Starting phenix.real_space_refine on Sat Feb 17 22:37:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw6_20918/02_2024/6uw6_20918_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw6_20918/02_2024/6uw6_20918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw6_20918/02_2024/6uw6_20918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw6_20918/02_2024/6uw6_20918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw6_20918/02_2024/6uw6_20918_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw6_20918/02_2024/6uw6_20918_updated.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 116 5.16 5 C 13100 2.51 5 N 3272 2.21 5 O 3572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 117": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A GLU 719": "OE1" <-> "OE2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 156": "OD1" <-> "OD2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ASP 340": "OD1" <-> "OD2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ASP 400": "OD1" <-> "OD2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B ASP 414": "OD1" <-> "OD2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B GLU 719": "OE1" <-> "OE2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ASP 340": "OD1" <-> "OD2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ASP 400": "OD1" <-> "OD2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C ASP 414": "OD1" <-> "OD2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 610": "OE1" <-> "OE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "C TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 714": "NH1" <-> "NH2" Residue "C GLU 719": "OE1" <-> "OE2" Residue "C ARG 729": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D ASP 156": "OD1" <-> "OD2" Residue "D ASP 166": "OD1" <-> "OD2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D ASP 240": "OD1" <-> "OD2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ASP 340": "OD1" <-> "OD2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ASP 400": "OD1" <-> "OD2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D ASP 414": "OD1" <-> "OD2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 610": "OE1" <-> "OE2" Residue "D ASP 627": "OD1" <-> "OD2" Residue "D TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 714": "NH1" <-> "NH2" Residue "D GLU 719": "OE1" <-> "OE2" Residue "D ARG 729": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20072 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4910 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 589} Chain breaks: 3 Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4910 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 589} Chain breaks: 3 Chain: "C" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4910 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 589} Chain breaks: 3 Chain: "D" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4910 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 589} Chain breaks: 3 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Unusual residues: {'6OU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-1': 4, '6OU:plan-2': 2, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Unusual residues: {'6OU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-1': 4, '6OU:plan-2': 2, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Unusual residues: {'6OU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-1': 4, '6OU:plan-2': 2, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Unusual residues: {'6OU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-1': 4, '6OU:plan-2': 2, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 10.35, per 1000 atoms: 0.52 Number of scatterers: 20072 At special positions: 0 Unit cell: (161.7, 161.7, 119.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 12 15.00 O 3572 8.00 N 3272 7.00 C 13100 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: 7.36 Conformation dependent library (CDL) restraints added in 3.6 seconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 4 sheets defined 56.6% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.806A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 416 through 419 No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 426 through 460 removed outlier: 3.856A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 506 removed outlier: 6.867A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 541 Processing helix chain 'A' and resid 547 through 566 removed outlier: 