 497 removed outlier: 3.659A pdb=" N PHE B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N SER B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 514 through 538 removed outlier: 4.127A pdb=" N LYS B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 526 " --> pdb=" O ILE B 522 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 536 " --> pdb=" O ASN B 532 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 537 " --> pdb=" O GLY B 533 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 572 Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 593 through 609 removed outlier: 3.576A pdb=" N ALA B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 627 removed outlier: 3.836A pdb=" N GLN B 625 " --> pdb=" O ASN B 621 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 646 removed outlier: 4.065A pdb=" N TYR B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 719 removed outlier: 3.837A pdb=" N HIS B 703 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN B 704 " --> pdb=" O ARG B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 removed outlier: 3.635A pdb=" N ILE B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 42 removed outlier: 3.656A pdb=" N TYR C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.826A pdb=" N ILE C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'C' and resid 99 through 106 Processing helix chain 'C' and resid 109 through 116 Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'C' and resid 155 through 164 removed outlier: 3.904A pdb=" N LYS C 164 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 216 through 233 removed outlier: 4.209A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 256 removed outlier: 3.966A pdb=" N LYS C 238 " --> pdb=" O ASN C 235 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA C 239 " --> pdb=" O GLU C 236 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 240 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE C 251 " --> pdb=" O CYS C 248 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 252 " --> pdb=" O LYS C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 269 removed outlier: 3.772A pdb=" N ILE C 268 " --> pdb=" O GLU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 298 through 301 No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.568A pdb=" N LEU C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 311 " --> pdb=" O GLN C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 338 removed outlier: 3.669A pdb=" N CYS C 333 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE C 335 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 337 " --> pdb=" O CYS C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 347 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 362 through 383 Processing helix chain 'C' and resid 403 through 424 Proline residue: C 408 - end of helix removed outlier: 3.546A pdb=" N GLY C 424 " --> pdb=" O GLN C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 457 removed outlier: 3.585A pdb=" N ILE C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR C 456 " --> pdb=" O LYS C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 497 removed outlier: 3.659A pdb=" N PHE C 487 " --> pdb=" O ILE C 483 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE C 493 " --> pdb=" O SER C 489 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N SER C 494 " --> pdb=" O LEU C 490 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 514 through 538 removed outlier: 4.127A pdb=" N LYS C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 525 " --> pdb=" O PHE C 521 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 526 " --> pdb=" O ILE C 522 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C 536 " --> pdb=" O ASN C 532 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 537 " --> pdb=" O GLY C 533 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 572 Processing helix chain 'C' and resid 581 through 583 No H-bonds generated for 'chain 'C' and resid 581 through 583' Processing helix chain 'C' and resid 593 through 609 removed outlier: 3.576A pdb=" N ALA C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 627 removed outlier: 3.836A pdb=" N GLN C 625 " --> pdb=" O ASN C 621 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS C 626 " --> pdb=" O ASN C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 