Starting phenix.real_space_refine on Sun Dec 10 04:05:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6du8_8912/12_2023/6du8_8912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6du8_8912/12_2023/6du8_8912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6du8_8912/12_2023/6du8_8912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6du8_8912/12_2023/6du8_8912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6du8_8912/12_2023/6du8_8912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6du8_8912/12_2023/6du8_8912.pdb" } resolution = 3.11 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= 0.030 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 44 5.16 5 C 8880 2.51 5 N 2136 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 518": "NH1" <-> "NH2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 518": "NH1" <-> "NH2" Residue "C PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13380 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3331 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 11, 'TRANS': 409} Chain breaks: 4 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3331 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 11, 'TRANS': 409} Chain breaks: 4 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3331 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 11, 'TRANS': 409} Chain breaks: 4 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3331 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 11, 'TRANS': 409} Chain breaks: 4 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.54, per 1000 atoms: 0.56 Number of scatterers: 13380 At special positions: 0 Unit cell: (115.44, 115.44, 93.6, 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 44 16.00 O 2320 8.00 N 2136 7.00 C 8880 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 Atom "HETATM13336 O5 NAG A 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM13364 O5 NAG C 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM13378 O5 NAG D 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM13350 O5 NAG B 901 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 207 " " NAG B 901 " - " ASN B 207 " " NAG C 901 " - " ASN C 207 " " NAG D 901 " - " ASN D 207 " Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 2.4 seconds 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 48.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 104 through 119 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.725A pdb=" N PHE A 137 " --> pdb=" O MET A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.793A pdb=" N ILE A 151 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 249 through 254 removed outlier: 4.056A pdb=" N LEU A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.675A pdb=" N ALA A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 376 removed outlier: 3.979A pdb=" N PHE A 359 " --> pdb=" O CYS A 355 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE A 364 " --> pdb=" O CYS A 360 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 368 " --> pdb=" O PHE A 364 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 420 removed outlier: 3.661A pdb=" N VAL A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 396 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 452 Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 481 through 499 removed outlier: 3.948A pdb=" N ILE A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 522 removed outlier: 4.142A pdb=" N GLN A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 521 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 560 removed outlier: 3.709A pdb=" N THR A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET A 555 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.725A pdb=" N PHE B 137 " --> pdb=" O MET B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.793A pdb=" N ILE B 151 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 249 through 254 removed outlier: 4.056A pdb=" N LEU B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.675A pdb=" N ALA B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 376 removed outlier: 3.979A pdb=" N PHE B 359 " --> pdb=" O CYS B 355 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE B 363 " --> pdb=" O PHE B 359 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE B 364 " --> pdb=" O CYS B 360 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 368 " --> pdb=" O PHE B 364 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 420 removed outlier: 3.661A pdb=" N VAL B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 396 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 452 Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 481 through 499 removed outlier: 3.948A pdb=" N ILE B 486 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 522 removed outlier: 4.142A pdb=" N GLN B 516 " --> pdb=" O CYS B 512 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE B 520 " --> pdb=" O GLN B 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 521 " --> pdb=" O PHE B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 560 removed outlier: 3.709A pdb=" N THR B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA B 558 " --> pdb=" O ASN B 554 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.725A pdb=" N PHE C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.793A pdb=" N ILE C 151 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 249 through 254 removed outlier: 4.056A pdb=" N LEU C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 291 removed outlier: 3.675A pdb=" N ALA C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU C 