4.003A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 608 removed outlier: 3.995A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 587 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 removed outlier: 4.516A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 665 Processing helix chain 'A' and resid 669 through 685 Processing helix chain 'A' and resid 688 through 705 Processing helix chain 'A' and resid 739 through 747 removed outlier: 3.569A pdb=" N LYS A 743 " --> pdb=" O TRP A 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 removed outlier: 3.806A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 184 through 196 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 416 through 419 No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 426 through 460 removed outlier: 3.856A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 506 removed outlier: 6.866A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 541 Processing helix chain 'B' and resid 547 through 566 removed outlier: 4.002A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 608 removed outlier: 3.995A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 587 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 removed outlier: 4.517A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 665 Processing helix chain 'B' and resid 669 through 685 Processing helix chain 'B' and resid 688 through 705 Processing helix chain 'B' and resid 739 through 747 removed outlier: 3.569A pdb=" N LYS B 743 " --> pdb=" O TRP B 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 129 removed outlier: 3.805A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 Processing helix chain 'C' and resid 155 through 162 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 275 through 282 Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 344 through 351 Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 416 through 419 No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 426 through 460 removed outlier: 3.857A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LYS C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET C 440 " --> pdb=" O PHE C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 506 removed outlier: 6.867A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 541 Processing helix chain 'C' and resid 547 through 566 removed outlier: 4.002A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 608 removed outlier: 3.994A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL C 587 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 removed outlier: 4.516A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 665 Processing helix chain 'C' and resid 669 through 685 Processing helix chain 'C' and resid 688 through 705 Processing helix chain 'C' and resid 739 through 747 removed outlier: 3.569A pdb=" N LYS C 743 " --> pdb=" O TRP C 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 removed outlier: 3.805A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 147 Processing helix chain 'D' and resid 155 through 162 Processing helix chain 'D' and resid 171 through 176 Processing helix chain 'D' and resid 184 through 196 Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 275 through 282 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 344 through 351 Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 426 through 460 removed outlier: 3.857A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET D 440 " --> pdb=" O PHE D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 506 removed outlier: 6.866A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 541 Processing helix chain 'D' and resid 547 through 566 removed outlier: 4.003A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 608 removed outlier: 3.995A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL D 587 " --> pdb=" O ILE D 583 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 removed outlier: 4.517A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 665 Processing helix chain 'D' and resid 669 through 685 Processing helix chain 'D' and resid 688 through 705 Processing helix chain 'D' and resid 739 through 747 removed outlier: 3.568A pdb=" N LYS D 743 " --> pdb=" O TRP D 739 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 733 through 737 removed outlier: 6.311A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 733 through 737 removed outlier: 6.311A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 733 