Starting phenix.real_space_refine on Sat Feb 17 17:50:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbe_20291/02_2024/6pbe_20291_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbe_20291/02_2024/6pbe_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_20291/02_2024/6pbe_20291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbe_20291/02_2024/6pbe_20291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbe_20291/02_2024/6pbe_20291_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pbe_20291/02_2024/6pbe_20291_updated.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 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. 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9.80, per 1000 atoms: 0.50 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: 7.19 Conformation dependent library (CDL) restraints added in 4.0 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: 4.05 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: 5.38 Time building geometry restraints manager: 7.87 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 - 31.71: 11260 31.71 - 63.43: 456 63.43 - 95.14: 52 95.14 - 126.85: 0 126.85 - 158.57: 4 Dihedral angle restraints: 11772 sinusoidal: 4716 harmonic: 7056 Sorted by residual: dihedral pdb=" C03 O6S A1001 " pdb=" C02 O6S A1001 " pdb=" O16 O6S A1001 " pdb=" C17 O6S A1001 " ideal model delta sinusoidal sigma weight residual 178.86 -22.57 -158.57 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C03 O6S B1001 " pdb=" C02 O6S B1001 " pdb=" O16 O6S B1001 " pdb=" C17 O6S B1001 " ideal model delta sinusoidal sigma weight residual 178.86 -22.57 -158.57 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C03 O6S C1001 " pdb=" C02 O6S C1001 " pdb=" O16 O6S C1001 " pdb=" C17 O6S C1001 " ideal model delta sinusoidal sigma weight residual 178.86 -22.58 -158.56 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 11769 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 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: 0.290 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: 2.750 Check model and map are aligned: 0.280 Set scattering table: 0.230 Process input model: 50.620 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.120 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:2.910 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 : 16.964 158.568 7212 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.18 % Allowed : 9.17 % Favored : 89.66 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 613 HIS 0.005 0.001 HIS B 201 PHE 0.012 0.002 PHE C 537 TYR 0.010 0.002 TYR C 222 ARG 0.003 0.000 ARG B 350 *********************** 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 : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7569 (mtp180) cc_final: 0.6980 (ttm170) REVERT: A 483 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8407 (tm-30) REVERT: A 628 ARG cc_start: 0.8030 (mtm180) cc_final: 0.7807 (mtp85) REVERT: B 113 GLU cc_start: 0.7301 (tp30) cc_final: 0.7089 (tp30) REVERT: B 483 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8371 (tm-30) REVERT: B 491 MET cc_start: 0.7342 (tpp) cc_final: 0.7095 (tpp) REVERT: B 495 TRP cc_start: 0.7649 (m100) cc_final: 0.7239 (m100) REVERT: C 483 GLN cc_start: 0.8522 (tm-30) cc_final: 0.7686 (tt0) REVERT: C 495 TRP cc_start: 0.7772 (m100) cc_final: 0.7571 (m100) REVERT: C 515 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7431 (mm-30) REVERT: C 628 ARG cc_start: 0.7988 (mtm180) cc_final: 0.7784 (mtp85) REVERT: D 483 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8346 (tm-30) REVERT: D 495 TRP cc_start: 0.7706 (m100) cc_final: 0.7328 (m100) REVERT: D 515 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7477 (mm-30) outliers start: 24 outliers final: 12 residues processed: 389 average time/residue: 0.3093 time to fit residues: 181.5678 Evaluate side-chains 293 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 281 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 394 THR 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: 10.0000 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 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: 0.7507 moved from start: 0.1578 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 7.555 27084 Z= 0.310 Chirality : 0.040 0.121 3048 Planarity : 0.005 0.040 3416 Dihedral : 11.638 168.652 2756 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.14 % Allowed : 16.96 % Favored : 79.90 % 