290 " --> pdb=" O ARG C 286 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 376 removed outlier: 3.979A pdb=" N PHE C 359 " --> pdb=" O CYS C 355 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 361 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE C 362 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE C 363 " --> pdb=" O PHE C 359 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE C 364 " --> pdb=" O CYS C 360 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 368 " --> pdb=" O PHE C 364 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 420 removed outlier: 3.661A pdb=" N VAL C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 396 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 398 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE C 405 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 406 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN C 412 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 452 Processing helix chain 'C' and resid 453 through 455 No H-bonds generated for 'chain 'C' and resid 453 through 455' Processing helix chain 'C' and resid 481 through 499 removed outlier: 3.948A pdb=" N ILE C 486 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL C 487 " --> pdb=" O MET C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 522 removed outlier: 4.142A pdb=" N GLN C 516 " --> pdb=" O CYS C 512 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE C 520 " --> pdb=" O GLN C 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 521 " --> pdb=" O PHE C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 560 removed outlier: 3.709A pdb=" N THR C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET C 555 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA C 558 " --> pdb=" O ASN C 554 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 126 through 138 removed outlier: 3.725A pdb=" N PHE D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 removed outlier: 3.793A pdb=" N ILE D 151 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 161 Processing helix chain 'D' and resid 249 through 254 removed outlier: 4.056A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 291 removed outlier: 3.675A pdb=" N ALA D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU D 290 " --> pdb=" O ARG D 286 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 376 removed outlier: 3.979A pdb=" N PHE D 359 " --> pdb=" O CYS D 355 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 361 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE D 362 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE D 363 " --> pdb=" O PHE D 359 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE D 364 " --> pdb=" O CYS D 360 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 368 " --> pdb=" O PHE D 364 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE D 376 " --> pdb=" O LEU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 420 removed outlier: 3.661A pdb=" N VAL D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 396 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER D 397 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE D 405 " --> pdb=" O VAL D 401 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE D 406 " --> pdb=" O GLY D 402 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN D 412 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 452 Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 481 through 499 removed outlier: 3.948A pdb=" N ILE D 486 " --> pdb=" O VAL D 482 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL D 487 " --> pdb=" O MET D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 522 removed outlier: 4.142A pdb=" N GLN D 516 " --> pdb=" O CYS D 512 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE D 520 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 521 " --> pdb=" O PHE D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 560 removed outlier: 3.709A pdb=" N THR D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET D 555 " --> pdb=" O VAL D 551 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE D 556 " --> pdb=" O LEU D 552 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA D 558 " --> pdb=" O ASN D 554 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 194 removed outlier: 4.145A pdb=" N VAL A 300 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 194 removed outlier: 3.601A pdb=" N ASN A 309 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 314 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 193 through 194 removed outlier: 4.145A pdb=" N VAL B 300 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 194 removed outlier: 3.601A pdb=" N ASN B 309 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 314 " --> pdb=" O ASN B 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 193 through 194 removed outlier: 4.145A pdb=" N VAL C 300 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 193 through 194 removed outlier: 3.601A pdb=" N ASN C 309 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU C 314 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 193 through 194 removed outlier: 4.145A pdb=" N VAL D 300 " --> pdb=" O LEU D 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 193 through 194 removed outlier: 3.601A pdb=" N ASN D 309 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D 314 " --> pdb=" O ASN D 309 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1608 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: 3.47 Time building geometry restraints manager: 6.