through 737 removed outlier: 6.312A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 733 through 737 removed outlier: 6.311A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2652 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: 5.55 Time building geometry restraints manager: 7.96 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: 6085 1.34 - 1.46: 4181 1.46 - 1.58: 9726 1.58 - 1.70: 260 1.70 - 1.81: 220 Bond restraints: 20472 Sorted by residual: bond pdb=" C16 6OU A 802 " pdb=" O18 6OU A 802 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C16 6OU D 802 " pdb=" O18 6OU D 802 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C16 6OU B 802 " pdb=" O18 6OU B 802 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C16 6OU C 802 " pdb=" O18 6OU C 802 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" C16 6OU C 804 " pdb=" O18 6OU C 804 " ideal model delta sigma weight residual 1.327 1.466 -0.139 2.00e-02 2.50e+03 4.85e+01 ... (remaining 20467 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.41: 253 105.41 - 112.61: 10531 112.61 - 119.82: 7639 119.82 - 127.02: 8934 127.02 - 134.23: 231 Bond angle restraints: 27588 Sorted by residual: angle pdb=" N GLU A 196 " pdb=" CA GLU A 196 " pdb=" C GLU A 196 " ideal model delta sigma weight residual 111.28 121.86 -10.58 1.09e+00 8.42e-01 9.43e+01 angle pdb=" N GLU C 196 " pdb=" CA GLU C 196 " pdb=" C GLU C 196 " ideal model delta sigma weight residual 111.28 121.86 -10.58 1.09e+00 8.42e-01 9.42e+01 angle pdb=" N GLU D 196 " pdb=" CA GLU D 196 " pdb=" C GLU D 196 " ideal model delta sigma weight residual 111.28 121.85 -10.57 1.09e+00 8.42e-01 9.41e+01 angle pdb=" N GLU B 196 " pdb=" CA GLU B 196 " pdb=" C GLU B 196 " ideal model delta sigma weight residual 111.28 121.84 -10.56 1.09e+00 8.42e-01 9.39e+01 angle pdb=" N ALA D 218 " pdb=" CA ALA D 218 " pdb=" C ALA D 218 " ideal model delta sigma weight residual 112.38 120.81 -8.43 1.22e+00 6.72e-01 4.77e+01 ... (remaining 27583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.41: 11502 27.41 - 54.81: 654 54.81 - 82.22: 96 82.22 - 109.63: 28 109.63 - 137.04: 4 Dihedral angle restraints: 12284 sinusoidal: 5200 harmonic: 7084 Sorted by residual: dihedral pdb=" CA LEU A 484 " pdb=" C LEU A 484 " pdb=" N LEU A 485 " pdb=" CA LEU A 485 " ideal model delta harmonic sigma weight residual 180.00 153.56 26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA LEU B 484 " pdb=" C LEU B 484 " pdb=" N LEU B 485 " pdb=" CA LEU B 485 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA LEU D 484 " pdb=" C LEU D 484 " pdb=" N LEU D 485 " pdb=" CA LEU D 485 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 12281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2940 0.115 - 0.230: 152 0.230 - 0.345: 8 0.345 - 0.460: 0 0.460 - 0.575: 12 Chirality restraints: 3112 Sorted by residual: chirality pdb=" C20 6OU D 802 " pdb=" C19 6OU D 802 " pdb=" C21 6OU D 802 " pdb=" O30 6OU D 802 " both_signs ideal model delta sigma weight residual False 2.35 2.92 -0.58 2.00e-01 2.50e+01 8.27e+00 chirality pdb=" C20 6OU B 802 " pdb=" C19 6OU B 802 " pdb=" C21 6OU B 802 " pdb=" O30 6OU B 802 " both_signs ideal model delta sigma weight residual False 2.35 2.92 -0.57 2.00e-01 2.50e+01 8.25e+00 chirality pdb=" C20 6OU A 802 " pdb=" C19 6OU A 802 " pdb=" C21 6OU A 802 " pdb=" O30 6OU A 802 " both_signs ideal model delta sigma weight residual False 2.35 2.92 -0.57 2.00e-01 2.50e+01 8.24e+00 ... (remaining 3109 not shown) Planarity restraints: 3392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 180 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.43e+00 pdb=" N PRO B 181 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 180 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO D 181 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 181 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 181 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 180 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO C 181 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " -0.037 5.00e-02 4.00e+02 ... (remaining 3389 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6296 2.82 - 3.34: 17971 3.34 - 3.86: 31185 3.86 - 4.38: 35542 4.38 - 4.90: 62538 Nonbonded interactions: 153532 Sorted by model distance: nonbonded pdb=" OG1 THR A 343 " pdb=" OE1 GLN A 346 " model vdw 2.299 2.440 nonbonded pdb=" OG1 THR D 343 " pdb=" OE1 GLN D 346 " model vdw 2.299 2.440 nonbonded pdb=" OG1 THR B 343 " pdb=" OE1 