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: -3.21 (0.15), residues: 2400 helix: -1.04 (0.13), residues: 1440 sheet: -4.53 (0.32), residues: 64 loop : -3.77 (0.16), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 629 HIS 0.003 0.001 HIS B 258 PHE 0.017 0.001 PHE A 574 TYR 0.019 0.001 TYR C 216 ARG 0.004 0.000 ARG D 628 *********************** 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 375 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 311 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7033 (ttm170) REVERT: A 466 MET cc_start: 0.8496 (mmp) cc_final: 0.8162 (mmt) REVERT: A 483 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8440 (tm-30) REVERT: A 491 MET cc_start: 0.7310 (tpp) cc_final: 0.7078 (mmt) REVERT: A 601 THR cc_start: 0.6979 (m) cc_final: 0.5467 (p) REVERT: B 146 ARG cc_start: 0.7688 (mtp180) cc_final: 0.7284 (ttm170) REVERT: B 466 MET cc_start: 0.8494 (mmp) cc_final: 0.8176 (mmt) REVERT: B 483 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8457 (tm-30) REVERT: B 491 MET cc_start: 0.7393 (tpp) cc_final: 0.7129 (tpp) REVERT: B 629 TRP cc_start: 0.9211 (m100) cc_final: 0.8980 (m100) REVERT: C 38 MET cc_start: 0.8261 (mmm) cc_final: 0.7924 (tpt) REVERT: C 466 MET cc_start: 0.8506 (mmp) cc_final: 0.8112 (mmt) REVERT: C 483 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8368 (tm-30) REVERT: C 601 THR cc_start: 0.6972 (m) cc_final: 0.5431 (p) REVERT: C 628 ARG cc_start: 0.8017 (mtm180) cc_final: 0.7800 (mtp85) REVERT: D 38 MET cc_start: 0.8302 (mmm) cc_final: 0.8030 (tpt) REVERT: D 466 MET cc_start: 0.8499 (mmp) cc_final: 0.8168 (mmt) REVERT: D 483 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8407 (tm-30) REVERT: D 554 MET cc_start: 0.6650 (tpp) cc_final: 0.6404 (tpp) REVERT: D 601 THR cc_start: 0.6982 (m) cc_final: 0.5425 (p) REVERT: D 629 TRP cc_start: 0.9171 (m100) cc_final: 0.8929 (m100) outliers start: 64 outliers final: 53 residues processed: 355 average time/residue: 0.2814 time to fit residues: 158.7338 Evaluate side-chains 336 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 283 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 602 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 30.0000 chunk 181 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 0.2980 chunk 235 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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: 0.7525 moved from start: 0.1915 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= 0.252 Angle : 0.601 8.852 27084 Z= 0.299 Chirality : 0.040 0.126 3048 Planarity : 0.004 0.043 3416 Dihedral : 11.459 177.525 2752 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.41 % Allowed : 19.66 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.16), residues: 2400 helix: -0.43 (0.14), residues: 1428 sheet: -3.92 (0.41), residues: 64 loop : -3.51 (0.16), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 583 HIS 0.003 0.001 HIS A 258 PHE 0.014 0.001 PHE A 611 TYR 0.016 0.001 TYR B 216 ARG 0.005 0.000 ARG A 628 *********************** 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 394 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 304 time to evaluate : 2.102 Fit side-chains REVERT: A 146 ARG cc_start: 0.7705 (mtp180) cc_final: 0.7126 (ttm170) REVERT: A 216 TYR cc_start: 0.8068 (t80) cc_final: 0.7858 (t80) REVERT: A 483 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8438 (tm-30) REVERT: A 547 TYR cc_start: 0.6373 (m-80) cc_final: 0.6169 (m-80) REVERT: A 601 THR cc_start: 0.7064 (m) cc_final: 0.5555 (p) REVERT: A 603 MET cc_start: 0.7511 (tmm) cc_final: 0.7235 (tmm) REVERT: B 126 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7493 (ttt) REVERT: B 146 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7358 (ttm170) REVERT: B 353 LYS cc_start: 0.7040 (tttm) cc_final: 0.6772 (ptmt) REVERT: B 483 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8433 (tm-30) REVERT: B 491 MET cc_start: 0.7333 (tpp) cc_final: 0.7053 (tpp) REVERT: B 547 TYR cc_start: 0.6430 (m-80) cc_final: 0.6209 (m-80) REVERT: B 601 THR cc_start: 0.7106 (m) cc_final: 0.5599 (p) REVERT: C 38 MET cc_start: 0.8356 (mmm) cc_final: 0.8060 (tpt) REVERT: C 126 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7606 (ttt) REVERT: C 146 ARG cc_start: 0.7681 (mtp180) cc_final: 0.7209 (ttm170) REVERT: C 353 LYS cc_start: 0.6742 (tttm) cc_final: 0.6442 (ptmt) REVERT: C 466 MET cc_start: 0.8347 (mmp) cc_final: 0.8083 (mmt) REVERT: C 483 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8432 (tm-30) REVERT: C 491 MET cc_start: 0.7197 (tpp) cc_final: 0.6963 (tpp) REVERT: C 547 TYR cc_start: 0.6381 (m-80) cc_final: 0.6181 (m-80) REVERT: C 601 THR cc_start: 0.7166 (m) cc_final: 0.5629 (p) REVERT: C 628 ARG cc_start: 0.8064 (mtm180) cc_final: 0.7856 (mtp85) REVERT: D 38 MET cc_start: 0.8304 (mmm) cc_final: 0.8095 (tpt) REVERT: D 146 ARG cc_start: 0.7622 (mtp180) cc_final: 0.7289 (ttm170) REVERT: D 466 MET cc_start: 0.8451 (mmp) cc_final: 0.8182 (mmt) REVERT: D 483 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8454 (tm-30) outliers start: 90 outliers final: 67 residues processed: 364 average time/residue: 0.2731 time to fit residues: 161.3249 Evaluate side-chains 354 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 285 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 602 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 146 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.7416 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19928 Z= 0.130 Angle : 0.534 9.617 27084 Z= 0.255 Chirality : 0.037 0.118 3048 Planarity : 0.003 0.040 3416 Dihedral : 11.150 169.869 2752 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.94 % Allowed : 22.40 % Favored : 74.66 % 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: 1424 sheet: -3.36 (0.46), residues: 64 loop : -3.22 (0.17), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 583 HIS 0.002 0.000 HIS B 582 PHE 0.009 0.001 PHE D 574 TYR 0.013 0.001 TYR D 216 ARG 0.004 0.000 ARG A 628 *********************** 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 391 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 331 time to evaluate : 2.186 Fit side-chains REVERT: A 353 LYS cc_start: 0.6979 (tttm) cc_final: 0.6663 (ptmt) REVERT: A 466 MET cc_start: 0.8409 (mmp) cc_final: 0.8173 (mmt) REVERT: A 483 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8432 (tm-30) REVERT: A 603 MET cc_start: 0.7344 (tmm) cc_final: 0.7024 (tmm) REVERT: B 146 ARG cc_start: 0.7593 (mtp180) cc_final: 0.7294 (ttm170) REVERT: B 466 MET cc_start: 0.8432 (mmp) cc_final: 0.8228 (mmt) REVERT: B 483 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8422 (tm-30) REVERT: B 491 MET cc_start: 0.7184 (tpp) cc_final: 0.6960 (tpp) REVERT: C 38 MET cc_start: 0.8283 (mmm) cc_final: 0.7974 (tpt) REVERT: C 483 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8407 (tm-30) REVERT: C 515 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7431 (mm-30) REVERT: D 38 MET cc_start: 0.8255 (mmm) cc_final: 0.8009 (tpt) REVERT: D 483 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8455 (tm-30) REVERT: D 515 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7457 (mm-30) outliers start: 60 outliers final: 53 residues processed: 375 average time/residue: 0.2932 time to fit residues: 172.5714 Evaluate side-chains 343 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 290 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 528 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 172 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 19928 Z= 0.489 Angle : 0.777 9.935 27084 Z= 0.382 Chirality : 0.046 0.269 3048 Planarity : 0.005 0.048 3416 Dihedral : 11.107 177.140 2752 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 6.32 % Allowed : 23.24 % Favored : 70.44 % 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 (0.16), residues: 2400 helix: -0.20 (0.14), residues: 1416 sheet: -3.51 (0.45), residues: 64 loop : -3.28 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 583 HIS 0.006 0.002 HIS B 509 PHE 0.020 0.002 PHE D 562 TYR 0.014 0.002 TYR A 623 ARG 0.004 0.000 ARG A 615 *********************** 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 412 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 283 time to evaluate : 2.374 Fit side-chains REVERT: A 341 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7681 (tp) REVERT: A 353 LYS cc_start: 0.6820 (tttm) cc_final: 0.6565 (ptmt) REVERT: A 570 MET cc_start: 0.6784 (tpp) cc_final: 0.6542 (tpp) REVERT: B 126 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7682 (ttt) REVERT: B 146 ARG cc_start: 0.7807 (mtp180) cc_final: 0.7372 (ttm170) REVERT: B 341 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7695 (tp) REVERT: B 570 MET cc_start: 0.6784 (tpp) cc_final: 0.6576 (tpp) REVERT: C 38 MET cc_start: 0.8395 (mmm) cc_final: 0.8125 (tpt) REVERT: C 126 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7700 (ttt) REVERT: C 450 GLU