Starting phenix.real_space_refine (version: dev) on Wed Dec 14 06:38:55 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbe_20291/12_2022/6pbe_20291_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbe_20291/12_2022/6pbe_20291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbe_20291/12_2022/6pbe_20291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbe_20291/12_2022/6pbe_20291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbe_20291/12_2022/6pbe_20291_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbe_20291/12_2022/6pbe_20291_updated.pdb" } resolution = 3.78 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= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 55": "OE1" <-> "OE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ASP 356": "OD1" <-> "OD2" Residue "B ASP 357": "OD1" <-> "OD2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B GLU 591": "OE1" <-> "OE2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ASP 356": "OD1" <-> "OD2" Residue "C ASP 357": "OD1" <-> "OD2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C GLU 403": "OE1" <-> "OE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C GLU 591": "OE1" <-> "OE2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C GLU 622": "OE1" <-> "OE2" Residue "C TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ASP 356": "OD1" <-> "OD2" Residue "D ASP 357": "OD1" <-> "OD2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 403": "OE1" <-> "OE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D GLU 591": "OE1" <-> "OE2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D GLU 622": "OE1" <-> "OE2" Residue "D TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 628": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 19452 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4797 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 4797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4797 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 4797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4797 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 4797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4797 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'O6S': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'O6S': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'O6S': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'O6S': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.99, per 1000 atoms: 0.51 Number of scatterers: 19452 At special positions: 0 Unit cell: (135.128, 134.064, 125.552, 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 144 16.00 O 3432 8.00 N 3268 7.00 C 12608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 2.7 seconds 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 8 sheets defined 56.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 31 through 46 removed outlier: 3.559A pdb=" N LEU A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 59 through 66 Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.672A pdb=" N TYR A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.094A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 253 through 262 removed outlier: 4.096A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 311 through 324 removed outlier: 4.663A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 348 removed outlier: 4.447A pdb=" N VAL A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 380 through 407 Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 423 through 444 removed outlier: 4.589A pdb=" N ILE A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 4.476A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N PHE A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 511 removed outlier: 3.768A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 553 through 566 removed outlier: 4.179A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 584 removed outlier: 4.185A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 607 removed outlier: 4.852A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 46 removed outlier: 3.559A pdb=" N LEU B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 59 through 66 Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.672A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 179 through 185 removed outlier: 4.094A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 253 through 262 removed outlier: 4.096A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 311 through 324 removed outlier: 4.663A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 348 removed outlier: 4.448A pdb=" N VAL B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 380 through 407 Proline residue: B 405 - end of helix Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 423 through 444 removed outlier: 4.589A pdb=" N ILE B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 468 removed outlier: 4.476A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N PHE B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 511 removed outlier: 3.767A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 553 through 566 removed outlier: 4.180A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 584 removed outlier: 4.185A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 607 removed outlier: 4.852A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 46 removed outlier: 3.559A pdb=" N LEU C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 59 through 66 Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.672A pdb=" N TYR C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 179 through 185 removed outlier: 4.094A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'C' and resid 243 through 250 Processing helix chain 'C' and resid 253 through 262 removed outlier: 4.096A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 311 through 324 removed outlier: 4.663A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 348 removed outlier: 4.447A pdb=" N VAL C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 380 through 407 Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 