Starting phenix.real_space_refine on Fri Feb 16 00:33:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1w_6877/02_2024/5z1w_6877_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1w_6877/02_2024/5z1w_6877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1w_6877/02_2024/5z1w_6877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1w_6877/02_2024/5z1w_6877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1w_6877/02_2024/5z1w_6877_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1w_6877/02_2024/5z1w_6877_neut.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 9124 2.51 5 N 2192 2.21 5 O 2456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 534": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13824 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3414 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 11, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3414 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 11, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3414 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 11, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "D" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3414 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 11, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.44, per 1000 atoms: 0.54 Number of scatterers: 13824 At special positions: 0 Unit cell: (108.24, 108.24, 97.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2456 8.00 N 2192 7.00 C 9124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 223 " distance=2.02 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 223 " distance=2.02 Simple disulfide: pdb=" SG CYS C 210 " - pdb=" SG CYS C 223 " distance=2.02 Simple disulfide: pdb=" SG CYS D 210 " - pdb=" SG CYS D 223 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 800 " - " ASN A 177 " " NAG A 801 " - " ASN A 207 " " NAG A 802 " - " ASN A 241 " " NAG B 800 " - " ASN B 177 " " NAG B 801 " - " ASN B 207 " " NAG B 802 " - " ASN B 241 " " NAG C 800 " - " ASN C 177 " " NAG C 801 " - " ASN C 207 " " NAG C 802 " - " ASN C 241 " " NAG D 800 " - " ASN D 177 " " NAG D 801 " - " ASN D 207 " " NAG D 802 " - " ASN D 241 " Time building additional restraints: 5.54 Conformation dependent library (CDL) restraints added in 2.3 seconds 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 53.2% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.573A pdb=" N VAL A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.520A pdb=" N TYR A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.575A pdb=" N ASP A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.859A pdb=" N SER A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 372 removed outlier: 3.778A pdb=" N PHE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 372 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 421 removed outlier: 3.718A pdb=" N GLY A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N HIS A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 452 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 480 through 480 No H-bonds generated for 'chain 'A' and resid 480 through 480' Processing helix chain 'A' and resid 481 through 499 removed outlier: 3.636A pdb=" N VAL A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.834A pdb=" N ILE A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 562 removed outlier: 3.644A pdb=" N VAL A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.520A pdb=" N TYR B 129 " --> pdb=" O SER B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.575A pdb=" N ASP B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.860A pdb=" N SER B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 372 removed outlier: 3.778A pdb=" N PHE B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 372 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 421 removed outlier: 3.718A pdb=" N GLY B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N HIS B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 452 Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'B' and resid 480 through 480 No H-bonds generated for 'chain 'B' and resid 480 through 480' Processing helix chain 'B' and resid 481 through 499 removed outlier: 3.635A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 525 through 533 removed outlier: 3.834A pdb=" N ILE B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 562 removed outlier: 3.643A pdb=" N VAL B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 120 Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.520A pdb=" N TYR C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.575A pdb=" N ASP C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 291 removed outlier: 