GLN B 346 " model vdw 2.299 2.440 nonbonded pdb=" OG1 THR C 343 " pdb=" OE1 GLN C 346 " model vdw 2.299 2.440 nonbonded pdb=" O SER C 518 " pdb=" OG SER C 518 " model vdw 2.312 2.440 ... (remaining 153527 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.950 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 51.850 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.015 0.141 20472 Z= 0.918 Angle : 1.236 16.843 27588 Z= 0.628 Chirality : 0.067 0.575 3112 Planarity : 0.007 0.068 3392 Dihedral : 18.262 137.037 7684 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.12), residues: 2376 helix: -2.93 (0.08), residues: 1540 sheet: -2.37 (0.50), residues: 84 loop : -3.55 (0.17), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 710 HIS 0.006 0.001 HIS D 417 PHE 0.019 0.002 PHE C 592 TYR 0.022 0.003 TYR B 208 ARG 0.005 0.001 ARG C 698 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ILE cc_start: 0.8485 (tp) cc_final: 0.8251 (pt) REVERT: A 590 PHE cc_start: 0.8515 (t80) cc_final: 0.8217 (t80) REVERT: B 128 SER cc_start: 0.8889 (m) cc_final: 0.8494 (p) REVERT: B 591 LEU cc_start: 0.8699 (mt) cc_final: 0.8485 (mp) REVERT: C 128 SER cc_start: 0.8793 (m) cc_final: 0.8415 (p) REVERT: C 493 TRP cc_start: 0.7023 (t-100) cc_final: 0.6757 (t-100) REVERT: C 555 MET cc_start: 0.7900 (ttp) cc_final: 0.7627 (ttm) REVERT: C 590 PHE cc_start: 0.8558 (t80) cc_final: 0.8321 (t80) REVERT: C 710 TRP cc_start: 0.7181 (t60) cc_final: 0.6946 (t60) REVERT: D 128 SER cc_start: 0.8718 (m) cc_final: 0.8324 (p) REVERT: D 368 LYS cc_start: 0.8295 (tptp) cc_final: 0.8086 (pttm) REVERT: D 591 LEU cc_start: 0.8792 (mt) cc_final: 0.8551 (mp) REVERT: D 631 GLU cc_start: 0.8255 (tp30) cc_final: 0.7785 (tp30) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.3161 time to fit residues: 168.4954 Evaluate side-chains 233 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 217 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 394 ASN A 417 HIS A 430 HIS A 523 HIS B 220 ASN B 314 ASN B 394 ASN B 417 HIS B 430 HIS B 523 HIS C 220 ASN C 314 ASN C 394 ASN C 417 HIS C 430 HIS C 523 HIS D 160 HIS D 220 ASN D 314 ASN D 394 ASN D 417 HIS D 430 HIS D 523 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20472 Z= 0.258 Angle : 0.584 6.267 27588 Z= 0.303 Chirality : 0.039 0.160 3112 Planarity : 0.004 0.036 3392 Dihedral : 13.796 138.105 2988 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.79 % Allowed : 18.28 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.53 (0.15), residues: 2376 helix: -0.85 (0.12), residues: 1532 sheet: -2.22 (0.52), residues: 84 loop : -3.22 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 433 HIS 0.005 0.001 HIS C 160 PHE 0.012 0.001 PHE C 633 TYR 0.013 0.002 TYR A 260 ARG 0.005 0.000 ARG B 716 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 270 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8589 (pp) REVERT: A 590 PHE cc_start: 0.8460 (t80) cc_final: 0.8102 (t80) REVERT: B 422 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8585 (pp) REVERT: B 430 HIS cc_start: 0.7786 (m-70) cc_final: 0.7511 (m-70) REVERT: B 575 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7821 (m-80) REVERT: C 128 SER cc_start: 0.8619 (m) cc_final: 0.8415 (p) REVERT: C 193 PHE cc_start: 0.8032 (t80) cc_final: 0.7804 (t80) REVERT: C 365 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8063 (mt) REVERT: C 422 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8642 (pp) REVERT: C 575 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: D 145 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7562 (tt) REVERT: D 368 LYS cc_start: 0.8385 (tptp) cc_final: 0.7896 (pttm) REVERT: D 422 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8614 (pp) REVERT: D 430 HIS cc_start: 0.7740 (m-70) cc_final: 0.7468 (m-70) REVERT: D 508 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7786 (tp) outliers start: 38 outliers final: 10 residues processed: 298 average time/residue: 0.3250 time to fit residues: 153.3206 Evaluate side-chains 228 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 209 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 508 LEU 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: 1.9990 chunk 181 optimal weight: 9.9990 chunk 148 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 chunk 235 optimal weight: 0.9990 chunk 194 optimal weight: 0.0050 chunk 216 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN B 160 HIS ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20472 