646 removed outlier: 4.065A pdb=" N TYR C 646 " --> pdb=" O LEU C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 719 removed outlier: 3.837A pdb=" N HIS C 703 " --> pdb=" O VAL C 699 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 752 removed outlier: 3.635A pdb=" N ILE C 742 " --> pdb=" O LEU C 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 42 removed outlier: 3.656A pdb=" N TYR D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 58 removed outlier: 3.826A pdb=" N ILE D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 79 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 99 through 106 Processing helix chain 'D' and resid 109 through 116 Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 155 through 164 removed outlier: 3.904A pdb=" N LYS D 164 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 203 Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 216 through 233 removed outlier: 4.209A pdb=" N LYS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.967A pdb=" N LYS D 238 " --> pdb=" O ASN D 235 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA D 239 " --> pdb=" O GLU D 236 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU D 240 " --> pdb=" O PHE D 237 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE D 251 " --> pdb=" O CYS D 248 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA D 252 " --> pdb=" O LYS D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 269 removed outlier: 3.772A pdb=" N ILE D 268 " --> pdb=" O GLU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 298 through 301 No H-bonds generated for 'chain 'D' and resid 298 through 301' Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.568A pdb=" N LEU D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA D 311 " --> pdb=" O GLN D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 338 removed outlier: 3.670A pdb=" N CYS D 333 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 335 " --> pdb=" O ILE D 331 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY D 337 " --> pdb=" O CYS D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 362 through 383 Processing helix chain 'D' and resid 403 through 424 Proline residue: D 408 - end of helix removed outlier: 3.547A pdb=" N GLY D 424 " --> pdb=" O GLN D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 457 removed outlier: 3.585A pdb=" N ILE D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL D 454 " --> pdb=" O SER D 450 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR D 456 " --> pdb=" O LYS D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 497 removed outlier: 3.659A pdb=" N PHE D 487 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU D 492 " --> pdb=" O SER D 488 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ILE D 493 " --> pdb=" O SER D 489 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N SER D 494 " --> pdb=" O LEU D 490 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU D 495 " --> pdb=" O ARG D 491 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR D 497 " --> pdb=" O ILE D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 514 through 538 removed outlier: 4.127A pdb=" N LYS D 518 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 525 " --> pdb=" O PHE D 521 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL D 526 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN D 536 " --> pdb=" O ASN D 532 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 537 " --> pdb=" O GLY D 533 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 572 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 593 through 609 removed outlier: 3.575A pdb=" N ALA D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 627 removed outlier: 3.835A pdb=" N GLN D 625 " --> pdb=" O ASN D 621 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS D 626 " --> pdb=" O ASN D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 646 removed outlier: 4.066A pdb=" N TYR D 646 " --> pdb=" O LEU D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 719 removed outlier: 3.836A pdb=" N HIS D 703 " --> pdb=" O VAL D 699 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN D 704 " --> pdb=" O ARG D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 752 removed outlier: 3.634A pdb=" N ILE D 742 " --> pdb=" O LEU D 738 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2844 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: 5.61 Time building geometry restraints manager: 8.