423 through 444 removed outlier: 4.588A pdb=" N ILE C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 468 removed outlier: 4.476A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N MET C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N PHE C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 511 removed outlier: 3.767A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N MET C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 507 " --> pdb=" O GLY C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 553 through 566 removed outlier: 4.180A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 584 removed outlier: 4.184A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 607 removed outlier: 4.853A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.559A pdb=" N LEU D 39 " --> pdb=" O ARG D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 59 through 66 Processing helix chain 'D' and resid 82 through 89 removed outlier: 3.672A pdb=" N TYR D 89 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 179 through 185 removed outlier: 4.093A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 213 through 222 Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 253 through 262 removed outlier: 4.096A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 311 through 324 removed outlier: 4.663A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 348 removed outlier: 4.448A pdb=" N VAL D 331 " --> pdb=" O PRO D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 380 through 407 Proline residue: D 405 - end of helix Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 423 through 444 removed outlier: 4.589A pdb=" N ILE D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 468 removed outlier: 4.475A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N PHE D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 511 removed outlier: 3.766A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA D 507 " --> pdb=" O GLY D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 553 through 566 removed outlier: 4.179A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 584 removed outlier: 4.184A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 607 removed outlier: 4.852A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 273 through 279 removed outlier: 3.562A pdb=" N THR A 276 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 352 through 354 Processing sheet with id= C, first strand: chain 'B' and resid 273 through 279 removed outlier: 3.562A pdb=" N THR B 276 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 352 through 354 Processing sheet with id= E, first strand: chain 'C' and resid 273 through 279 removed outlier: 3.562A pdb=" N THR C 276 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 352 through 354 Processing sheet with id= G, first strand: chain 'D' and resid 273 through 279 removed outlier: 3.562A pdb=" N THR D 276 " --> pdb=" O VAL D 633 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 352 through 354 820 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 7.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6165 1.34 - 1.46: 4021 1.46 - 1.58: 9498 1.58 - 1.69: 4 1.69 - 1.81: 240 Bond restraints: 19928 Sorted by residual: bond pdb=" C03 O6S D1002 " pdb=" C04 O6S D1002 " ideal model delta sigma weight residual 1.523 1.581 -0.058 2.00e-02 2.50e+03 8.38e+00 bond pdb=" C03 O6S B1002 " pdb=" C04 O6S B1002 " ideal model delta sigma weight residual 1.523 1.581 -0.058 2.00e-02 2.50e+03 8.30e+00 bond pdb=" C03 O6S A1002 " pdb=" C04 O6S A1002 " ideal model delta sigma weight residual 1.523 1.580 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" C03 O6S C1002 " pdb=" C04 O6S C1002 " ideal model delta sigma weight residual 1.523 1.580 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" C20 O6S A1001 " pdb=" N19 O6S A1001 " ideal model delta sigma weight residual 1.352 1.405 -0.053 2.00e-02 2.50e+03 7.01e+00 ... (remaining 19923 not shown) Histogram of bond angle deviations from ideal: 92.56 - 100.89: 56 100.89 - 109.22: 1679 109.22 - 117.56: 12333 117.56 - 125.89: 12660 125.89 - 134.23: 356 Bond angle restraints: 27084 Sorted by residual: angle pdb=" C ASN C 208 " pdb=" N LYS C 209 " pdb=" CA LYS C 209 " ideal model delta sigma weight residual 121.54 130.10 -8.56 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C ASN A 208 " pdb=" N LYS A 209 " pdb=" CA LYS A 209 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C ASN B 208 " pdb=" N LYS B 209 " pdb=" CA LYS B 209 " ideal model delta sigma weight residual 121.54 130.02 -8.48 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C ASN D 208 " pdb=" N LYS D 209 " pdb=" CA LYS D 209 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C SER B 285 " pdb=" N TRP B 286 " pdb=" CA TRP B 286 " ideal model delta sigma weight residual 121.54 128.32 -6.78 1.91e+00 2.74e-01 1.26e+01 ... (remaining 27079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 10282 17.79 - 35.58: 1138 35.58 - 53.37: 216 53.37 - 71.15: 56 71.15 - 88.94: 32 Dihedral angle restraints: 11724 sinusoidal: 4668 harmonic: 7056 Sorted by residual: dihedral pdb=" CA CYS D 112 " pdb=" C CYS D 112 " pdb=" N GLU D 113 " pdb=" CA GLU D 113 " ideal model delta harmonic sigma weight residual 180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA CYS C 112 " pdb=" C CYS C 112 " pdb=" N GLU C 113 " pdb=" CA GLU C 113 " ideal model delta harmonic sigma weight residual 180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA CYS B 112 " pdb=" C CYS B 112 " pdb=" N GLU B 113 " pdb=" CA GLU B 113 " ideal model delta harmonic sigma weight residual -180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 11721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1769 0.040 - 0.080: 886 0.080 - 0.120: 295 0.120 - 0.161: 58 0.161 - 0.201: 40 Chirality restraints: 3048 Sorted by residual: chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.83e-01 ... (remaining 3045 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 209 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C LYS C 209 