Z= 0.138 Angle : 0.493 7.403 27588 Z= 0.253 Chirality : 0.036 0.123 3112 Planarity : 0.003 0.033 3392 Dihedral : 12.305 107.177 2988 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.49 % Allowed : 20.11 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2376 helix: 0.09 (0.13), residues: 1544 sheet: -1.76 (0.58), residues: 84 loop : -2.86 (0.19), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 710 HIS 0.004 0.001 HIS D 160 PHE 0.008 0.001 PHE D 633 TYR 0.010 0.001 TYR A 594 ARG 0.003 0.000 ARG D 716 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 282 time to evaluate : 2.448 Fit side-chains revert: symmetry clash REVERT: A 575 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7703 (m-80) REVERT: A 590 PHE cc_start: 0.8327 (t80) cc_final: 0.7977 (t80) REVERT: B 430 HIS cc_start: 0.7735 (m-70) cc_final: 0.7377 (m90) REVERT: B 575 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: C 422 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8705 (pp) REVERT: C 430 HIS cc_start: 0.7746 (m-70) cc_final: 0.7435 (m90) REVERT: C 575 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: C 590 PHE cc_start: 0.8359 (t80) cc_final: 0.8035 (t80) REVERT: D 145 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7595 (tt) REVERT: D 368 LYS cc_start: 0.8191 (tptp) cc_final: 0.7570 (pttm) REVERT: D 369 ARG cc_start: 0.7402 (ttp80) cc_final: 0.7114 (ttp80) REVERT: D 422 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8705 (pp) outliers start: 53 outliers final: 24 residues processed: 321 average time/residue: 0.2974 time to fit residues: 149.7847 Evaluate side-chains 271 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 241 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 508 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 1.9990 chunk 164 optimal weight: 0.0370 chunk 113 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 297 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN C 143 GLN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20472 Z= 0.159 Angle : 0.503 7.541 27588 Z= 0.253 Chirality : 0.037 0.150 3112 Planarity : 0.003 0.032 3392 Dihedral : 11.733 96.952 2988 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.34 % Allowed : 20.21 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.81 (0.17), residues: 2376 helix: 0.53 (0.13), residues: 1548 sheet: -1.84 (0.56), residues: 84 loop : -2.67 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 710 HIS 0.005 0.001 HIS B 160 PHE 0.031 0.001 PHE C 193 TYR 0.011 0.001 TYR C 594 ARG 0.002 0.000 ARG D 716 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 251 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: A 626 SER cc_start: 0.8566 (m) cc_final: 0.8246 (p) REVERT: A 741 GLU cc_start: 0.7383 (mp0) cc_final: 0.7151 (mp0) REVERT: B 368 LYS cc_start: 0.8148 (tptt) cc_final: 0.7867 (pttm) REVERT: B 430 HIS cc_start: 0.7735 (m-70) cc_final: 0.7492 (m-70) REVERT: B 575 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: B 590 PHE cc_start: 0.8417 (t80) cc_final: 0.8045 (t80) REVERT: C 422 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8757 (pp) REVERT: C 430 HIS cc_start: 0.7744 (m-70) cc_final: 0.7417 (m90) REVERT: C 575 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: C 626 SER cc_start: 0.8582 (m) cc_final: 0.8282 (p) REVERT: D 145 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7642 (tt) REVERT: D 368 LYS cc_start: 0.8261 (tptp) cc_final: 0.8032 (tptm) REVERT: D 422 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8706 (pp) REVERT: D 590 PHE cc_start: 0.8390 (t80) cc_final: 0.8029 (t80) REVERT: D 626 SER cc_start: 0.8583 (m) cc_final: 0.8205 (p) outliers start: 71 outliers final: 32 residues processed: 305 average time/residue: 0.2837 time to fit residues: 139.2504 Evaluate side-chains 271 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 233 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 508 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 3 optimal weight: 30.0000 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 208 optimal weight: 0.0370 chunk 58 optimal weight: 2.9990 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20472 Z= 0.237 Angle : 0.549 10.079 27588 Z= 0.275 Chirality : 0.038 0.132 3112 Planarity : 0.003 0.033 3392 Dihedral : 11.888 99.444 2988 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.91 % Allowed : 21.24 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.66 (0.17), residues: 2376 