3.858A pdb=" N SER C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 372 removed outlier: 3.778A pdb=" N PHE C 350 " --> pdb=" O ASN C 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU C 372 " --> pdb=" O VAL C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 421 removed outlier: 3.718A pdb=" N GLY C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N HIS C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE C 405 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 452 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 480 through 480 No H-bonds generated for 'chain 'C' and resid 480 through 480' Processing helix chain 'C' and resid 481 through 499 removed outlier: 3.635A pdb=" N VAL C 487 " --> pdb=" O MET C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 525 through 533 removed outlier: 3.834A pdb=" N ILE C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 562 removed outlier: 3.644A pdb=" N VAL C 539 " --> pdb=" O ILE C 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.519A pdb=" N TYR D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 162 Processing helix chain 'D' and resid 163 through 168 removed outlier: 3.575A pdb=" N ASP D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 291 removed outlier: 3.858A pdb=" N SER D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY D 291 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 372 removed outlier: 3.779A pdb=" N PHE D 350 " --> pdb=" O ASN D 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU D 372 " --> pdb=" O VAL D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 421 removed outlier: 3.718A pdb=" N GLY D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N HIS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE D 405 " --> pdb=" O VAL D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 452 Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 480 through 480 No H-bonds generated for 'chain 'D' and resid 480 through 480' Processing helix chain 'D' and resid 481 through 499 removed outlier: 3.635A pdb=" N VAL D 487 " --> pdb=" O MET D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 525 through 533 removed outlier: 3.833A pdb=" N ILE D 529 " --> pdb=" O ASP D 525 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 562 removed outlier: 3.643A pdb=" N VAL D 539 " --> pdb=" O ILE D 535 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 removed outlier: 6.832A pdb=" N LEU A 195 " --> pdb=" O TYR A 308 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR A 308 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA A 197 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER A 306 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 300 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 314 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'B' and resid 187 through 188 Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 188 removed outlier: 6.832A pdb=" N LEU B 195 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR B 308 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA B 197 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER B 306 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 300 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 314 " --> pdb=" O ASN B 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 188 Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 188 removed outlier: 6.832A pdb=" N LEU C 195 " --> pdb=" O TYR C 308 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR C 308 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA C 197 " --> pdb=" O SER C 306 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER C 306 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 300 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 314 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 258 through 259 Processing sheet with id=AB1, first strand: chain 'D' and resid 187 through 188 Processing sheet with id=AB2, first strand: chain 'D' and resid 187 through 188 removed outlier: 6.832A pdb=" N LEU D 195 " --> pdb=" O TYR D 308 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR D 308 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA D 197 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER D 306 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 300 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D 314 " --> pdb=" O ASN D 309 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 258 through 259 784 hydrogen bonds defined for protein. 2268 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: 3.82 Time building geometry restraints manager: 6.