Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 20:40:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6du8_8912/04_2023/6du8_8912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6du8_8912/04_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_8912/04_2023/6du8_8912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6du8_8912/04_2023/6du8_8912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6du8_8912/04_2023/6du8_8912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6du8_8912/04_2023/6du8_8912.pdb" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 chiralities: 1 Time building chain proxies: 7.05, per 1000 atoms: 0.53 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: 4.71 Conformation dependent library (CDL) restraints added in 1.7 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: 0.47 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: 3.28 Time building geometry restraints manager: 5.13 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: 7008 15.72 - 31.43: 524 31.43 - 47.14: 120 47.14 - 62.86: 8 62.86 - 78.57: 12 Dihedral angle restraints: 7672 sinusoidal: 2764 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 7669 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: 0.990 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: 4.930 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 32.480 Find NCS groups from input model: 0.900 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.560 ------------------------------------------------------------------------------- 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 : 12.565 78.570 4520 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 % 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 *********************** 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 : 1.362 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 412 average time/residue: 0.2019 time to fit residues: 127.8902 Evaluate side-chains 320 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 308 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1142 time to fit residues: 4.4407 ------------------------------------------------------------------------------- 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: 0.5844 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 0.034 13768 Z= 0.234 Angle : 0.691 7.782 18764 Z= 0.366 Chirality : 0.053 0.536 2104 Planarity : 0.005 0.067 2344 Dihedral : 5.954 26.923 1820 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 3.85 % 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: -1.06 (0.39), residues: 176 loop : -3.11 (0.20), residues: 712 *********************** 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 : 1.447 Fit side-chains outliers start: 52 outliers final: 20 residues processed: 360 average time/residue: 0.2264 time to fit residues: 124.3311 Evaluate side-chains 296 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 276 time to evaluate : 1.468 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1198 time to fit residues: 6.4985 ------------------------------------------------------------------------------- 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: 5.9990 chunk 126 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.5938 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 13768 Z= 0.404 Angle : 0.809 9.395 18764 Z= 0.419 Chirality : 0.056 0.551 2104 Planarity : 0.006 0.062 2344 Dihedral : 6.129 27.876 1820 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.90 % Favored : 87.10 % Rotamer Outliers : 2.07 % 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: -3.11 (0.19), residues: 1644 helix: -1.27 (0.18), residues: 756 sheet: -1.20 (0.40), residues: 176 loop : -3.18 (0.21), residues: 712 *********************** 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 324 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 296 time to evaluate : 1.532 Fit side-chains outliers start: 28 outliers final: 16 residues processed: 320 average time/residue: 0.2119 time to fit residues: 104.3364 Evaluate side-chains 292 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 276 time to evaluate : 1.584 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1192 time to fit residues: 5.7200 ------------------------------------------------------------------------------- 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: 7.9990 chunk 114 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 0.3980 chunk 102 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.5850 moved from start: 0.2913 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= 0.196 Angle : 0.717 11.997 18764 Z= 0.356 Chirality : 0.050 0.482 2104 Planarity : 0.004 0.057 2344 Dihedral : 5.301 23.412 1820 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer Outliers : 2.07 % 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: -2.45 (0.20), residues: 1644 helix: -0.74 (0.19), residues: 744 sheet: -0.85 (0.40), residues: 176 loop : -2.81 (0.21), residues: 724 *********************** 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 334 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 306 time to evaluate : 1.486 Fit side-chains outliers start: 28 outliers final: 20 residues processed: 318 average time/residue: 0.2220 time to fit residues: 106.8156 Evaluate side-chains 292 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 272 time to evaluate : 1.410 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1243 time to fit residues: 6.5692 ------------------------------------------------------------------------------- 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: 4.9990 chunk 92 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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: 0.5904 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 13768 Z= 0.289 Angle : 0.723 12.168 18764 Z= 0.367 Chirality : 0.051 0.476 2104 Planarity : 0.005 0.059 2344 Dihedral : 5.430 27.629 1820 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer Outliers : 2.96 % 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: -2.30 (0.20), residues: 1644 helix: -0.63 (0.19), residues: 724 sheet: -0.97 (0.39), residues: 176 loop : -2.59 (0.22), residues: 744 *********************** 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 326 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 286 time to evaluate : 1.476 Fit side-chains outliers start: 40 outliers final: 8 residues processed: 310 average time/residue: 0.2156 time to fit residues: 102.0027 Evaluate side-chains 288 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 280 time to evaluate : 1.455 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1193 time to fit residues: 3.8899 ------------------------------------------------------------------------------- 