helix: 0.71 (0.14), residues: 1524 sheet: -1.87 (0.54), residues: 84 loop : -2.64 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.009 0.001 HIS D 160 PHE 0.027 0.001 PHE D 193 TYR 0.013 0.001 TYR D 213 ARG 0.003 0.000 ARG D 716 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 238 time to evaluate : 2.419 Fit side-chains revert: symmetry clash REVERT: A 575 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: A 626 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8341 (p) REVERT: B 193 PHE cc_start: 0.7963 (t80) cc_final: 0.7743 (t80) REVERT: B 368 LYS cc_start: 0.8199 (tptt) cc_final: 0.7920 (pttm) REVERT: B 575 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: C 422 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8762 (pp) REVERT: C 575 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: C 626 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8326 (p) REVERT: C 710 TRP cc_start: 0.7153 (t60) cc_final: 0.6807 (t60) REVERT: D 145 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7638 (tt) REVERT: D 368 LYS cc_start: 0.8348 (tptp) cc_final: 0.8074 (tptm) REVERT: D 422 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8715 (pp) REVERT: D 626 SER cc_start: 0.8717 (m) cc_final: 0.8365 (p) outliers start: 62 outliers final: 40 residues processed: 284 average time/residue: 0.3116 time to fit residues: 140.9682 Evaluate side-chains 272 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 224 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.7980 chunk 208 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20472 Z= 0.160 Angle : 0.512 8.928 27588 Z= 0.254 Chirality : 0.037 0.126 3112 Planarity : 0.003 0.033 3392 Dihedral : 11.258 106.316 2988 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.77 % Allowed : 22.42 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.34 (0.17), residues: 2376 helix: 0.93 (0.14), residues: 1520 sheet: -1.69 (0.54), residues: 84 loop : -2.43 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.004 0.001 HIS D 160 PHE 0.029 0.001 PHE A 193 TYR 0.015 0.001 TYR D 213 ARG 0.002 0.000 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 244 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 TRP cc_start: 0.7446 (t-100) cc_final: 0.6908 (t-100) REVERT: A 555 MET cc_start: 0.7082 (ttp) cc_final: 0.6729 (ttm) REVERT: A 575 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: A 626 SER cc_start: 0.8507 (m) cc_final: 0.8293 (p) REVERT: B 368 LYS cc_start: 0.8029 (tptt) cc_final: 0.7746 (pttm) REVERT: B 575 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: B 626 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8271 (p) REVERT: C 145 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7282 (tp) REVERT: C 575 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7953 (m-80) REVERT: C 626 SER cc_start: 0.8495 (m) cc_final: 0.8289 (p) REVERT: D 145 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7523 (tp) REVERT: D 422 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8716 (pp) REVERT: D 626 SER cc_start: 0.8630 (m) cc_final: 0.8207 (p) outliers start: 59 outliers final: 40 residues processed: 292 average time/residue: 0.2911 time to fit residues: 134.8026 Evaluate side-chains 275 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 228 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20472 Z= 0.192 Angle : 0.531 7.977 27588 Z= 0.264 Chirality : 0.037 0.118 3112 Planarity : 0.003 0.033 3392 Dihedral : 11.104 102.604 2988 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.05 % Allowed : 23.73 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.22 (0.17), residues: 2376 helix: 1.01 (0.14), residues: 1520 sheet: -1.73 (0.54), residues: 84 loop : -2.34 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.004 0.001 HIS D 160 PHE 0.029 0.001 PHE D 193 TYR 0.015 0.001 TYR D 213 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 232 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8075 (tm-30) REVERT: A 255 GLN cc_start: 0.6183 (OUTLIER) cc_final: 0.5710 (tt0) REVERT: A 493 TRP cc_start: 0.7430 (t-100) cc_final: 0.6880 (t-100) REVERT: A 575 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: A 626 SER cc_start: 0.8526 (m) cc_final: 0.8272 (p) REVERT: B 368 LYS cc_start: 0.8052 (tptt) cc_final: 0.7781 (pttm) REVERT: B 575 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: B 626 SER cc_start: 0.8504 (m) cc_final: 0.8219 (p) REVERT: C 145 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7301 (tp) REVERT: C 255 GLN cc_start: 0.6274 (OUTLIER) cc_final: 0.5740 (tt0) REVERT: C 575 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: C 626 SER cc_start: 0.8519 (m) cc_final: 0.8276 (p) REVERT: D 145 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7502 (tp) REVERT: D 255 GLN cc_start: 0.6153 (OUTLIER) cc_final: 0.5679 (tt0) REVERT: D 422 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8697 (pp) REVERT: D 626 SER cc_start: 0.8591 (m) cc_final: 0.8156 (p) outliers start: 65 outliers final: 45 residues processed: 287 average time/residue: 0.2911 time to fit residues: 132.6728 Evaluate side-chains 279 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 225 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 0.0870 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20472 Z= 0.178 Angle : 0.526 12.682 27588 Z= 0.261 Chirality : 0.037 0.129 3112 Planarity : 0.003 0.034 3392 Dihedral : 10.815 102.151 2988 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.48 % Allowed : 23.64 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.05 (0.18), residues: 2376 helix: 1.13 (0.14), residues: 1512 sheet: -1.61 (0.55), residues: 84 loop : -2.22 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 380 HIS 0.004 0.001 HIS D 160 PHE 0.027 0.001 PHE D 193 TYR 0.015 0.001 TYR D 213 ARG 0.002 0.000 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 240 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8253 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 255 GLN cc_start: 0.6155 (OUTLIER) cc_final: 0.5699 (tt0) REVERT: A 485 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7183 (tt) REVERT: A 493 TRP cc_start: 0.7393 (t-100) cc_final: 0.6868 (t-100) REVERT: A 575 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: A 626 SER cc_start: 0.8517 (m) cc_final: 0.8266 (p) REVERT: B 255 GLN cc_start: 0.6291 (OUTLIER) cc_final: 0.5770 (tt0) REVERT: B 368 LYS cc_start: 0.7957 (tptt) cc_final: 0.7717 (pttm) REVERT: B 575 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: B 626 SER cc_start: 0.8503 (m) cc_final: 0.8139 (p) REVERT: C 145 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7318 (tp) REVERT: C 255 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.5775 (tt0) REVERT: C 485 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7263 (tt) REVERT: C 575 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: C 626 SER cc_start: 0.8515 (m) cc_final: 0.8274 (p) REVERT: D 145 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7400 (tp) REVERT: D 255 GLN cc_start: 0.6166 (OUTLIER) cc_final: 0.5705 (tt0) REVERT: D 368 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7967 (tptm) REVERT: D 422 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8698 (pp) REVERT: D 626 SER cc_start: 0.8598 (m) cc_final: 0.8203 (p) outliers start: 74 outliers final: 49 residues processed: 301 average time/residue: 0.2901 time to fit residues: 139.2976 Evaluate side-chains 293 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 231 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 202 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 129 optimal weight: 0.0670 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 194 optimal weight: 0.0030 chunk 203 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 overall best weight: 0.5528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20472 Z= 0.127 Angle : 0.515 13.793 27588 Z= 0.251 Chirality : 0.036 0.136 3112 Planarity : 0.003 0.033 3392 Dihedral : 10.115 96.939 2988 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.96 % Allowed : 24.30 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.22 (0.18), residues: 2376 helix: 1.31 (0.14), residues: 1488 sheet: -0.78 (0.59), residues: 76 loop : -2.02 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 380 HIS 0.004 0.000 HIS D 160 PHE 0.030 0.001 PHE D 193 TYR 0.015 0.001 TYR D 213 ARG 0.003 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 266 time to evaluate : 2.519 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8023 (tm-30) REVERT: A 255 GLN cc_start: 0.6142 (OUTLIER) cc_final: 0.5712 (tt0) REVERT: A 485 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7128 (tt) REVERT: A 493 TRP cc_start: 0.7357 (t-100) cc_final: 0.6820 (t-100) REVERT: A 575 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: A 626 SER cc_start: 0.8450 (m) cc_final: 0.8112 (p) REVERT: B 255 GLN cc_start: 0.6286 (OUTLIER) cc_final: 0.5802 (tt0) REVERT: B 575 