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4214 1.34 - 1.46: 3436 1.46 - 1.57: 6486 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 14216 Sorted by residual: bond pdb=" CA TRP C 259 " pdb=" CB TRP C 259 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.39e-02 5.18e+03 7.86e+00 bond pdb=" CA TRP A 259 " pdb=" CB TRP A 259 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.39e-02 5.18e+03 7.86e+00 bond pdb=" CA TRP B 259 " pdb=" CB TRP B 259 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.39e-02 5.18e+03 7.81e+00 bond pdb=" CA TRP D 259 " pdb=" CB TRP D 259 " ideal model delta sigma weight residual 1.528 1.489 0.038 1.39e-02 5.18e+03 7.55e+00 bond pdb=" C GLN C 234 " pdb=" N LEU C 235 " ideal model delta sigma weight residual 1.329 1.259 0.070 3.03e-02 1.09e+03 5.33e+00 ... (remaining 14211 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.23: 251 106.23 - 113.18: 7630 113.18 - 120.13: 5569 120.13 - 127.08: 5791 127.08 - 134.04: 143 Bond angle restraints: 19384 Sorted by residual: angle pdb=" N GLY A 183 " pdb=" CA GLY A 183 " pdb=" C GLY A 183 " ideal model delta sigma weight residual 110.97 116.54 -5.57 1.56e+00 4.11e-01 1.28e+01 angle pdb=" N GLY B 183 " pdb=" CA GLY B 183 " pdb=" C GLY B 183 " ideal model delta sigma weight residual 110.97 116.54 -5.57 1.56e+00 4.11e-01 1.28e+01 angle pdb=" N GLY C 183 " pdb=" CA GLY C 183 " pdb=" C GLY C 183 " ideal model delta sigma weight residual 110.97 116.53 -5.56 1.56e+00 4.11e-01 1.27e+01 angle pdb=" N GLY D 183 " pdb=" CA GLY D 183 " pdb=" C GLY D 183 " ideal model delta sigma weight residual 110.97 116.48 -5.51 1.56e+00 4.11e-01 1.25e+01 angle pdb=" C ILE B 451 " pdb=" N LYS B 452 " pdb=" CA LYS B 452 " ideal model delta sigma weight residual 120.63 125.87 -5.24 1.61e+00 3.86e-01 1.06e+01 ... (remaining 19379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 7852 16.28 - 32.57: 232 32.57 - 48.85: 60 48.85 - 65.14: 20 65.14 - 81.42: 12 Dihedral angle restraints: 8176 sinusoidal: 3156 harmonic: 5020 Sorted by residual: dihedral pdb=" CA ASN B 311 " pdb=" C ASN B 311 " pdb=" N ILE B 312 " pdb=" CA ILE B 312 " ideal model delta harmonic sigma weight residual 180.00 158.05 21.95 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASN D 311 " pdb=" C ASN D 311 " pdb=" N ILE D 312 " pdb=" CA ILE D 312 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASN C 311 " pdb=" C ASN C 311 " pdb=" N ILE C 312 " pdb=" CA ILE C 312 " ideal model delta harmonic sigma weight residual 180.00 158.09 21.91 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 8173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1090 0.039 - 0.078: 721 0.078 - 0.116: 295 0.116 - 0.155: 78 0.155 - 0.194: 8 Chirality restraints: 2192 Sorted by residual: chirality pdb=" CA ARG C 299 " pdb=" N ARG C 299 " pdb=" C ARG C 299 " pdb=" CB ARG C 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA ARG D 299 " pdb=" N ARG D 299 " pdb=" C ARG D 299 " pdb=" CB ARG D 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" CA ARG B 299 " pdb=" N ARG B 299 " pdb=" C ARG B 299 " pdb=" CB ARG B 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 2189 not shown) Planarity restraints: 2428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 171 " -0.015 2.00e-02 2.50e+03 1.76e-02 7.73e+00 pdb=" CG TRP C 171 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 171 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 171 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 171 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 171 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 171 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 171 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 171 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP C 171 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 171 " -0.015 2.00e-02 2.50e+03 1.75e-02 7.62e+00 pdb=" CG TRP D 171 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP D 171 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 171 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 171 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 171 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 171 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 171 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 171 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 171 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 171 " -0.015 2.00e-02 2.50e+03 1.74e-02 7.58e+00 pdb=" CG TRP B 171 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 171 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 171 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 171 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 171 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 171 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 