Starting phenix.real_space_refine on Sat Feb 24 12:23:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lr0_23493/02_2024/7lr0_23493_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lr0_23493/02_2024/7lr0_23493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lr0_23493/02_2024/7lr0_23493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lr0_23493/02_2024/7lr0_23493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lr0_23493/02_2024/7lr0_23493_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lr0_23493/02_2024/7lr0_23493_trim_updated.pdb" } resolution = 3.81 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= 0.015 sd= 0.095 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: 7 Type Number sf(0) Gaussians P 20 5.49 5 S 124 5.16 5 Na 1 4.78 5 C 14364 2.51 5 N 3440 2.21 5 O 3964 1.98 5 H 20936 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 42849 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 10445 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 17, 'TRANS': 628} Chain breaks: 1 Chain: "B" Number of atoms: 10445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 10445 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 17, 'TRANS': 628} Chain breaks: 1 Chain: "C" Number of atoms: 10445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 10445 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 17, 'TRANS': 628} Chain breaks: 1 Chain: "D" Number of atoms: 10445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 10445 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 17, 'TRANS': 628} Chain breaks: 1 Chain: "A" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 312 Unusual residues: {' NA': 1, '4DY': 1, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 267 Unusual residues: {'4DY': 1, 'POV': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 267 Unusual residues: {'4DY': 1, 'POV': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 223 Unusual residues: {'4DY': 1, 'POV': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 19.84, per 1000 atoms: 0.46 Number of scatterers: 42849 At special positions: 0 Unit cell: (131.97, 131.97, 118.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 124 16.00 P 20 15.00 Na 1 11.00 O 3964 8.00 N 3440 7.00 C 14364 6.00 H 20936 1.00 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: 34.62 Conformation dependent library (CDL) restraints added in 4.2 seconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4888 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 4 sheets defined 54.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.12 Creating SS restraints... Processing helix chain 'A' and resid 116 through 125 removed outlier: 3.561A pdb=" N ALA A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.526A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 No H-bonds generated for 'chain 'A' and resid 189 through 192' Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 263 through 271 Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.513A pdb=" N GLU A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 321 removed outlier: 3.503A pdb=" N THR A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 348 through 356 removed outlier: 3.533A pdb=" N LEU A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 removed outlier: 3.669A pdb=" N ALA A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.918A pdb=" N LEU A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 416 " --> pdb=" O HIS A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 411 through 416' Processing helix chain 'A' and resid 418 through 429 removed outlier: 3.500A pdb=" N GLN A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 455 Processing helix chain 'A' and resid 471 through 498 removed outlier: 3.765A pdb=" N TYR A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.655A pdb=" N VAL A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.616A pdb=" N LEU A 517 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 558 removed outlier: 3.590A pdb=" N VAL A 540 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 545 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP A 551 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 574 removed outlier: 4.072A pdb=" N TYR A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 571 " --> pdb=" O TYR A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 600 removed outlier: 3.642A pdb=" N VAL A 588 " --> pdb=" O PHE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 644 removed outlier: 4.314A pdb=" N THR A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 644 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 687 removed outlier: 3.853A pdb=" N LEU A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 683 " --> pdb=" O MET A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 713 removed outlier: 3.526A pdb=" N LYS A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 125 removed outlier: 3.561A pdb=" N ALA B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 174 through 184 removed outlier: 3.525A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 192 No H-bonds generated for 'chain 'B' and resid 189 through 192' Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 216 through 225 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 263 through 271 Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.513A pdb=" N GLU B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 321 removed outlier: 3.503A pdb=" N THR B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 338 through 345 Processing helix chain 'B' and resid 348 through 356 removed outlier: 3.533A pdb=" N LEU B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 403 removed outlier: 3.670A pdb=" N ALA B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.918A pdb=" N LEU B 415 " --> pdb=" O ARG B 411 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 416 " --> pdb=" O HIS B 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 411 through 416' Processing helix chain 'B' and resid 418 through 429 Processing helix chain 'B' and resid 433 through 455 Processing helix chain 'B' and resid 471 through 498 removed outlier: 3.766A pdb=" N TYR B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 removed outlier: 3.655A pdb=" N VAL B 510 " --> pdb=" O LYS B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.619A pdb=" N LEU B 517 " --> pdb=" O TYR B 513 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 522 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 558 removed outlier: 3.590A pdb=" N VAL B 540 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 545 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET B 549 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP B 551 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 574 removed outlier: 4.073A pdb=" N TYR B 567 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 571 " --> pdb=" O TYR B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 600 removed outlier: 3.641A pdb=" N VAL B 588 " --> pdb=" O PHE B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 644 removed outlier: 4.315A pdb=" N THR B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 644 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 687 removed outlier: 3.853A pdb=" N LEU B 665 " --> pdb=" O PHE B 661 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 683 " --> pdb=" O MET B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 713 removed outlier: 3.526A pdb=" N LYS B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 125 removed outlier: 3.561A pdb=" N ALA C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 159 through 165 Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 174 through 184 