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: B 626 SER cc_start: 0.8461 (m) cc_final: 0.8110 (p) REVERT: C 145 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7379 (tp) REVERT: C 255 GLN cc_start: 0.6281 (OUTLIER) cc_final: 0.5810 (tt0) REVERT: C 368 LYS cc_start: 0.8108 (tptm) cc_final: 0.7538 (pttm) REVERT: C 485 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7177 (tt) REVERT: C 575 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7840 (m-80) REVERT: C 626 SER cc_start: 0.8462 (m) cc_final: 0.8128 (p) REVERT: D 145 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7456 (tp) REVERT: D 255 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.5772 (tt0) REVERT: D 368 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7681 (tptm) REVERT: D 422 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8734 (pp) REVERT: D 626 SER cc_start: 0.8350 (m) cc_final: 0.8069 (p) outliers start: 63 outliers final: 41 residues processed: 319 average time/residue: 0.2808 time to fit residues: 144.1361 Evaluate side-chains 292 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 238 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 7.9990 chunk 227 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 239 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20472 Z= 0.152 Angle : 0.528 14.901 27588 Z= 0.257 Chirality : 0.037 0.162 3112 Planarity : 0.003 0.033 3392 Dihedral : 9.889 94.726 2988 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.87 % Allowed : 25.23 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.32 (0.18), residues: 2376 helix: 1.39 (0.14), residues: 1484 sheet: -1.35 (0.57), residues: 84 loop : -1.91 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.004 0.001 HIS B 160 PHE 0.029 0.001 PHE D 193 TYR 0.015 0.001 TYR D 213 ARG 0.003 0.000 ARG D 714 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 252 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLN cc_start: 0.6289 (OUTLIER) cc_final: 0.5768 (tt0) REVERT: A 485 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7134 (tt) REVERT: A 493 TRP cc_start: 0.7354 (t-100) cc_final: 0.6845 (t-100) REVERT: A 555 MET cc_start: 0.7200 (ttp) cc_final: 0.6683 (ttm) REVERT: A 575 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: A 626 SER cc_start: 0.8482 (m) cc_final: 0.8123 (p) REVERT: B 255 GLN cc_start: 0.6289 (OUTLIER) cc_final: 0.5819 (tt0) REVERT: B 575 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: B 626 SER cc_start: 0.8482 (m) cc_final: 0.8122 (p) REVERT: C 145 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7390 (tp) REVERT: C 255 GLN cc_start: 0.6301 (OUTLIER) cc_final: 0.5823 (tt0) REVERT: C 485 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7193 (tt) REVERT: C 575 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: C 626 SER cc_start: 0.8485 (m) cc_final: 0.8135 (p) REVERT: D 145 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7451 (tp) REVERT: D 255 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.5770 (tt0) REVERT: D 368 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7719 (tptm) REVERT: D 626 SER cc_start: 0.8352 (m) cc_final: 0.7994 (p) outliers start: 61 outliers final: 44 residues processed: 306 average time/residue: 0.2786 time to fit residues: 135.6667 Evaluate side-chains 296 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 240 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.8980 chunk 202 optimal weight: 0.0270 chunk 58 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 195 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.129653 restraints weight = 25803.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132320 restraints weight = 19221.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134171 restraints weight = 15822.968| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20472 Z= 0.148 Angle : 0.534 14.881 27588 Z= 0.259 Chirality : 0.036 0.161 3112 Planarity : 0.003 0.033 3392 Dihedral : 9.539 92.143 2988 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.77 % Allowed : 25.28 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.38 (0.18), residues: 2376 helix: 1.42 (0.14), residues: 1484 sheet: -1.33 (0.57), residues: 84 loop : -1.84 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.004 0.001 HIS B 160 PHE 0.028 0.001 PHE D 193 TYR 0.016 0.001 TYR A 213 ARG 0.002 0.000 ARG A 716 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3679.67 seconds wall clock time: 68 minutes 42.20 seconds (4122.20 seconds total)