171 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 171 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 171 " 0.000 2.00e-02 2.50e+03 ... (remaining 2425 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3259 2.77 - 3.30: 13614 3.30 - 3.84: 22586 3.84 - 4.37: 26689 4.37 - 4.90: 44611 Nonbonded interactions: 110759 Sorted by model distance: nonbonded pdb=" NH2 ARG B 182 " pdb=" NH1 ARG D 296 " model vdw 2.239 3.200 nonbonded pdb=" NH1 ARG A 296 " pdb=" NH2 ARG D 182 " model vdw 2.242 3.200 nonbonded pdb=" NH1 ARG B 296 " pdb=" NH2 ARG C 182 " model vdw 2.242 3.200 nonbonded pdb=" NH2 ARG A 182 " pdb=" NH1 ARG C 296 " model vdw 2.254 3.200 nonbonded pdb=" OD1 ASP B 427 " pdb=" N GLU B 429 " model vdw 2.316 2.520 ... (remaining 110754 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.850 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: 6.560 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 37.120 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.070 14216 Z= 0.723 Angle : 0.928 7.032 19384 Z= 0.543 Chirality : 0.057 0.194 2192 Planarity : 0.006 0.052 2416 Dihedral : 10.296 81.422 4948 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -3.34 (0.16), residues: 1692 helix: -2.55 (0.13), residues: 912 sheet: -0.44 (0.33), residues: 184 loop : -1.89 (0.20), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP C 171 HIS 0.007 0.002 HIS D 213 PHE 0.022 0.003 PHE A 364 TYR 0.040 0.003 TYR D 129 ARG 0.006 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7967 (tt0) REVERT: A 363 ILE cc_start: 0.8102 (pt) cc_final: 0.7891 (tp) REVERT: A 482 ILE cc_start: 0.9063 (tt) cc_final: 0.8702 (mm) REVERT: A 530 ASP cc_start: 0.8846 (t70) cc_final: 0.8575 (t70) REVERT: B 290 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7967 (tt0) REVERT: B 363 ILE cc_start: 0.8125 (pt) cc_final: 0.7918 (tp) REVERT: B 482 ILE cc_start: 0.9067 (tt) cc_final: 0.8702 (mm) REVERT: B 530 ASP cc_start: 0.8843 (t70) cc_final: 0.8574 (t70) REVERT: C 290 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7969 (tt0) REVERT: C 363 ILE cc_start: 0.8102 (pt) cc_final: 0.7889 (tp) REVERT: C 482 ILE cc_start: 0.9061 (tt) cc_final: 0.8701 (mm) REVERT: C 530 ASP cc_start: 0.8848 (t70) cc_final: 0.8582 (t70) REVERT: D 290 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7980 (tt0) REVERT: D 363 ILE cc_start: 0.8101 (pt) cc_final: 0.7888 (tp) REVERT: D 482 ILE cc_start: 0.9063 (tt) cc_final: 0.8700 (mm) REVERT: D 530 ASP cc_start: 0.8846 (t70) cc_final: 0.8571 (t70) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2288 time to fit residues: 110.8373 Evaluate side-chains 217 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 202 GLN A 222 ASN A 437 GLN A 493 GLN A 516 GLN A 533 ASN A 554 ASN B 139 HIS B 202 GLN B 222 ASN B 437 GLN B 493 GLN B 516 GLN B 533 ASN B 554 ASN C 139 HIS C 202 GLN C 222 ASN C 437 GLN C 493 GLN C 516 GLN C 533 ASN C 554 ASN D 139 HIS D 202 GLN D 222 ASN D 437 GLN D 493 GLN D 516 GLN D 533 ASN D 554 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.004 0.031 14216 Z= 0.282 Angle : 0.583 5.725 19384 Z= 0.317 Chirality : 0.045 0.210 2192 Planarity : 0.004 0.034 2416 Dihedral : 6.317 47.220 2120 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.97 % Allowed : 5.67 % Favored : 91.36 % 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: -0.42 (0.19), residues: 1692 helix: 0.36 (0.17), residues: 880 sheet: 0.06 (0.33), residues: 184 loop : -1.20 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 434 HIS 0.009 0.002 HIS C 213 PHE 0.029 0.002 PHE C 550 TYR 0.024 0.002 TYR A 129 ARG 0.002 0.001 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 235 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ILE cc_start: 0.9090 (tt) cc_final: 0.8593 (mm) REVERT: A 483 MET cc_start: 0.8369 (tmm) cc_final: 0.7999 (tmm) REVERT: B 482 ILE cc_start: 0.9100 (tt) cc_final: 0.8605 (mm) REVERT: B 483 MET cc_start: 0.8370 (tmm) cc_final: 0.7997 (tmm) REVERT: C 482 ILE cc_start: 0.9093 (tt) cc_final: 0.8597 (mm) REVERT: C 483 MET cc_start: 0.8376 (tmm) cc_final: 0.8005 (tmm) REVERT: D 482 ILE cc_start: 0.9092 (tt) cc_final: 0.8594 (mm) REVERT: D 483 MET cc_start: 0.8355 (tmm) cc_final: 0.7980 (tmm) REVERT: D 550 PHE cc_start: 0.7571 (t80) cc_final: 0.7366 (t80) outliers start: 42 outliers final: 23 residues processed: 259 average time/residue: 0.2185 time to fit residues: 87.2947 Evaluate side-chains 223 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 126 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 437 GLN C 437 GLN D 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14216 Z= 0.240 Angle : 0.539 5.318 19384 Z= 0.295 Chirality : 0.044 0.206 2192 Planarity : 0.004 