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: 3.9990 chunk 146 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 0.0060 chunk 53 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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** ** 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: 0.5853 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 0.025 13768 Z= 0.195 Angle : 0.707 13.545 18764 Z= 0.347 Chirality : 0.049 0.452 2104 Planarity : 0.004 0.053 2344 Dihedral : 5.119 26.110 1820 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer Outliers : 1.78 % 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: -2.14 (0.20), residues: 1644 helix: -0.47 (0.19), residues: 728 sheet: -0.88 (0.39), residues: 176 loop : -2.56 (0.22), residues: 740 *********************** 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 328 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 304 time to evaluate : 1.363 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 312 average time/residue: 0.2056 time to fit residues: 97.6812 Evaluate side-chains 291 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 279 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1162 time to fit residues: 4.6763 ------------------------------------------------------------------------------- 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: 10.0000 chunk 118 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 289 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 13768 Z= 0.339 Angle : 0.774 13.120 18764 Z= 0.391 Chirality : 0.053 0.458 2104 Planarity : 0.005 0.060 2344 Dihedral : 5.501 29.874 1820 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer Outliers : 1.48 % 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: -2.17 (0.21), residues: 1644 helix: -0.50 (0.19), residues: 724 sheet: -1.00 (0.39), residues: 176 loop : -2.54 (0.22), residues: 744 *********************** 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 296 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 276 time to evaluate : 1.339 Fit side-chains outliers start: 20 outliers final: 4 residues processed: 284 average time/residue: 0.2133 time to fit residues: 93.2853 Evaluate side-chains 278 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 274 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1209 time to fit residues: 3.0391 ------------------------------------------------------------------------------- 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: 9.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.5849 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 13768 Z= 0.194 Angle : 0.741 14.303 18764 Z= 0.360 Chirality : 0.049 0.432 2104 Planarity : 0.004 0.052 2344 Dihedral : 5.108 31.704 1820 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.97 (0.20), residues: 1644 helix: -0.35 (0.19), residues: 728 sheet: -0.76 (0.39), residues: 176 loop : -2.46 (0.22), residues: 740 *********************** 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 310 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 288 time to evaluate : 1.605 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 306 average time/residue: 0.2063 time to fit residues: 98.2007 Evaluate side-chains 279 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 265 time to evaluate : 1.513 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1365 time to fit residues: 5.4268 ------------------------------------------------------------------------------- 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: 8.9990 chunk 141 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 99 optimal weight: 0.0980 chunk 159 optimal weight: 0.0470 overall best weight: 3.8284 ------------------------------------------------------------------------------- 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: 0.5907 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 13768 Z= 0.304 Angle : 0.788 14.076 18764 Z= 0.389 Chirality : 0.052 0.438 2104 Planarity : 0.005 0.060 2344 Dihedral : 5.335 32.867 1820 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.00 (0.20), residues: 1644 helix: -0.43 (0.19), residues: 728 sheet: -0.86 (0.38), residues: 176 loop : -2.38 (0.23), residues: 740 *********************** 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 300 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 277 time to evaluate : 1.503 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 283 average time/residue: 0.2234 time to fit residues: 95.4788 Evaluate side-chains 290 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 275 time to evaluate : 1.463 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1183 time to fit residues: 5.4252 ------------------------------------------------------------------------------- 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: 9.9990 chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 133 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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: 0.5913 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 13768 Z= 0.324 Angle : 0.813 14.314 18764 Z= 0.401 Chirality : 0.052 0.439 2104 Planarity : 0.005 0.055 2344 Dihedral : 5.474 33.154 1820 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.13 (0.20), residues: 1644 helix: -0.68 (0.18), residues: 752 sheet: -0.91 (0.39), residues: 176 loop : -2.33 (0.23), residues: 716 ********************** 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 277 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 267 time to evaluate : 1.530 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 271 average time/residue: 0.2203 time to fit residues: 90.7683 Evaluate side-chains 261 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 259 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1134 time to fit residues: 2.2843 ------------------------------------------------------------------------------- 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: 1.9990 chunk 122 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4342 r_free = 0.4342 target = 0.168297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.134315 restraints weight = 16431.827| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 3.53 r_work: 0.3838 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 13768 Z= 0.246 Angle : 0.772 14.593 18764 Z= 0.386 Chirality : 0.051 0.428 2104 Planarity : 0.004 0.057 2344 Dihedral : 5.261 32.849 1820 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.95 (0.20), residues: 1644 helix: -0.42 (0.19), residues: 728 sheet: -0.80 (0.39), residues: 176 loop : -2.33 (0.23), residues: 740 =============================================================================== Job complete usr+sys time: 3164.69 seconds wall clock time: 57 minutes 55.50 seconds (3475.50 seconds total)