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 3324 1.31 - 1.45: 5989 1.45 - 1.59: 12127 1.59 - 1.73: 32 1.73 - 1.87: 180 Bond restraints: 21652 Sorted by residual: bond pdb=" C11 SKQ B1002 " pdb=" N10 SKQ B1002 " ideal model delta sigma weight residual 1.287 1.551 -0.264 2.00e-02 2.50e+03 1.75e+02 bond pdb=" C11 SKQ D1002 " pdb=" N10 SKQ D1002 " ideal model delta sigma weight residual 1.287 1.551 -0.264 2.00e-02 2.50e+03 1.75e+02 bond pdb=" C11 SKQ C1002 " pdb=" N10 SKQ C1002 " ideal model delta sigma weight residual 1.287 1.551 -0.264 2.00e-02 2.50e+03 1.75e+02 bond pdb=" C11 SKQ A1001 " pdb=" N10 SKQ A1001 " ideal model delta sigma weight residual 1.287 1.551 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" N09 SKQ C1002 " pdb=" N10 SKQ C1002 " ideal model delta sigma weight residual 1.317 1.541 -0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 21647 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.36: 496 106.36 - 113.30: 11892 113.30 - 120.23: 8618 120.23 - 127.17: 8022 127.17 - 134.10: 272 Bond angle restraints: 29300 Sorted by residual: angle pdb=" N ILE C 387 " pdb=" CA ILE C 387 " pdb=" C ILE C 387 " ideal model delta sigma weight residual 112.12 108.95 3.17 8.40e-01 1.42e+00 1.42e+01 angle pdb=" N ILE B 387 " pdb=" CA ILE B 387 " pdb=" C ILE B 387 " ideal model delta sigma weight residual 112.12 108.95 3.17 8.40e-01 1.42e+00 1.42e+01 angle pdb=" N ILE D 387 " pdb=" CA ILE D 387 " pdb=" C ILE D 387 " ideal model delta sigma weight residual 112.12 108.97 3.15 8.40e-01 1.42e+00 1.40e+01 angle pdb=" N ILE A 387 " pdb=" CA ILE A 387 " pdb=" C ILE A 387 " ideal model delta sigma weight residual 112.12 108.97 3.15 8.40e-01 1.42e+00 1.40e+01 angle pdb=" N PRO D 655 " pdb=" CA PRO D 655 " pdb=" C PRO D 655 " ideal model delta sigma weight residual 110.70 114.66 -3.96 1.22e+00 6.72e-01 1.05e+01 ... (remaining 29295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 12173 23.43 - 46.85: 644 46.85 - 70.28: 79 70.28 - 93.71: 16 93.71 - 117.13: 4 Dihedral angle restraints: 12916 sinusoidal: 5320 harmonic: 7596 Sorted by residual: dihedral pdb=" C18 SKQ B1002 " pdb=" C19 SKQ B1002 " pdb=" C20 SKQ B1002 " pdb=" C21 SKQ B1002 " ideal model delta sinusoidal sigma weight residual 63.74 -53.39 117.13 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" C18 SKQ A1001 " pdb=" C19 SKQ A1001 " pdb=" C20 SKQ A1001 " pdb=" C21 SKQ A1001 " ideal model delta sinusoidal sigma weight residual 63.74 -53.38 117.12 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" C18 SKQ C1002 " pdb=" C19 SKQ C1002 " pdb=" C20 SKQ C1002 " pdb=" C21 SKQ C1002 " ideal model delta sinusoidal sigma weight residual 63.74 -53.32 117.06 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 12913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3235 0.122 - 0.244: 37 0.244 - 0.366: 4 0.366 - 0.488: 0 0.488 - 0.610: 4 Chirality restraints: 3280 Sorted by residual: chirality pdb=" C16 SKQ A1001 " pdb=" C17 SKQ A1001 " pdb=" C21 SKQ A1001 " pdb=" N15 SKQ A1001 " both_signs ideal model delta sigma weight residual False -2.38 -2.99 0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" C16 SKQ C1002 " pdb=" C17 SKQ C1002 " pdb=" C21 SKQ C1002 " pdb=" N15 SKQ C1002 " both_signs ideal model delta sigma weight residual False -2.38 -2.99 0.61 2.00e-01 2.50e+01 9.26e+00 chirality pdb=" C16 SKQ B1002 " pdb=" C17 SKQ B1002 " pdb=" C21 SKQ B1002 " pdb=" N15 SKQ B1002 " both_signs ideal model delta sigma weight residual False -2.38 -2.99 0.61 2.00e-01 2.50e+01 9.24e+00 ... (remaining 3277 not shown) Planarity restraints: 3620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 350 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO D 351 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 351 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 351 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 350 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 351 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 351 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 351 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 350 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO C 351 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 