0.038 2416 Dihedral : 5.490 31.010 2120 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.62 % Allowed : 7.37 % Favored : 90.01 % 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: 0.48 (0.20), residues: 1692 helix: 1.25 (0.17), residues: 880 sheet: 0.31 (0.34), residues: 184 loop : -0.99 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 434 HIS 0.007 0.001 HIS A 213 PHE 0.022 0.002 PHE D 550 TYR 0.017 0.001 TYR C 129 ARG 0.001 0.000 ARG C 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 238 time to evaluate : 1.487 Fit side-chains REVERT: A 482 ILE cc_start: 0.9001 (tt) cc_final: 0.8464 (mm) REVERT: A 483 MET cc_start: 0.8389 (tmm) cc_final: 0.8014 (tmm) REVERT: A 557 LEU cc_start: 0.8386 (tp) cc_final: 0.8082 (tp) REVERT: B 482 ILE cc_start: 0.9001 (tt) cc_final: 0.8468 (mm) REVERT: B 483 MET cc_start: 0.8389 (tmm) cc_final: 0.8017 (tmm) REVERT: B 557 LEU cc_start: 0.8357 (tp) cc_final: 0.8061 (tp) REVERT: C 482 ILE cc_start: 0.9010 (tt) cc_final: 0.8474 (mm) REVERT: C 483 MET cc_start: 0.8388 (tmm) cc_final: 0.8019 (tmm) REVERT: C 557 LEU cc_start: 0.8359 (tp) cc_final: 0.8061 (tp) REVERT: D 429 GLU cc_start: 0.8005 (mp0) cc_final: 0.7493 (mp0) REVERT: D 482 ILE cc_start: 0.8995 (tt) cc_final: 0.8459 (mm) REVERT: D 483 MET cc_start: 0.8374 (tmm) cc_final: 0.7997 (tmm) REVERT: D 557 LEU cc_start: 0.8348 (tp) cc_final: 0.8055 (tp) outliers start: 37 outliers final: 29 residues processed: 259 average time/residue: 0.2284 time to fit residues: 89.3225 Evaluate side-chains 234 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 205 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14216 Z= 0.185 Angle : 0.509 5.768 19384 Z= 0.274 Chirality : 0.042 0.198 2192 Planarity : 0.004 0.038 2416 Dihedral : 4.840 25.190 2120 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.19 % Allowed : 8.43 % Favored : 88.39 % 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: 0.91 (0.20), residues: 1692 helix: 1.77 (0.17), residues: 852 sheet: 0.42 (0.33), residues: 184 loop : -0.91 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 434 HIS 0.006 0.001 HIS C 213 PHE 0.026 0.001 PHE C 549 TYR 0.012 0.001 TYR C 129 ARG 0.001 0.000 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 227 time to evaluate : 1.740 Fit side-chains REVERT: A 173 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8104 (mmtp) REVERT: A 482 ILE cc_start: 0.8928 (tt) cc_final: 0.8364 (mm) REVERT: A 483 MET cc_start: 0.8398 (tmm) cc_final: 0.8019 (tmm) REVERT: A 557 LEU cc_start: 0.8370 (tp) cc_final: 0.8095 (tp) REVERT: B 173 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8107 (mmtp) REVERT: B 482 ILE cc_start: 0.8930 (tt) cc_final: 0.8368 (mm) REVERT: B 483 MET cc_start: 0.8396 (tmm) cc_final: 0.8017 (tmm) REVERT: B 557 LEU cc_start: 0.8351 (tp) cc_final: 0.8073 (tp) REVERT: C 173 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8104 (mmtp) REVERT: C 482 ILE cc_start: 0.8935 (tt) cc_final: 0.8377 (mm) REVERT: C 483 MET cc_start: 0.8376 (tmm) cc_final: 0.7997 (tmm) REVERT: C 557 LEU cc_start: 0.8353 (tp) cc_final: 0.8076 (tp) REVERT: D 482 ILE cc_start: 0.8925 (tt) cc_final: 0.8367 (mm) REVERT: D 483 MET cc_start: 0.8362 (tmm) cc_final: 0.7972 (tmm) REVERT: D 557 LEU cc_start: 0.8337 (tp) cc_final: 0.8061 (tp) outliers start: 45 outliers final: 25 residues processed: 255 average time/residue: 0.2279 time to fit residues: 87.9058 Evaluate side-chains 224 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14216 Z= 0.212 Angle : 0.524 10.692 19384 Z= 0.276 Chirality : 0.042 0.199 2192 Planarity : 0.004 0.041 2416 Dihedral : 4.619 23.091 2120 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.97 % Allowed : 9.70 % Favored : 87.32 % 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: 1.13 (0.20), residues: 1692 helix: 1.94 (0.17), residues: 852 sheet: 0.72 (0.33), residues: 184 loop : -0.86 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 434 HIS 0.005 0.001 HIS B 213 PHE 0.027 0.002 PHE A 549 TYR 0.011 0.001 TYR B 129 ARG 0.001 0.000 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 225 time to evaluate : 1.518 Fit side-chains REVERT: A 173 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8112 (mmtp) REVERT: A 482 ILE cc_start: 0.8901 (tt) cc_final: 0.8320 (mm) REVERT: A 483 MET cc_start: 0.8411 (tmm) cc_final: 0.8035 (tmm) REVERT: A 557 LEU cc_start: 0.8353 (tp) cc_final: 0.8098 (tp) REVERT: B 173 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8109 (mmtp) REVERT: B 482 ILE cc_start: 0.8902 (tt) cc_final: 0.8322 (mm) REVERT: B 483 MET cc_start: 0.8407 (tmm) cc_final: 0.8033 (tmm) REVERT: B 557 LEU cc_start: 0.8342 (tp) cc_final: 0.8081 (tp) REVERT: C 173 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8106 (mmtp) REVERT: C 482 ILE cc_start: 0.8905 (tt) cc_final: 0.8325 (mm) REVERT: C 483 MET cc_start: 0.8408 (tmm) cc_final: 0.8034 (tmm) REVERT: C 557 LEU cc_start: 0.8356 (tp) cc_final: 0.8095 (tp) REVERT: D 173 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8109 (mmtp) REVERT: D 482 ILE cc_start: 0.8897 (tt) cc_final: 0.8315 (mm) REVERT: D 483 MET cc_start: 0.8403 (tmm) cc_final: 0.8022 (tmm) REVERT: D 557 LEU cc_start: 0.8336 (tp) cc_final: 0.8082 (tp) outliers start: 42 outliers final: 29 residues processed: 249 average time/residue: 0.2437 time to fit residues: 90.9980 Evaluate side-chains 243 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 214 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 0.0000 chunk 53 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN B 404 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN C 404 HIS C 554 ASN D 404 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14216 Z= 0.215 Angle : 0.521 10.698 19384 Z= 0.277 Chirality : 0.043 0.200 2192 Planarity : 0.004 0.040 2416 Dihedral : 4.524 22.292 2120 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.48 % Allowed : 11.47 % Favored : 86.05 % 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: 1.05 (0.20), residues: 1692 helix: 1.78 (0.17), residues: 880 sheet: 0.67 (0.34), residues: 184 loop : -0.87 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 434 HIS 0.004 0.001 HIS C 213 PHE 0.029 0.001 PHE C 549 TYR 0.010 0.001 TYR C 129 ARG 0.001 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 219 time to evaluate : 1.592 Fit side-chains REVERT: A 173 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8087 (mmtp) REVERT: A 482 ILE cc_start: 0.8838 (tt) cc_final: 0.8243 (mm) REVERT: A 483 MET cc_start: 0.8395 (tmm) cc_final: 0.8029 (tmm) REVERT: A 557 LEU cc_start: 0.8355 (tp) cc_final: 0.8091 (tp) REVERT: B 173 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8090 (mmtp) REVERT: B 482 ILE cc_start: 0.8845 (tt) cc_final: 0.8258 (mm) REVERT: B 483 MET cc_start: 0.8386 (tmm) cc_final: 0.8000 (tmm) REVERT: B 557 LEU cc_start: 0.8350 (tp) cc_final: 0.8085 (tp) REVERT: C 173 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8091 (mmtp) REVERT: C 482 ILE cc_start: 0.8838 (tt) cc_final: 0.8243 (mm) REVERT: C 483 MET cc_start: 0.8388 (tmm) cc_final: 0.8000 (tmm) REVERT: C 557 LEU cc_start: 0.8352 (tp) cc_final: 0.8088 (tp) REVERT: D 173 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8087 (mmtp) REVERT: D 482 ILE cc_start: 0.8837 (tt) cc_final: 0.8242 (mm) REVERT: D 483 MET cc_start: 0.8383 (tmm) cc_final: 0.7992 (tmm) REVERT: D 496 TYR cc_start: 0.8970 (t80) cc_final: 0.8731 (t80) REVERT: D 557 LEU cc_start: 0.8344 (tp) cc_final: 0.8088 (tp) outliers start: 35 outliers final: 31 residues processed: 242 average time/residue: 0.2387 time to fit residues: 86.7733 Evaluate side-chains 244 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 213 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN B 404 HIS B 554 ASN C 404 HIS C 554 ASN D 404 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14216 Z= 0.205 Angle : 0.516 10.260 19384 Z= 0.274 Chirality : 0.042 0.197 2192 Planarity : 0.003 0.040 2416 Dihedral : 4.401 21.224 2120 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.69 % Allowed : 11.54 % Favored : 85.76 % 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: 1.27 (0.21), residues: 1692 helix: 2.04 (0.17), residues: 856 sheet: 0.71 (0.34), residues: 184 loop : -0.76 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 434 HIS 0.004 0.001 HIS D 213 PHE 0.029 0.001 PHE A 549 TYR 0.010 0.001 TYR D 127 ARG 0.002 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 224 time to evaluate : 1.612 Fit side-chains REVERT: A 173 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8077 (mmtp) REVERT: A 482 ILE cc_start: 0.8811 (tt) cc_final: 0.8206 (mm) REVERT: A 483 MET cc_start: 0.8382 (tmm) cc_final: 0.7996 (tmm) REVERT: A 557 LEU cc_start: 0.8346 (tp) cc_final: 0.8086 (tp) REVERT: B 173 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8080 (mmtp) REVERT: B 482 ILE cc_start: 0.8806 (tt) cc_final: 0.8198 (mm) REVERT: B 483 MET cc_start: 0.8389 (tmm) cc_final: 0.8006 (tmm) REVERT: B 557 LEU cc_start: 0.8341 (tp) cc_final: 0.8084 (tp) REVERT: C 173 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8077 (mmtp) REVERT: C 482 ILE cc_start: 0.8806 (tt) cc_final: 0.8197 (mm) REVERT: C 483 MET cc_start: 0.8387 (tmm) cc_final: 0.8003 (tmm) REVERT: C 557 LEU cc_start: 0.8343 (tp) cc_final: 0.8085 (tp) REVERT: D 173 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8078 (mmtp) REVERT: D 482 ILE cc_start: 0.8808 (tt) cc_final: 0.8199 (mm) REVERT: D 483 MET cc_start: 0.8389 (tmm) cc_final: 