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3312 1.33 - 1.45: 3260 1.45 - 1.57: 7132 1.57 - 1.69: 4 1.69 - 1.81: 60 Bond restraints: 13768 Sorted by residual: bond pdb=" CA GLY B 500 " pdb=" C GLY B 500 " ideal model delta sigma weight residual 1.515 1.498 0.017 6.20e-03 2.60e+04 7.49e+00 bond pdb=" CA GLY A 500 " pdb=" C GLY A 500 " ideal model delta sigma weight residual 1.515 1.498 0.017 6.20e-03 2.60e+04 7.49e+00 bond pdb=" CA GLY D 500 " pdb=" C GLY D 500 " ideal model delta sigma weight residual 1.515 1.498 0.017 6.20e-03 2.60e+04 7.49e+00 bond pdb=" CA GLY C 500 " pdb=" C GLY C 500 " ideal model delta sigma weight residual 1.515 1.498 0.017 6.20e-03 2.60e+04 7.49e+00 bond pdb=" CA LEU A 104 " pdb=" CB LEU A 104 " ideal model delta sigma weight residual 1.532 1.570 -0.038 1.57e-02 4.06e+03 6.01e+00 ... (remaining 13763 not shown) Histogram of bond angle deviations from ideal: 95.92 - 103.55: 112 103.55 - 111.18: 4836 111.18 - 118.81: 5600 118.81 - 126.45: 7980 126.45 - 134.08: 236 Bond angle restraints: 18764 Sorted by residual: angle pdb=" N LYS B 340 " pdb=" CA LYS B 340 " pdb=" C LYS B 340 " ideal model delta sigma weight residual 111.07 120.95 -9.88 1.07e+00 8.73e-01 8.53e+01 angle pdb=" N LYS A 340 " pdb=" CA LYS A 340 " pdb=" C LYS A 340 " ideal model delta sigma weight residual 111.07 120.95 -9.88 1.07e+00 8.73e-01 8.53e+01 angle pdb=" N LYS C 340 " pdb=" CA LYS C 340 " pdb=" C LYS C 340 " ideal model delta sigma weight residual 111.07 120.95 -9.88 1.07e+00 8.73e-01 8.53e+01 angle pdb=" N LYS D 340 " pdb=" CA LYS D 340 " pdb=" C LYS D 340 " ideal model delta sigma weight residual 111.07 120.95 -9.88 1.07e+00 8.73e-01 8.53e+01 angle pdb=" N GLY C 500 " pdb=" CA GLY C 500 " pdb=" C GLY C 500 " ideal model delta sigma weight residual 110.21 102.15 8.06 9.10e-01 1.21e+00 7.84e+01 ... (remaining 18759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 7084 15.72 - 31.43: 532 31.43 - 47.14: 120 47.14 - 62.86: 8 62.86 - 78.57: 12 Dihedral angle restraints: 7756 sinusoidal: 2848 harmonic: 4908 Sorted by residual: dihedral pdb=" CA TYR C 189 " pdb=" C TYR C 189 " pdb=" N TYR C 190 " pdb=" CA TYR C 190 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR A 189 " pdb=" C TYR A 189 " pdb=" N TYR A 190 " pdb=" CA TYR A 190 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR B 189 " pdb=" C TYR B 189 " pdb=" N TYR B 190 " pdb=" CA TYR B 190 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 7753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 2080 0.185 - 0.370: 20 0.370 - 0.555: 0 0.555 - 0.740: 0 0.740 - 0.924: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" C1 NAG D 901 " pdb=" ND2 ASN D 207 " pdb=" C2 NAG D 901 " pdb=" O5 NAG D 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 207 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 207 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.14e+01 ... (remaining 2101 not shown) Planarity restraints: 2348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 207 " 0.041 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" CG ASN C 207 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN C 207 " 0.217 2.00e-02 2.50e+03 pdb=" ND2 ASN C 207 " -0.536 2.00e-02 2.50e+03 pdb=" C1 NAG C 901 " 0.364 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 207 " -0.041 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" CG ASN D 207 " 0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN D 207 " -0.217 2.00e-02 2.50e+03 pdb=" ND2 ASN D 207 " 0.536 2.00e-02 2.50e+03 pdb=" C1 NAG D 901 " -0.364 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 207 " 0.041 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" CG ASN A 207 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN A 207 " 0.217 2.00e-02 2.50e+03 pdb=" ND2 ASN A 207 " -0.536 2.00e-02 2.50e+03 pdb=" C1 NAG A 901 " 0.364 2.00e-02 2.50e+03 ... (remaining 2345 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 128 2.62 - 3.19: 11312 3.19 - 3.76: 20708 3.76 - 4.33: 26952 4.33 - 4.90: 44754 Nonbonded interactions: 103854 Sorted by model distance: nonbonded pdb=" CB PHE A 315 " pdb=" CD2 LEU A 341 " model vdw 2.046 3.860 nonbonded pdb=" CB PHE C 315 " pdb=" CD2 LEU C 341 " model vdw 2.046 3.860 nonbonded pdb=" CB PHE D 315 " pdb=" CD2 LEU D 341 " model vdw 2.046 3.860 nonbonded pdb=" CB PHE B 315 " pdb=" CD2 LEU B 341 " model vdw 2.046 3.860 nonbonded pdb=" OD1 ASN C 505 " pdb=" OG1 THR C 515 " model vdw 2.218 2.440 ... (remaining 103849 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: 0.750 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: 0.010 Extract box with map and model: 4.470 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 36.920 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 13768 Z= 0.474 Angle : 1.142 13.668 18764 Z= 0.643 Chirality : 0.077 0.924 2104 Planarity : 0.007 0.067 2344 Dihedral : 12.525 78.570 4604 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.89 % Allowed : 5.62 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.16), residues: 1644 helix: -3.25 (0.12), residues: 764 sheet: -1.67 (0.40), residues: 168 loop : -3.42 (0.19), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 259 HIS 0.007 0.003 HIS A 258 PHE 0.032 0.003 PHE D 305 TYR 0.054 0.005 TYR C 129 ARG 0.008 0.001 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 400 time to evaluate : 1.436 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 412 average time/residue: 0.1991 time to fit residues: 126.3695 Evaluate side-chains 320 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 308 time to evaluate : 1.341 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1105 time to fit residues: 4.4684 ------------------------------------------------------------------------------- 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: 1.9990 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 152 optimal weight: 0.0970 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 ASN ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5843 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13768 Z= 0.232 Angle : 0.690 7.665 18764 Z= 0.368 Chirality : 0.054 0.612 2104 Planarity : 0.005 0.067 2344 Dihedral : 6.149 26.811 1904 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.85 % Allowed : 10.06 % Favored : 86.09 % 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: -3.45 (0.18), residues: 1644 helix: -1.82 (0.16), residues: 756 sheet: -1.03 (0.39), residues: 176 loop : -3.12 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 434 HIS 0.005 0.001 HIS C 258 PHE 0.017 0.002 PHE B 556 TYR 0.021 0.002 TYR B 129 ARG 0.003 0.001 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 332 time to evaluate : 1.380 Fit side-chains outliers start: 52 outliers final: 20 residues processed: 360 average time/residue: 0.2087 time to fit residues: 114.4212 Evaluate side-chains 304 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 284 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1119 time to fit residues: 6.0804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 126 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 136 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 13768 Z= 0.531 Angle : 0.898 9.335 18764 Z= 0.473 Chirality : 0.061 0.626 2104 Planarity : 0.006 0.065 2344 Dihedral : 6.986 28.075 1904 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.36 % Favored : 85.64 % Rotamer: Outliers : 2.96 % Allowed : 18.05 % Favored : 78.99 % 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: -3.33 (0.19), residues: 1644 helix: -1.40 (0.18), residues: 756 sheet: -1.33 (0.39), residues: 176 loop : -3.37 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP C 259 HIS 0.006 0.002 HIS C 182 PHE 0.035 0.003 PHE C 324 TYR 0.036 0.004 TYR B 129 ARG 0.004 0.001 ARG C 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 288 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 16 residues processed: 316 average time/residue: 0.2099 time to fit residues: 102.7954 Evaluate side-chains 280 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 264 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1263 time to fit residues: 5.9792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 30.0000 chunk 79 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 162 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13768 Z= 0.222 Angle : 0.751 11.881 18764 Z= 0.375 Chirality : 0.052 0.538 2104 Planarity : 0.004 0.058 2344 Dihedral : 6.054 28.066 1904 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 2.66 % Allowed : 20.71 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.20), residues: 1644 helix: -0.84 (0.19), residues: 748 sheet: -1.01 (0.40), residues: 176 loop : -2.87 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 434 HIS 0.005 0.001 HIS C 258 PHE 0.021 0.002 PHE B 546 TYR 0.023 0.002 TYR B 526 ARG 0.003 0.000 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 300 time to evaluate : 1.589 Fit side-chains outliers start: 36 outliers final: 16 residues processed: 320 average time/residue: 0.2152 time to fit residues: 105.5550 Evaluate side-chains 280 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 264 time to evaluate : 1.398 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1251 time to fit residues: 5.6064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 120 optimal weight: 0.0170 chunk 67 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 145 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 overall best weight: 1.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13768 Z= 0.205 Angle : 0.706 12.615 18764 Z= 0.353 Chirality : 0.051 0.510 2104 Planarity : 0.004 0.058 2344 Dihedral : 5.678 28.910 1904 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.07 % Allowed : 21.60 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.20), residues: 1644 helix: -0.53 (0.19), residues: 720 sheet: -1.05 (0.39), residues: 176 loop : -2.56 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 434 HIS 0.004 0.001 HIS B 258 PHE 0.017 0.002 PHE C 556 TYR 0.023 0.002 TYR B 526 ARG 0.003 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 284 time to evaluate : 1.538 Fit side-chains outliers start: 28 outliers final: 8 residues processed: 300 average time/residue: 0.2102 time to fit residues: 97.4470 Evaluate side-chains 276 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 268 time to evaluate : 1.591 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1214 time to fit residues: 3.8674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13768 Z= 0.345 Angle : 0.786 12.637 18764 Z= 0.397 Chirality : 0.053 0.509 2104 Planarity : 0.005 0.060 2344 Dihedral : 6.032 28.838 1904 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 2.66 % Allowed : 23.96 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.20), residues: 1644 helix: -0.71 (0.19), residues: 748 sheet: -1.26 (0.38), residues: 176 loop : -2.69 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 434 HIS 0.005 0.002 HIS C 404 PHE 0.020 0.002 PHE D 351 TYR 0.030 0.003 TYR D 526 ARG 0.002 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 276 time to evaluate : 1.508 Fit side-chains outliers start: 36 outliers final: 4 residues processed: 288 average time/residue: 0.2123 time to fit residues: 93.7389 