351 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 351 " 0.030 5.00e-02 4.00e+02 ... (remaining 3617 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4383 2.77 - 3.30: 19790 3.30 - 3.84: 32175 3.84 - 4.37: 38657 4.37 - 4.90: 67821 Nonbonded interactions: 162826 Sorted by model distance: nonbonded pdb=" NH2 ARG C 746 " pdb=" OE1 GLU D 748 " model vdw 2.239 2.520 nonbonded pdb=" NH2 ARG A 746 " pdb=" OE1 GLU B 748 " model vdw 2.239 2.520 nonbonded pdb=" OE1 GLU A 748 " pdb=" NH2 ARG D 746 " model vdw 2.239 2.520 nonbonded pdb=" NH2 ARG B 746 " pdb=" OE1 GLU C 748 " model vdw 2.240 2.520 nonbonded pdb=" OD1 ASP C 257 " pdb=" NE2 GLN C 303 " model vdw 2.243 2.520 ... (remaining 162821 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' and resid 29 through 754) selection = (chain 'B' and resid 29 through 754) selection = (chain 'C' and resid 29 through 754) selection = (chain 'D' and resid 29 through 754) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 6.240 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 53.490 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.012 0.264 21652 Z= 0.794 Angle : 0.839 13.003 29300 Z= 0.427 Chirality : 0.051 0.610 3280 Planarity : 0.005 0.055 3620 Dihedral : 13.872 117.134 7972 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2516 helix: 0.16 (0.12), residues: 1792 sheet: None (None), residues: 0 loop : -2.74 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 422 HIS 0.011 0.002 HIS A 151 PHE 0.034 0.003 PHE B 519 TYR 0.016 0.002 TYR D 36 ARG 0.008 0.001 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 2.488 Fit side-chains REVERT: A 429 TYR cc_start: 0.7758 (t80) cc_final: 0.7246 (t80) REVERT: A 737 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6498 (mt-10) REVERT: B 429 TYR cc_start: 0.7739 (t80) cc_final: 0.7237 (t80) REVERT: B 737 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6501 (mt-10) REVERT: C 429 TYR cc_start: 0.7757 (t80) cc_final: 0.7239 (t80) REVERT: C 737 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6503 (mt-10) REVERT: D 429 TYR cc_start: 0.7756 (t80) cc_final: 0.7241 (t80) REVERT: D 737 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6505 (mt-10) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.3212 time to fit residues: 139.3224 Evaluate side-chains 224 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0070 chunk 149 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN B 247 GLN C 247 GLN D 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21652 Z= 0.166 Angle : 0.532 11.503 29300 Z= 0.253 Chirality : 0.036 0.123 3280 Planarity : 0.005 0.042 3620 Dihedral : 8.843 85.222 3008 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.71 % Allowed : 5.91 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2516 helix: 0.83 (0.13), residues: 1804 sheet: None (None), residues: 0 loop : -2.32 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 422 HIS 0.002 0.001 HIS A 151 PHE 0.015 0.001 PHE D 340 TYR 0.011 0.001 TYR D 582 ARG 0.003 0.000 ARG D 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 211 time to evaluate : 2.421 Fit side-chains REVERT: A 621 ASN cc_start: 0.8122 (m110) cc_final: 0.7903 (m-40) REVERT: B 336 ILE cc_start: 0.8549 (mm) cc_final: 0.8223 (mt) REVERT: B 621 ASN cc_start: 0.8126 (m110) cc_final: 0.7906 (m-40) REVERT: C 336 ILE cc_start: 0.8555 (mm) cc_final: 0.8227 (mt) REVERT: C 621 ASN cc_start: 0.8122 (m110) cc_final: 0.7905 (m-40) REVERT: D 336 ILE cc_start: 0.8554 (mm) cc_final: 0.8227 (mt) REVERT: D 621 ASN cc_start: 0.8121 (m110) cc_final: 0.7903 (m-40) outliers start: 16 outliers final: 8 residues processed: 219 average time/residue: 0.2922 time to fit residues: 105.2728 Evaluate side-chains 195 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 187 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 117 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 186 optimal weight: 0.0870 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 ASN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 ASN ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 21652 Z= 0.245 Angle : 0.526 10.814 29300 Z= 0.255 Chirality : 0.037 0.136 3280 Planarity : 0.004 0.038 3620 Dihedral : 7.381 54.622 3008 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.23 % Allowed : 9.83 