0.7998 (tmm) REVERT: D 557 LEU cc_start: 0.8343 (tp) cc_final: 0.8092 (tp) outliers start: 38 outliers final: 33 residues processed: 249 average time/residue: 0.2384 time to fit residues: 88.1152 Evaluate side-chains 254 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 110 optimal weight: 0.0000 chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 554 ASN B 404 HIS B 554 ASN C 404 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 ASN D 404 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14216 Z= 0.137 Angle : 0.480 9.362 19384 Z= 0.255 Chirality : 0.041 0.183 2192 Planarity : 0.003 0.038 2416 Dihedral : 4.014 17.967 2120 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.05 % Allowed : 12.18 % Favored : 85.76 % 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: 1.35 (0.20), residues: 1692 helix: 2.02 (0.17), residues: 880 sheet: 0.73 (0.34), residues: 184 loop : -0.67 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 434 HIS 0.003 0.001 HIS D 213 PHE 0.028 0.001 PHE C 549 TYR 0.012 0.001 TYR C 127 ARG 0.001 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 238 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8108 (mmtp) REVERT: A 330 THR cc_start: 0.9234 (m) cc_final: 0.8999 (m) REVERT: A 480 PHE cc_start: 0.6709 (t80) cc_final: 0.6428 (m-80) REVERT: A 482 ILE cc_start: 0.8667 (tt) cc_final: 0.8109 (mm) REVERT: A 483 MET cc_start: 0.8316 (tmm) cc_final: 0.7888 (tmm) REVERT: A 557 LEU cc_start: 0.8389 (tp) cc_final: 0.8117 (tp) REVERT: B 173 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8109 (mmtp) REVERT: B 480 PHE cc_start: 0.6715 (t80) cc_final: 0.6419 (m-80) REVERT: B 482 ILE cc_start: 0.8674 (tt) cc_final: 0.8119 (mm) REVERT: B 483 MET cc_start: 0.8319 (tmm) cc_final: 0.7900 (tmm) REVERT: B 557 LEU cc_start: 0.8387 (tp) cc_final: 0.8128 (tp) REVERT: C 173 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8109 (mmtp) REVERT: C 480 PHE cc_start: 0.6716 (t80) cc_final: 0.6419 (m-80) REVERT: C 482 ILE cc_start: 0.8675 (tt) cc_final: 0.8118 (mm) REVERT: C 483 MET cc_start: 0.8315 (tmm) cc_final: 0.7902 (tmm) REVERT: C 557 LEU cc_start: 0.8386 (tp) cc_final: 0.8124 (tp) REVERT: D 173 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8107 (mmtp) REVERT: D 330 THR cc_start: 0.9235 (m) cc_final: 0.9000 (m) REVERT: D 480 PHE cc_start: 0.6719 (t80) cc_final: 0.6441 (m-80) REVERT: D 482 ILE cc_start: 0.8676 (tt) cc_final: 0.8112 (mm) REVERT: D 483 MET cc_start: 0.8315 (tmm) cc_final: 0.7886 (tmm) REVERT: D 557 LEU cc_start: 0.8370 (tp) cc_final: 0.8105 (tp) outliers start: 29 outliers final: 21 residues processed: 255 average time/residue: 0.2423 time to fit residues: 91.9125 Evaluate side-chains 240 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 219 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 397 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 46 optimal weight: 0.0060 chunk 136 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 554 ASN B 404 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN C 404 HIS C 554 ASN D 404 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14216 Z= 0.149 Angle : 0.488 8.838 19384 Z= 0.260 Chirality : 0.041 0.186 2192 Planarity : 0.003 0.039 2416 Dihedral : 3.941 16.148 2120 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.12 % Allowed : 11.97 % Favored : 85.91 % 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: 1.64 (0.21), residues: 1692 helix: 2.39 (0.17), residues: 856 sheet: 0.80 (0.35), residues: 184 loop : -0.61 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 434 HIS 0.003 0.000 HIS C 213 PHE 0.029 0.001 PHE C 549 TYR 0.011 0.001 TYR C 127 ARG 0.001 0.000 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 1.436 Fit side-chains REVERT: A 173 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8089 (mmtp) REVERT: A 231 LYS cc_start: 0.9147 (mtpp) cc_final: 0.8883 (mtpp) REVERT: A 330 THR cc_start: 0.9276 (m) cc_final: 0.9041 (m) REVERT: A 480 PHE cc_start: 0.6865 (t80) cc_final: 0.6573 (m-80) REVERT: A 482 ILE cc_start: 0.8671 (tt) cc_final: 0.8094 (mm) REVERT: A 483 MET cc_start: 0.8345 (tmm) cc_final: 0.7949 (tmm) REVERT: A 557 LEU cc_start: 0.8382 (tp) cc_final: 0.8125 (tp) REVERT: B 173 LYS cc_start: 0.8529 (mtmm) cc_final: 0.8092 (mmtp) REVERT: B 231 LYS cc_start: 0.9147 (mtpp) cc_final: 0.8884 (mtpp) REVERT: B 480 PHE cc_start: 0.6860 (t80) cc_final: 0.6594 (m-80) REVERT: B 482 ILE cc_start: 0.8650 (tt) cc_final: 0.8063 (mm) REVERT: B 483 MET cc_start: 0.8363 (tmm) cc_final: 0.7967 (tmm) REVERT: B 557 LEU cc_start: 0.8381 (tp) cc_final: 0.8123 (tp) REVERT: C 173 LYS cc_start: 0.8525 (mtmm) cc_final: 0.8078 (mmtp) REVERT: C 231 LYS cc_start: 0.9146 (mtpp) cc_final: 0.8882 (mtpp) REVERT: C 480 PHE cc_start: 0.6860 (t80) cc_final: 0.6571 (m-80) REVERT: C 482 ILE cc_start: 0.8652 (tt) cc_final: 0.8067 (mm) REVERT: C 483 MET cc_start: 0.8365 (tmm) cc_final: 0.7971 (tmm) REVERT: C 557 LEU cc_start: 0.8377 (tp) cc_final: 0.8120 (tp) REVERT: D 173 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8078 (mmtp) REVERT: D 231 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8882 (mtpp) REVERT: D 330 THR cc_start: 0.9274 (m) cc_final: 0.9040 (m) REVERT: D 480 PHE cc_start: 0.6870 (t80) cc_final: 0.6606 (m-80) REVERT: D 482 ILE cc_start: 0.8653 (tt) cc_final: 0.8067 (mm) REVERT: D 483 MET cc_start: 0.8364 (tmm) cc_final: 0.7966 (tmm) REVERT: D 557 LEU cc_start: 0.8386 (tp) cc_final: 0.8133 (tp) outliers start: 30 outliers final: 21 residues processed: 255 average time/residue: 0.2397 time to fit residues: 90.9425 Evaluate side-chains 253 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 397 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 133 optimal weight: 0.0170 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN B 404 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN C 404 HIS ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 ASN D 404 HIS ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14216 Z= 0.220 Angle : 0.521 8.974 19384 Z= 0.276 Chirality : 0.043 0.199 2192 Planarity : 0.004 0.043 2416 Dihedral : 4.219 17.055 2120 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.84 % Allowed : 12.54 % Favored : 85.62 % 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: 1.50 (0.20), residues: 1692 helix: 2.21 (0.17), residues: 880 sheet: 0.73 (0.35), residues: 184 loop : -0.70 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 434 HIS 0.004 0.001 HIS A 213 PHE 0.030 0.002 PHE A 549 TYR 0.010 0.001 TYR C 496 ARG 0.002 0.000 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 222 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8067 (mmtp) REVERT: A 480 PHE cc_start: 0.6901 (t80) cc_final: 0.6547 (m-80) REVERT: A 482 ILE cc_start: 0.8660 (tt) cc_final: 0.8100 (mm) REVERT: A 483 MET cc_start: 0.8382 (tmm) cc_final: 0.7982 (tmm) REVERT: A 557 LEU cc_start: 0.8410 (tp) cc_final: 0.8142 (tp) REVERT: B 173 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8071 (mmtp) REVERT: B 480 PHE cc_start: 0.6897 (t80) cc_final: 0.6548 (m-80) REVERT: B 482 ILE cc_start: 0.8647 (tt) cc_final: 0.8099 (mm) REVERT: B 483 MET cc_start: 0.8410 (tmm) cc_final: 0.8006 (tmm) REVERT: B 557 LEU cc_start: 0.8402 (tp) cc_final: 0.8136 (tp) REVERT: C 173 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8067 (mmtp) REVERT: C 480 PHE cc_start: 0.6905 (t80) cc_final: 0.6579 (m-80) REVERT: C 482 ILE cc_start: 0.8642 (tt) cc_final: 0.8092 (mm) REVERT: C 483 MET cc_start: 0.8402 (tmm) cc_final: 0.8000 (tmm) REVERT: C 557 LEU cc_start: 0.8402 (tp) cc_final: 0.8134 (tp) REVERT: D 173 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8067 (mmtp) REVERT: D 480 PHE cc_start: 0.6944 (t80) cc_final: 0.6602 (m-80) REVERT: D 482 ILE cc_start: 0.8648 (tt) cc_final: 0.8100 (mm) REVERT: D 483 MET cc_start: 0.8403 (tmm) cc_final: 0.8001 (tmm) REVERT: D 557 LEU cc_start: 0.8377 (tp) cc_final: 0.8130 (tp) outliers start: 26 outliers final: 25 residues processed: 235 average time/residue: 0.2454 time to fit residues: 85.8538 Evaluate side-chains 240 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 215 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 397 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 55 optimal weight: 0.0870 chunk 137 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.2980 chunk 117 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.6764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN B 404 HIS ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN C 404 HIS C 554 ASN D 404 HIS ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.102575 restraints weight = 20985.091| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.54 r_work: 0.3074 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14216 Z= 0.156 Angle : 0.507 8.819 19384 Z= 0.270 Chirality : 0.041 0.189 2192 Planarity : 0.003 0.041 2416 Dihedral : 3.943 15.776 2120 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.12 % Allowed : 12.46 % Favored : 85.41 % 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: 1.73 (0.21), residues: 1692 helix: 2.47 (0.17), residues: 856 sheet: 0.78 (0.34), residues: 184 loop : -0.57 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 434 HIS 0.002 0.000 HIS C 213 PHE 0.029 0.001 PHE C 549 TYR 0.013 0.001 TYR C 107 ARG 0.001 0.000 ARG D 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2794.03 seconds wall clock time: 51 minutes 41.39 seconds (3101.39 seconds total)