Evaluate side-chains 256 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 252 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1196 time to fit residues: 2.8859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13768 Z= 0.226 Angle : 0.737 13.506 18764 Z= 0.363 Chirality : 0.051 0.487 2104 Planarity : 0.004 0.054 2344 Dihedral : 5.600 28.251 1904 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 2.07 % Allowed : 25.44 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.20), residues: 1644 helix: -0.40 (0.19), residues: 724 sheet: -1.11 (0.38), residues: 176 loop : -2.48 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 434 HIS 0.004 0.001 HIS B 258 PHE 0.033 0.002 PHE A 305 TYR 0.022 0.002 TYR D 526 ARG 0.001 0.000 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 292 time to evaluate : 1.408 Fit side-chains outliers start: 28 outliers final: 12 residues processed: 308 average time/residue: 0.2068 time to fit residues: 98.8257 Evaluate side-chains 276 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 264 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1315 time to fit residues: 4.9024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 0.0980 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13768 Z= 0.197 Angle : 0.729 13.995 18764 Z= 0.354 Chirality : 0.049 0.468 2104 Planarity : 0.004 0.055 2344 Dihedral : 5.295 27.979 1904 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.37 % Allowed : 24.56 % Favored : 73.08 % 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: -1.89 (0.21), residues: 1644 helix: -0.25 (0.19), residues: 728 sheet: -1.01 (0.39), residues: 176 loop : -2.36 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 434 HIS 0.004 0.001 HIS A 258 PHE 0.035 0.002 PHE A 305 TYR 0.019 0.002 TYR A 526 ARG 0.001 0.000 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 272 time to evaluate : 1.465 Fit side-chains outliers start: 32 outliers final: 12 residues processed: 292 average time/residue: 0.2290 time to fit residues: 100.3688 Evaluate side-chains 276 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 264 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1298 time to fit residues: 4.7995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 150 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 136 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13768 Z= 0.187 Angle : 0.745 14.151 18764 Z= 0.361 Chirality : 0.049 0.447 2104 Planarity : 0.004 0.053 2344 Dihedral : 5.116 26.999 1904 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 26.04 % Favored : 73.96 % 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: -1.89 (0.20), residues: 1644 helix: -0.29 (0.19), residues: 728 sheet: -1.07 (0.39), residues: 176 loop : -2.29 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 434 HIS 0.003 0.001 HIS D 258 PHE 0.032 0.002 PHE A 305 TYR 0.018 0.002 TYR A 526 ARG 0.002 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 1.733 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2181 time to fit residues: 94.9243 Evaluate side-chains 276 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 110 optimal weight: 0.3980 chunk 167 optimal weight: 10.0000 chunk 154 optimal weight: 0.5980 chunk 133 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 141 optimal weight: 0.0970 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5812 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13768 Z= 0.185 Angle : 0.764 14.306 18764 Z= 0.375 Chirality : 0.050 0.435 2104 Planarity : 0.004 0.051 2344 Dihedral : 4.948 25.832 1904 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.30 % Allowed : 26.63 % Favored : 73.08 % 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: -1.89 (0.20), residues: 1644 helix: -0.29 (0.19), residues: 712 sheet: -1.04 (0.39), residues: 176 loop : -2.26 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 434 HIS 0.003 0.001 HIS A 258 PHE 0.031 0.002 PHE A 305 TYR 0.025 0.002 TYR B 128 ARG 0.002 0.000 ARG A 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 292 time to evaluate : 1.341 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 292 average time/residue: 0.2253 time to fit residues: 100.3852 Evaluate side-chains 280 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.459 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 133 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 137 optimal weight: 0.0980 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 117 optimal weight: 0.0040 chunk 7 optimal weight: 20.0000 overall best weight: 1.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** 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 = 0.4360 r_free = 0.4360 target = 0.171042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.136645 restraints weight = 16075.750| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 3.49 r_work: 0.3914 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13768 Z= 0.195 Angle : 0.725 12.622 18764 Z= 0.360 Chirality : 0.049 0.423 2104 Planarity : 0.004 0.054 2344 Dihedral : 4.881 24.686 1904 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.30 % Allowed : 26.63 % Favored : 73.08 % 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: -1.84 (0.20), residues: 1644 helix: -0.26 (0.19), residues: 720 sheet: -0.94 (0.40), residues: 176 loop : -2.28 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 434 HIS 0.003 0.001 HIS C 258 PHE 0.032 0.002 PHE C 406 TYR 0.023 0.002 TYR C 128 ARG 0.001 0.000 ARG C 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3385.47 seconds wall clock time: 61 minutes 34.73 seconds (3694.73 seconds total)