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2516 helix: 0.92 (0.13), residues: 1812 sheet: None (None), residues: 0 loop : -2.15 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 314 HIS 0.003 0.001 HIS A 325 PHE 0.019 0.002 PHE A 340 TYR 0.011 0.001 TYR B 582 ARG 0.002 0.000 ARG D 511 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 2.494 Fit side-chains REVERT: A 336 ILE cc_start: 0.8526 (mm) cc_final: 0.8149 (mt) REVERT: A 702 ASN cc_start: 0.8094 (m-40) cc_final: 0.7736 (m110) REVERT: B 336 ILE cc_start: 0.8606 (mm) cc_final: 0.8238 (mt) REVERT: B 702 ASN cc_start: 0.8118 (m-40) cc_final: 0.7758 (m110) REVERT: C 336 ILE cc_start: 0.8606 (mm) cc_final: 0.8238 (mt) REVERT: C 702 ASN cc_start: 0.8117 (m-40) cc_final: 0.7757 (m110) REVERT: D 336 ILE cc_start: 0.8608 (mm) cc_final: 0.8240 (mt) REVERT: D 702 ASN cc_start: 0.8108 (m-40) cc_final: 0.7745 (m110) outliers start: 28 outliers final: 28 residues processed: 224 average time/residue: 0.2910 time to fit residues: 105.8080 Evaluate side-chains 212 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 652 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 0.4980 chunk 175 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 233 optimal weight: 0.8980 chunk 247 optimal weight: 0.5980 chunk 122 optimal weight: 0.0770 chunk 221 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN B 305 ASN C 305 ASN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21652 Z= 0.107 Angle : 0.447 9.614 29300 Z= 0.215 Chirality : 0.034 0.121 3280 Planarity : 0.004 0.036 3620 Dihedral : 6.876 53.688 3008 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.41 % Allowed : 10.63 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2516 helix: 1.32 (0.13), residues: 1812 sheet: None (None), residues: 0 loop : -1.98 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 314 HIS 0.001 0.000 HIS B 325 PHE 0.015 0.001 PHE C 340 TYR 0.009 0.001 TYR B 582 ARG 0.003 0.000 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 215 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7406 (mt-10) REVERT: A 336 ILE cc_start: 0.8530 (mm) cc_final: 0.8212 (mt) REVERT: A 418 ILE cc_start: 0.8218 (tp) cc_final: 0.7958 (tp) REVERT: A 702 ASN cc_start: 0.7896 (m-40) cc_final: 0.7507 (m110) REVERT: B 81 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7211 (mt-10) REVERT: B 336 ILE cc_start: 0.8493 (mm) cc_final: 0.8191 (mt) REVERT: B 418 ILE cc_start: 0.8224 (tp) cc_final: 0.7959 (tp) REVERT: B 702 ASN cc_start: 0.7911 (m-40) cc_final: 0.7518 (m110) REVERT: C 81 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7211 (mt-10) REVERT: C 336 ILE cc_start: 0.8495 (mm) cc_final: 0.8193 (mt) REVERT: C 702 ASN cc_start: 0.7914 (m-40) cc_final: 0.7520 (m110) REVERT: D 81 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7409 (mt-10) REVERT: D 336 ILE cc_start: 0.8496 (mm) cc_final: 0.8191 (mt) REVERT: D 418 ILE cc_start: 0.8223 (tp) cc_final: 0.7962 (tp) REVERT: D 702 ASN cc_start: 0.7909 (m-40) cc_final: 0.7512 (m110) outliers start: 32 outliers final: 32 residues processed: 243 average time/residue: 0.2817 time to fit residues: 113.4953 Evaluate side-chains 232 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 731 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 102 optimal weight: 0.0980 chunk 211 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21652 Z= 0.176 Angle : 0.476 9.252 29300 Z= 0.230 Chirality : 0.035 0.130 3280 Planarity : 0.004 0.035 3620 Dihedral : 6.913 57.802 3008 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.94 % Allowed : 11.51 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2516 helix: 1.44 (0.13), residues: 1808 sheet: None (None), residues: 0 loop : -1.87 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.002 0.001 HIS A 325 PHE 0.017 0.001 PHE A 340 TYR 0.010 0.001 TYR C 582 ARG 0.003 0.000 ARG D 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 208 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7222 (mt-10) REVERT: A 336 ILE cc_start: 0.8577 (mm) cc_final: 0.8240 (mt) REVERT: A 418 ILE cc_start: 0.8301 (tp) cc_final: 0.8014 (tp) REVERT: A 702 ASN cc_start: 0.7947 (m-40) cc_final: 0.7583 (m-40) REVERT: B 81 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7246 (mt-10) REVERT: B 336 ILE cc_start: 0.8550 (mm) cc_final: 0.8234 (mt) REVERT: B 418 ILE cc_start: 0.8308 (tp) cc_final: 0.8022 (tp) REVERT: B 702 ASN cc_start: 0.7944 (m-40) cc_final: 0.7575 (m-40) REVERT: C 81 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7244 (mt-10) REVERT: C 336 ILE cc_start: 0.8550 (mm) cc_final: 0.8232 (mt) REVERT: C 418 ILE cc_start: 0.8346 (tp) cc_final: 0.8103 (tp) REVERT: C 702 ASN cc_start: 0.7945 (m-40) cc_final: 0.7577 (m-40) REVERT: D 81 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7225 (mt-10) REVERT: D 336 ILE cc_start: 0.8550 (mm) cc_final: 0.8234 (mt) REVERT: D 418 ILE cc_start: 0.8308 (tp) cc_final: 0.8021 (tp) REVERT: D 702 ASN cc_start: 0.7958 (m-40) cc_final: 0.7585 (m-40) outliers start: 44 outliers final: 44 residues processed: 252 average time/residue: 0.3108 time to fit residues: 127.6915 Evaluate side-chains 240 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 196 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 652 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 145 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 247 optimal weight: 0.6980 chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 0.0570 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21652 Z= 0.128 Angle : 0.442 8.718 29300 Z= 0.215 Chirality : 0.035 0.120 3280 Planarity : 0.004 0.034 3620 Dihedral : 6.658 57.754 3008 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.29 % Allowed : 12.17 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.17), residues: 2516 helix: 1.68 (0.13), residues: 1804 sheet: None (None), residues: 0 loop : -1.80 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 314 HIS 0.002 0.000 HIS C 325 PHE 0.015 0.001 PHE B 340 TYR 0.010 0.001 TYR C 582 ARG 0.003 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 208 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7379 (mt-10) REVERT: A 336 ILE cc_start: 0.8545 (mm) cc_final: 0.8205 (mt) REVERT: A 418 ILE cc_start: 0.8240 (tp) cc_final: 0.7989 (tp) REVERT: A 702 ASN cc_start: 0.7941 (m-40) cc_final: 0.7552 (m-40) REVERT: A 723 ASP cc_start: 0.8031 (t0) cc_final: 0.7802 (t0) REVERT: B 81 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7280 (mt-10) REVERT: B 336 ILE cc_start: 0.8575 (mm) cc_final: 0.8235 (mt) REVERT: B 418 ILE cc_start: 0.8250 (tp) cc_final: 0.8005 (tp) REVERT: B 702 ASN cc_start: 0.7953 (m-40) cc_final: 0.7563 (m-40) REVERT: B 723 ASP cc_start: 0.8033 (t0) cc_final: 0.7804 (t0) REVERT: C 81 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7295 (mt-10) REVERT: C 336 ILE cc_start: 0.8576 (mm) cc_final: 0.8236 (mt) REVERT: C 702 ASN cc_start: 0.7955 (m-40) cc_final: 0.7565 (m-40) REVERT: C 723 ASP cc_start: 0.8026 (t0) cc_final: 0.7799 (t0) REVERT: D 81 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7383 (mt-10) REVERT: D 336 ILE cc_start: 0.8576 (mm) cc_final: 0.8235 (mt) REVERT: D 418 ILE cc_start: 0.8243 (tp) cc_final: 0.7993 (tp) REVERT: D 702 ASN cc_start: 0.7952 (m-40) cc_final: 0.7555 (m-40) REVERT: D 723 ASP cc_start: 0.8030 (t0) cc_final: 0.7802 (t0) outliers start: 52 outliers final: 48 residues processed: 256 average time/residue: 0.2996 time to fit residues: 126.0100 Evaluate side-chains 252 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 204 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 731 THR Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 4.9990 chunk 27 optimal weight: 0.0770 chunk 141 optimal weight: 6.9990 chunk 180 optimal weight: 0.5980 chunk 140 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 246 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 150 optimal weight: 0.0170 chunk 113 optimal weight: 0.9980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 614 ASN C 442 ASN D 151 HIS ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21652 Z= 0.099 Angle : 0.417 7.977 29300 Z= 0.205 Chirality : 0.034 0.128 3280 Planarity : 0.004 0.033 3620 Dihedral : 6.165 55.967 3008 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.81 % Allowed : 12.26 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.17), residues: 2516 helix: 1.94 (0.13), residues: 1808 sheet: None (None), residues: 0 loop : -1.76 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 314 HIS 0.001 0.000 HIS A 325 PHE 0.014 0.001 PHE D 340 TYR 0.009 0.001 TYR A 582 ARG 0.006 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 232 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 ILE