cc_start: 0.8149 (tp30) cc_final: 0.7914 (tp30) REVERT: C 554 MET cc_start: 0.7066 (tpp) cc_final: 0.6760 (tpp) REVERT: C 628 ARG cc_start: 0.8204 (mtm180) cc_final: 0.7956 (mtp85) REVERT: D 38 MET cc_start: 0.8372 (mmm) cc_final: 0.8153 (tpt) REVERT: D 126 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7738 (ttt) REVERT: D 341 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7760 (tp) REVERT: D 515 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7463 (mm-30) REVERT: D 570 MET cc_start: 0.6665 (tpp) cc_final: 0.6403 (tpp) outliers start: 129 outliers final: 96 residues processed: 377 average time/residue: 0.2576 time to fit residues: 158.7178 Evaluate side-chains 368 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 266 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 602 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 GLN B 596 GLN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19928 Z= 0.164 Angle : 0.567 9.129 27084 Z= 0.274 Chirality : 0.039 0.253 3048 Planarity : 0.004 0.041 3416 Dihedral : 10.656 179.016 2752 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.71 % Allowed : 26.08 % Favored : 69.22 % 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: -1.63 (0.17), residues: 2400 helix: 0.22 (0.14), residues: 1416 sheet: -3.32 (0.46), residues: 64 loop : -3.07 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 583 HIS 0.003 0.001 HIS D 258 PHE 0.010 0.001 PHE C 574 TYR 0.014 0.001 TYR A 216 ARG 0.004 0.000 ARG A 45 *********************** 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 400 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 304 time to evaluate : 2.280 Fit side-chains REVERT: A 264 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8336 (tttt) REVERT: A 353 LYS cc_start: 0.6792 (tttm) cc_final: 0.6574 (ptmt) REVERT: A 483 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8543 (tm-30) REVERT: A 554 MET cc_start: 0.7103 (tpp) cc_final: 0.6827 (tpp) REVERT: B 146 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7314 (ttm170) REVERT: B 483 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8548 (tm-30) REVERT: C 38 MET cc_start: 0.8293 (mmm) cc_final: 0.8064 (tpt) REVERT: C 341 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7643 (tp) REVERT: C 483 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8499 (tm-30) REVERT: C 491 MET cc_start: 0.7080 (tpp) cc_final: 0.6833 (tpp) REVERT: C 515 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7240 (mm-30) REVERT: D 38 MET cc_start: 0.8305 (mmm) cc_final: 0.8086 (tpt) REVERT: D 483 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8553 (tm-30) REVERT: D 491 MET cc_start: 0.7165 (tpp) cc_final: 0.6937 (tpp) REVERT: D 515 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7397 (mm-30) REVERT: D 554 MET cc_start: 0.6958 (tpp) cc_final: 0.6683 (tpp) outliers start: 96 outliers final: 85 residues processed: 377 average time/residue: 0.2538 time to fit residues: 156.9827 Evaluate side-chains 375 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 289 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 369 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 602 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN A 635 ASN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2652 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= 0.314 Angle : 0.640 9.087 27084 Z= 0.314 Chirality : 0.042 0.175 3048 Planarity : 0.004 0.042 3416 Dihedral : 10.509 176.900 2752 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 5.78 % Allowed : 26.13 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.17), residues: 2400 helix: 0.12 (0.14), residues: 1416 sheet: -3.27 (0.47), residues: 64 loop : -3.15 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 583 HIS 0.004 0.001 HIS B 509 PHE 0.016 0.001 PHE D 562 TYR 0.013 0.001 TYR D 216 ARG 0.006 0.000 ARG C 628 *********************** 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 408 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 290 time to evaluate : 2.294 Fit side-chains revert: symmetry clash REVERT: A 126 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7722 (ttt) REVERT: A 264 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8367 (tttt) REVERT: A 483 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8561 (tm-30) REVERT: B 440 MET cc_start: 0.7949 (tpt) cc_final: 0.7717 (tpt) REVERT: B 483 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8567 (tm-30) REVERT: C 38 MET cc_start: 