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS C 209 " 0.017 2.00e-02 2.50e+03 pdb=" N THR C 210 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 209 " -0.014 2.00e-02 2.50e+03 2.72e-02 7.41e+00 pdb=" C LYS D 209 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS D 209 " -0.017 2.00e-02 2.50e+03 pdb=" N THR D 210 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 209 " -0.014 2.00e-02 2.50e+03 2.71e-02 7.35e+00 pdb=" C LYS B 209 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS B 209 " -0.017 2.00e-02 2.50e+03 pdb=" N THR B 210 " -0.016 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4197 2.78 - 3.31: 17275 3.31 - 3.84: 31135 3.84 - 4.37: 33543 4.37 - 4.90: 58590 Nonbonded interactions: 144740 Sorted by model distance: nonbonded pdb=" O SER A 464 " pdb=" OG SER A 464 " model vdw 2.248 2.440 nonbonded pdb=" O SER C 464 " pdb=" OG SER C 464 " model vdw 2.249 2.440 nonbonded pdb=" O SER D 464 " pdb=" OG SER D 464 " model vdw 2.249 2.440 nonbonded pdb=" O SER B 464 " pdb=" OG SER B 464 " model vdw 2.249 2.440 nonbonded pdb=" OG SER A 506 " pdb=" OH TYR A 526 " model vdw 2.336 2.440 ... (remaining 144735 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 12608 2.51 5 N 3268 2.21 5 O 3432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.430 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.150 Process input model: 45.010 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.006 0.060 19928 Z= 0.415 Angle : 1.018 10.005 27084 Z= 0.513 Chirality : 0.054 0.201 3048 Planarity : 0.007 0.059 3416 Dihedral : 16.229 88.943 7164 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer Outliers : 1.18 % 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: -5.02 (0.12), residues: 2400 helix: -2.71 (0.10), residues: 1452 sheet: -4.18 (0.58), residues: 40 loop : -4.21 (0.14), residues: 908 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 371 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 389 average time/residue: 0.3049 time to fit residues: 180.2561 Evaluate side-chains 285 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 273 time to evaluate : 2.115 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1587 time to fit residues: 6.6316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 509 HIS A 519 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 56 ASN B 131 ASN B 369 GLN B 509 HIS B 519 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 131 ASN C 509 HIS C 519 ASN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 56 ASN D 131 ASN D 369 GLN D 509 HIS D 519 ASN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 19928 Z= 0.254 Angle : 0.622 7.461 27084 Z= 0.311 Chirality : 0.040 0.120 3048 Planarity : 0.005 0.041 3416 Dihedral : 8.236 80.365 2696 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.15), residues: 2400 helix: -1.04 (0.13), residues: 1440 sheet: -4.49 (0.33), residues: 64 loop : -3.79 (0.16), residues: 896 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 292 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 46 residues processed: 328 average time/residue: 0.2665 time to fit residues: 140.8315 Evaluate side-chains 316 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 270 time to evaluate : 2.427 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.1707 time to fit residues: 17.9635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 19928 Z= 0.209 Angle : 0.575 8.250 27084 Z= 0.286 Chirality : 0.039 0.135 3048 Planarity : 0.004 0.039 3416 Dihedral : 7.935 76.502 2696 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.16), residues: 2400 helix: -0.38 (0.14), residues: 1432 sheet: -3.91 (0.40), residues: 64 loop : -3.57 (0.16), residues: 904 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 300 time to evaluate : 2.409 Fit side-chains outliers start: 36 outliers final: 19 residues processed: 318 average time/residue: 0.2586 time to fit residues: 133.9735 Evaluate side-chains 289 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 270 time to evaluate : 2.379 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1699 time to fit residues: 9.2743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 2.9990 chunk 164 optimal weight: 0.0980 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 207 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 19928 Z= 0.144 Angle : 0.546 9.987 27084 Z= 0.262 Chirality : 0.038 0.129 3048 Planarity : 0.004 0.039 3416 Dihedral : 7.834 72.050 2696 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 1.67 % 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: -1.75 (0.17), residues: 2400 helix: 0.16 (0.14), residues: 1424 sheet: -3.37 (0.46), residues: 64 loop : -3.23 (0.17), residues: 912 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 305 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 26 residues processed: 327 average time/residue: 0.2824 time to fit residues: 146.8069 Evaluate side-chains 305 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 279 time to evaluate : 2.319 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1763 time to fit residues: 11.6136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 10.0000 chunk 131 optimal weight: 0.0270 chunk 3 optimal weight: 20.0000 chunk 172 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN D 369 GLN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 19928 Z= 0.233 Angle : 0.593 10.873 27084 Z= 0.288 Chirality : 0.040 0.129 3048 Planarity : 0.004 0.041 3416 Dihedral : 7.562 65.644 2696 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 1.86 % 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: -1.70 (0.17), residues: 2400 helix: 0.22 (0.14), residues: 1428 sheet: -3.36 (0.46), residues: 64 loop : -3.24 (0.17), residues: 908 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 281 time to evaluate : 2.336 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 27 residues processed: 300 average time/residue: 0.2505 time to fit residues: 123.5400 Evaluate side-chains 293 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 266 time to evaluate : 2.055 