cc_start: 0.8517 (mm) cc_final: 0.8217 (mt) REVERT: A 418 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7992 (tp) REVERT: A 702 ASN cc_start: 0.7836 (m-40) cc_final: 0.7459 (m-40) REVERT: A 723 ASP cc_start: 0.7963 (t0) cc_final: 0.7744 (t0) REVERT: B 336 ILE cc_start: 0.8504 (mm) cc_final: 0.8113 (mt) REVERT: B 418 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7998 (tp) REVERT: B 702 ASN cc_start: 0.7848 (m-40) cc_final: 0.7445 (m-40) REVERT: B 723 ASP cc_start: 0.7961 (t0) cc_final: 0.7744 (t0) REVERT: C 336 ILE cc_start: 0.8506 (mm) cc_final: 0.8114 (mt) REVERT: C 702 ASN cc_start: 0.7850 (m-40) cc_final: 0.7472 (m-40) REVERT: C 723 ASP cc_start: 0.7955 (t0) cc_final: 0.7737 (t0) REVERT: D 336 ILE cc_start: 0.8505 (mm) cc_final: 0.8114 (mt) REVERT: D 418 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7999 (tp) REVERT: D 702 ASN cc_start: 0.7848 (m-40) cc_final: 0.7463 (m-40) REVERT: D 723 ASP cc_start: 0.7958 (t0) cc_final: 0.7741 (t0) outliers start: 41 outliers final: 32 residues processed: 266 average time/residue: 0.2872 time to fit residues: 123.3780 Evaluate side-chains 247 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 212 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 731 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 156 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 193 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 614 ASN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21652 Z= 0.111 Angle : 0.469 12.156 29300 Z= 0.220 Chirality : 0.034 0.120 3280 Planarity : 0.004 0.033 3620 Dihedral : 6.034 58.278 3008 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.72 % Allowed : 13.71 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.17), residues: 2516 helix: 2.02 (0.13), residues: 1808 sheet: None (None), residues: 0 loop : -1.72 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.001 0.000 HIS A 325 PHE 0.014 0.001 PHE A 340 TYR 0.009 0.001 TYR C 582 ARG 0.007 0.000 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 213 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 ILE cc_start: 0.8542 (mm) cc_final: 0.8237 (mt) REVERT: A 418 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.8012 (tp) REVERT: A 702 ASN cc_start: 0.7853 (m-40) cc_final: 0.7471 (m-40) REVERT: A 723 ASP cc_start: 0.7959 (t0) cc_final: 0.7745 (t0) REVERT: B 336 ILE cc_start: 0.8535 (mm) cc_final: 0.8143 (mt) REVERT: B 702 ASN cc_start: 0.7863 (m-40) cc_final: 0.7479 (m-40) REVERT: B 723 ASP cc_start: 0.7959 (t0) cc_final: 0.7743 (t0) REVERT: C 336 ILE cc_start: 0.8535 (mm) cc_final: 0.8153 (mt) REVERT: C 702 ASN cc_start: 0.7867 (m-40) cc_final: 0.7481 (m-40) REVERT: C 723 ASP cc_start: 0.7957 (t0) cc_final: 0.7740 (t0) REVERT: D 336 ILE cc_start: 0.8534 (mm) cc_final: 0.8143 (mt) REVERT: D 418 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.8019 (tp) REVERT: D 702 ASN cc_start: 0.7865 (m-40) cc_final: 0.7472 (m-40) REVERT: D 723 ASP cc_start: 0.7958 (t0) cc_final: 0.7742 (t0) outliers start: 39 outliers final: 36 residues processed: 245 average time/residue: 0.2922 time to fit residues: 116.3295 Evaluate side-chains 244 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 206 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 731 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 229 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 217 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 614 ASN ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21652 Z= 0.165 Angle : 0.501 12.322 29300 Z= 0.237 Chirality : 0.035 0.123 3280 Planarity : 0.004 0.034 3620 Dihedral : 6.153 57.926 3008 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.85 % Allowed : 13.36 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.17), residues: 2516 helix: 1.95 (0.13), residues: 1808 sheet: None (None), residues: 0 loop : -1.69 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.002 0.000 HIS A 325 PHE 0.016 0.001 PHE A 340 TYR 0.009 0.001 TYR C 582 ARG 0.007 0.000 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 217 time to evaluate : 2.479 Fit side-chains REVERT: A 336 ILE cc_start: 0.8533 (mm) cc_final: 0.8176 (mt) REVERT: A 409 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.6775 (m-90) REVERT: A 418 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8065 (tp) REVERT: A 702 ASN