0.8301 (mmm) cc_final: 0.8085 (tpt) REVERT: C 341 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7654 (tp) REVERT: C 491 MET cc_start: 0.7254 (tpp) cc_final: 0.7040 (tpp) REVERT: C 513 GLN cc_start: 0.8169 (tt0) cc_final: 0.7854 (tt0) REVERT: C 554 MET cc_start: 0.7216 (tpp) cc_final: 0.6910 (tpp) REVERT: C 603 MET cc_start: 0.7508 (tmm) cc_final: 0.7291 (tmm) REVERT: D 483 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8549 (tm-30) REVERT: D 491 MET cc_start: 0.7271 (tpp) cc_final: 0.7069 (tpp) REVERT: D 570 MET cc_start: 0.6508 (tpp) cc_final: 0.6209 (tpp) outliers start: 118 outliers final: 100 residues processed: 374 average time/residue: 0.2554 time to fit residues: 158.3996 Evaluate side-chains 383 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 281 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 369 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 602 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN B 128 GLN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2746 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= 0.148 Angle : 0.557 12.567 27084 Z= 0.265 Chirality : 0.038 0.137 3048 Planarity : 0.003 0.039 3416 Dihedral : 9.709 162.762 2752 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.36 % Allowed : 27.25 % Favored : 68.38 % 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: -1.33 (0.17), residues: 2400 helix: 0.44 (0.14), residues: 1416 sheet: -3.06 (0.48), residues: 64 loop : -2.91 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 583 HIS 0.004 0.001 HIS D 258 PHE 0.009 0.001 PHE A 562 TYR 0.010 0.001 TYR C 162 ARG 0.006 0.000 ARG C 628 *********************** 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 395 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 306 time to evaluate : 2.190 Fit side-chains revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8321 (tttt) REVERT: A 286 TRP cc_start: 0.5316 (t60) cc_final: 0.4464 (t60) REVERT: A 483 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8556 (tm-30) REVERT: B 146 ARG cc_start: 0.7779 (mtp180) cc_final: 0.7335 (ttm170) REVERT: B 483 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8541 (tm-30) REVERT: C 38 MET cc_start: 0.8291 (mmm) cc_final: 0.8023 (tpt) REVERT: C 483 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8487 (tm-30) REVERT: C 491 MET cc_start: 0.6945 (tpp) cc_final: 0.6735 (tpp) REVERT: C 513 GLN cc_start: 0.8141 (tt0) cc_final: 0.7848 (tt0) REVERT: C 515 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7290 (mm-30) REVERT: C 554 MET cc_start: 0.7118 (tpp) cc_final: 0.6757 (tpp) REVERT: D 483 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8540 (tm-30) REVERT: D 491 MET cc_start: 0.7077 (tpp) cc_final: 0.6835 (tpp) REVERT: D 515 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7470 (mm-30) outliers start: 89 outliers final: 83 residues processed: 365 average time/residue: 0.2513 time to fit residues: 150.2093 Evaluate side-chains 378 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 295 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 602 VAL 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: 0.8980 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 214 optimal weight: 0.0370 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7490 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19928 Z= 0.193 Angle : 0.581 13.007 27084 Z= 0.276 Chirality : 0.039 0.136 3048 Planarity : 0.004 0.038 3416 Dihedral : 9.427 153.678 2752 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.75 % Allowed : 27.11 % Favored : 68.14 % 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: -1.28 (0.17), residues: 2400 helix: 0.50 (0.14), residues: 1420 sheet: -3.03 (0.49), residues: 64 loop : -2.94 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 583 HIS 0.003 0.001 HIS D 258 PHE 0.012 0.001 PHE A 562 TYR 0.015 0.001 TYR D 216 ARG 0.006 0.000 ARG C 628 *********************** 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 394 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 297 time to evaluate : 2.191 Fit side-chains revert: symmetry clash REVERT: A 286 TRP cc_start: 0.5257 (OUTLIER) cc_final: 0.4444 (t60) REVERT: A 483 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8559 (tm-30) REVERT: B 146 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7364 (ttm170) REVERT: B 483 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8542 (tm-30) REVERT: C 38 MET cc_start: 0.8246 (mmm) cc_final: 