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1593 time to fit residues: 11.0205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 310 GLN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN B 310 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN C 310 GLN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN D 310 GLN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 19928 Z= 0.316 Angle : 0.670 10.143 27084 Z= 0.327 Chirality : 0.043 0.248 3048 Planarity : 0.004 0.041 3416 Dihedral : 6.972 63.540 2696 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 2.30 % 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: -1.79 (0.17), residues: 2400 helix: 0.09 (0.14), residues: 1412 sheet: -3.28 (0.47), residues: 64 loop : -3.12 (0.17), residues: 924 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 286 time to evaluate : 2.371 Fit side-chains outliers start: 47 outliers final: 32 residues processed: 314 average time/residue: 0.2609 time to fit residues: 135.3832 Evaluate side-chains 296 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 264 time to evaluate : 2.291 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1772 time to fit residues: 13.8988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 132 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 131 optimal weight: 20.0000 chunk 195 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 144 optimal weight: 0.0050 chunk 141 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN B 369 GLN B 596 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 19928 Z= 0.149 Angle : 0.550 9.030 27084 Z= 0.267 Chirality : 0.038 0.268 3048 Planarity : 0.004 0.039 3416 Dihedral : 6.466 61.917 2696 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 0.59 % 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: -1.34 (0.17), residues: 2400 helix: 0.44 (0.14), residues: 1420 sheet: -3.09 (0.48), residues: 64 loop : -2.96 (0.18), residues: 916 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 300 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 308 average time/residue: 0.2700 time to fit residues: 135.0461 Evaluate side-chains 277 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 271 time to evaluate : 2.236 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1874 time to fit residues: 5.3138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN B 635 ASN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 19928 Z= 0.219 Angle : 0.581 9.078 27084 Z= 0.284 Chirality : 0.040 0.159 3048 Planarity : 0.004 0.039 3416 Dihedral : 6.464 63.128 2696 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2400 helix: 0.45 (0.14), residues: 1420 sheet: -3.06 (0.49), residues: 64 loop : -2.97 (0.18), residues: 916 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 281 time to evaluate : 2.518 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 288 average time/residue: 0.2626 time to fit residues: 124.9691 Evaluate side-chains 286 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 275 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1900 time to fit residues: 7.0603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 169 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 203 optimal weight: 0.5980 chunk 214 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN B 635 ASN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 19928 Z= 0.228 Angle : 0.604 12.899 27084 Z= 0.292 Chirality : 0.040 0.146 3048 Planarity : 0.004 0.039 3416 Dihedral : 6.437 62.462 2696 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer Outliers : 0.78 % 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: -1.38 (0.17), residues: 2400 helix: 0.40 (0.14), residues: 1420 sheet: -2.92 (0.50), residues: 64 loop : -2.97 (0.18), residues: 916 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 285 time to evaluate : 2.416 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 291 average time/residue: 0.2588 time to fit residues: 124.2528 Evaluate side-chains 277 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 271 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1864 time to fit residues: 5.3859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN B 635 ASN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 19928 Z= 0.274 Angle : 0.649 13.188 27084 Z= 0.313 Chirality : 0.042 0.224 3048 Planarity : 0.004 0.040 3416 Dihedral : 6.498 62.184 2696 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 0.29 % 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: -1.47 (0.17), residues: 2400 helix: 0.30 (0.14), residues: 1416 sheet: -2.99 (0.49), residues: 64 loop : -2.93 (0.18), residues: 920 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 273 time to evaluate : 2.258 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 275 average time/residue: 0.2619 time to fit residues: 119.9645 Evaluate side-chains 270 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 266 time to evaluate : 2.420 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2445 time to fit residues: 4.7692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 24 optimal weight: 0.0170 chunk 35 optimal weight: 3.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN B 635 ASN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.155382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149954 restraints weight = 23658.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.148716 restraints weight = 34471.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.147456 restraints weight = 36363.968| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 19928 Z= 0.145 Angle : 0.576 12.729 27084 Z= 0.272 Chirality : 0.038 0.207 3048 Planarity : 0.004 0.038 3416 Dihedral : 6.325 62.916 2696 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2400 helix: 0.58 (0.14), residues: 1416 sheet: -2.85 (0.50), residues: 64 loop : -2.76 (0.19), residues: 920 =============================================================================== Job complete usr+sys time: 3239.69 seconds wall clock time: 60 minutes 1.76 seconds (3601.76 seconds total)