cc_start: 0.7865 (m-40) cc_final: 0.7499 (m-40) REVERT: B 336 ILE cc_start: 0.8549 (mm) cc_final: 0.8179 (mt) REVERT: B 339 MET cc_start: 0.7162 (ppp) cc_final: 0.6750 (mmt) REVERT: B 409 TRP cc_start: 0.8642 (OUTLIER) cc_final: 0.6801 (m-90) REVERT: B 702 ASN cc_start: 0.7877 (m-40) cc_final: 0.7510 (m-40) REVERT: C 336 ILE cc_start: 0.8564 (mm) cc_final: 0.8199 (mt) REVERT: C 339 MET cc_start: 0.7476 (ppp) cc_final: 0.6999 (mmt) REVERT: C 409 TRP cc_start: 0.8659 (OUTLIER) cc_final: 0.6775 (m-90) REVERT: C 702 ASN cc_start: 0.7882 (m-40) cc_final: 0.7513 (m-40) REVERT: D 336 ILE cc_start: 0.8549 (mm) cc_final: 0.8179 (mt) REVERT: D 339 MET cc_start: 0.7164 (ppp) cc_final: 0.6749 (mmt) REVERT: D 409 TRP cc_start: 0.8643 (OUTLIER) cc_final: 0.6774 (m-90) REVERT: D 418 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8081 (tp) REVERT: D 702 ASN cc_start: 0.7879 (m-40) cc_final: 0.7504 (m-40) outliers start: 42 outliers final: 34 residues processed: 251 average time/residue: 0.2837 time to fit residues: 116.1145 Evaluate side-chains 247 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 749 VAL 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: 3.9990 chunk 115 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 161 optimal weight: 0.0870 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 614 ASN ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21652 Z= 0.169 Angle : 0.507 12.455 29300 Z= 0.241 Chirality : 0.036 0.122 3280 Planarity : 0.004 0.034 3620 Dihedral : 6.222 57.348 3008 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.85 % Allowed : 13.45 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.17), residues: 2516 helix: 2.01 (0.12), residues: 1788 sheet: None (None), residues: 0 loop : -1.64 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 314 HIS 0.002 0.000 HIS D 325 PHE 0.016 0.001 PHE D 340 TYR 0.009 0.001 TYR D 582 ARG 0.007 0.000 ARG D 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 211 time to evaluate : 2.439 Fit side-chains REVERT: A 336 ILE cc_start: 0.8544 (mm) cc_final: 0.8182 (mt) REVERT: A 409 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.6793 (m-90) REVERT: A 418 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8077 (tp) REVERT: A 702 ASN cc_start: 0.7863 (m-40) cc_final: 0.7496 (m-40) REVERT: B 336 ILE cc_start: 0.8547 (mm) cc_final: 0.8174 (mt) REVERT: B 409 TRP cc_start: 0.8634 (OUTLIER) cc_final: 0.6788 (m-90) REVERT: B 702 ASN cc_start: 0.7942 (m-40) cc_final: 0.7568 (m-40) REVERT: C 336 ILE cc_start: 0.8558 (mm) cc_final: 0.8186 (mt) REVERT: C 409 TRP cc_start: 0.8637 (OUTLIER) cc_final: 0.6758 (m-90) REVERT: C 418 ILE cc_start: 0.8327 (tp) cc_final: 0.8098 (tp) REVERT: C 702 ASN cc_start: 0.7945 (m-40) cc_final: 0.7572 (m-40) REVERT: D 336 ILE cc_start: 0.8548 (mm) cc_final: 0.8175 (mt) REVERT: D 409 TRP cc_start: 0.8636 (OUTLIER) cc_final: 0.6812 (m-90) REVERT: D 418 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8082 (tp) REVERT: D 702 ASN cc_start: 0.7878 (m-40) cc_final: 0.7502 (m-40) outliers start: 42 outliers final: 35 residues processed: 243 average time/residue: 0.2929 time to fit residues: 116.1649 Evaluate side-chains 243 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 202 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 731 THR Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 187 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 178 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.142918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112270 restraints weight = 27283.900| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.02 r_work: 0.2819 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21652 Z= 0.223 Angle : 0.554 14.028 29300 Z= 0.264 Chirality : 0.037 0.138 3280 Planarity : 0.004 0.035 3620 Dihedral : 6.538 57.842 3008 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.85 % Allowed : 13.40 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.17), residues: 2516 helix: 1.83 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : -1.60 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 314 HIS 0.002 0.001 HIS B 325 PHE 0.018 0.001 PHE D 340 TYR 0.009 0.001 TYR A 582 ARG 0.007 0.000 ARG D 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3824.20 seconds wall clock time: 71 minutes 15.93 seconds (4275.93 seconds total)