0.8028 (tpt) REVERT: C 515 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7300 (mm-30) REVERT: D 126 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7611 (ttt) REVERT: D 483 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8546 (tm-30) REVERT: D 491 MET cc_start: 0.7104 (tpp) cc_final: 0.6892 (tpp) REVERT: D 515 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7443 (mm-30) REVERT: D 554 MET cc_start: 0.6994 (tpp) cc_final: 0.6714 (tpp) REVERT: D 570 MET cc_start: 0.6431 (tpp) cc_final: 0.6196 (tpp) outliers start: 97 outliers final: 90 residues processed: 361 average time/residue: 0.2541 time to fit residues: 151.3908 Evaluate side-chains 383 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 291 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 369 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 602 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 108 optimal weight: 0.0070 chunk 158 optimal weight: 0.9980 chunk 239 optimal weight: 0.0000 chunk 220 optimal weight: 9.9990 chunk 190 optimal weight: 0.0670 chunk 19 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 overall best weight: 0.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS A 635 ASN B 258 HIS B 635 ASN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN D 258 HIS ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19928 Z= 0.123 Angle : 0.547 12.281 27084 Z= 0.257 Chirality : 0.037 0.127 3048 Planarity : 0.003 0.038 3416 Dihedral : 8.529 131.207 2752 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.48 % Allowed : 28.63 % Favored : 67.89 % 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: -0.92 (0.18), residues: 2400 helix: 0.79 (0.14), residues: 1424 sheet: -2.70 (0.51), residues: 64 loop : -2.82 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 29 HIS 0.003 0.000 HIS C 201 PHE 0.007 0.001 PHE C 574 TYR 0.008 0.001 TYR B 162 ARG 0.008 0.000 ARG C 45 ********************** 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 395 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 324 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 TRP cc_start: 0.5087 (t60) cc_final: 0.4341 (t60) REVERT: A 483 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8505 (tm-30) REVERT: A 515 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: B 184 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7560 (tp30) REVERT: B 483 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8501 (tm-30) REVERT: B 554 MET cc_start: 0.6892 (tpp) cc_final: 0.6673 (tpp) REVERT: C 38 MET cc_start: 0.8259 (mmm) cc_final: 0.7980 (tpt) REVERT: C 286 TRP cc_start: 0.4960 (t60) cc_final: 0.4242 (t60) REVERT: C 341 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7537 (tp) REVERT: C 515 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7184 (mm-30) REVERT: D 483 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8486 (tm-30) REVERT: D 554 MET cc_start: 0.6843 (tpp) cc_final: 0.6577 (tpp) outliers start: 71 outliers final: 65 residues processed: 371 average time/residue: 0.2665 time to fit residues: 159.3352 Evaluate side-chains 382 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 315 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 597 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 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 635 ASN B 635 ASN ** C 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN D 513 GLN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.152753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.145680 restraints weight = 23947.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.144410 restraints weight = 32799.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144119 restraints weight = 38951.864| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19928 Z= 0.204 Angle : 0.593 11.990 27084 Z= 0.280 Chirality : 0.040 0.135 3048 Planarity : 0.005 0.097 3416 Dihedral : 8.540 132.463 2752 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.17 % Allowed : 27.99 % Favored : 67.84 % 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: -1.01 (0.17), residues: 2400 helix: 0.71 (0.14), residues: 1428 sheet: -2.73 (0.51), residues: 64 loop : -2.86 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 583 HIS 0.003 0.001 HIS C 258 PHE 0.013 0.001 PHE A 562 TYR 0.020 0.001 TYR D 216 ARG 0.007 0.000 ARG C 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3739.29 seconds wall clock time: 68 minutes 45.16 seconds (4125.16 seconds total)