removed outlier: 3.526A pdb=" N ALA C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 192 No H-bonds generated for 'chain 'C' and resid 189 through 192' Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 263 through 271 Processing helix chain 'C' and resid 289 through 296 removed outlier: 3.513A pdb=" N GLU C 295 " --> pdb=" O HIS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 321 removed outlier: 3.503A pdb=" N THR C 308 " --> pdb=" O THR C 304 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 315 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 329 No H-bonds generated for 'chain 'C' and resid 327 through 329' Processing helix chain 'C' and resid 338 through 345 Processing helix chain 'C' and resid 348 through 356 removed outlier: 3.532A pdb=" N LEU C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 403 removed outlier: 3.669A pdb=" N ALA C 402 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 403 " --> pdb=" O GLU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.918A pdb=" N LEU C 415 " --> pdb=" O ARG C 411 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 416 " --> pdb=" O HIS C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 411 through 416' Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 433 through 455 Processing helix chain 'C' and resid 471 through 498 removed outlier: 3.766A pdb=" N TYR C 489 " --> pdb=" O SER C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 511 removed outlier: 3.654A pdb=" N VAL C 510 " --> pdb=" O LYS C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.619A pdb=" N LEU C 517 " --> pdb=" O TYR C 513 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 522 " --> pdb=" O PHE C 518 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 558 removed outlier: 3.590A pdb=" N VAL C 540 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 545 " --> pdb=" O SER C 542 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET C 549 " --> pdb=" O SER C 546 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP C 551 " --> pdb=" O ALA C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 574 removed outlier: 4.073A pdb=" N TYR C 567 " --> pdb=" O GLN C 563 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE C 571 " --> pdb=" O TYR C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 600 removed outlier: 3.642A pdb=" N VAL C 588 " --> pdb=" O PHE C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 644 removed outlier: 4.314A pdb=" N THR C 643 " --> pdb=" O LEU C 639 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 644 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 687 removed outlier: 3.853A pdb=" N LEU C 665 " --> pdb=" O PHE C 661 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU C 683 " --> pdb=" O MET C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 713 removed outlier: 3.525A pdb=" N LYS C 696 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR C 706 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 125 removed outlier: 3.561A pdb=" N ALA D 124 " --> pdb=" O PHE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 159 through 165 Processing helix chain 'D' and resid 168 through 170 No H-bonds generated for 'chain 'D' and resid 168 through 170' Processing helix chain 'D' and resid 174 through 184 removed outlier: 3.525A pdb=" N ALA D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 192 No H-bonds generated for 'chain 'D' and resid 189 through 192' Processing helix chain 'D' and resid 206 through 212 Processing helix chain 'D' and resid 216 through 225 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 263 through 271 Processing helix chain 'D' and resid 289 through 296 removed outlier: 3.513A pdb=" N GLU D 295 " --> pdb=" O HIS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 321 removed outlier: 3.503A pdb=" N THR D 308 " --> pdb=" O THR D 304 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 338 through 345 Processing helix chain 'D' and resid 348 through 356 removed outlier: 3.533A pdb=" N LEU D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 removed outlier: 3.669A pdb=" N ALA D 402 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 403 " --> pdb=" O GLU D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.917A pdb=" N LEU D 415 " --> pdb=" O ARG D 411 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 416 " --> pdb=" O HIS D 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 411 through 416' Processing helix chain 'D' and resid 418 through 429 Processing helix chain 'D' and resid 433 through 455 Processing helix chain 'D' and resid 471 through 498 removed outlier: 3.766A pdb=" N TYR D 489 " --> pdb=" O SER D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 511 removed outlier: 3.654A pdb=" N VAL D 510 " --> pdb=" O LYS D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.622A pdb=" N LEU D 517 " --> pdb=" O TYR D 513 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 522 " --> pdb=" O PHE D 518 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 558 removed outlier: 3.591A pdb=" N VAL D 540 " --> pdb=" O LYS D 537 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE D 545 " --> pdb=" O SER D 542 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET D 549 " --> pdb=" O SER D 546 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP D 551 " --> pdb=" O ALA D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 574 removed outlier: 4.072A pdb=" N TYR D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE D 571 " --> pdb=" O TYR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 600 removed outlier: 3.642A pdb=" N VAL D 588 " --> pdb=" O PHE D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 644 removed outlier: 4.315A pdb=" N THR D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 644 " --> pdb=" O PHE D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 687 removed outlier: 3.852A pdb=" N LEU D 665 " --> pdb=" O PHE D 661 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU D 683 " --> pdb=" O MET D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 713 removed outlier: 3.525A pdb=" N LYS D 696 " --> pdb=" O ALA D 692 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR D 706 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 379 through 382 removed outlier: 3.501A pdb=" N HIS A 380 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 379 through 382 removed outlier: 3.501A pdb=" N HIS B 380 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 379 through 382 removed outlier: 3.502A pdb=" N HIS C 380 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 379 through 382 removed outlier: 3.502A pdb=" N HIS D 380 " --> pdb=" O GLU D 748 " (cutoff:3.500A) 847 hydrogen bonds defined for protein. 2349 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: 15.05 Time building geometry restraints manager: 35.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 20888 1.02 - 1.22: 95 1.22 - 1.42: 9231 1.42 - 1.62: 12822 1.62 - 1.82: 240 Bond restraints: 43276 Sorted by residual: bond pdb=" C31 POV A 909 " pdb=" O31 POV A 909 " ideal model delta sigma weight residual 1.327 1.407 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C31 POV A 901 " pdb=" O31 POV A 901 " ideal model delta sigma weight residual 1.327 1.406 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C31 POV B 901 " pdb=" O31 POV B 901 " ideal model delta sigma weight residual 1.327 1.405 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C31 POV C 901 " pdb=" O31 POV C 901 " ideal model delta sigma weight residual 1.327 1.404 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C31 POV B 907 " pdb=" O31 POV B 907 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 43271 not shown) Histogram of bond angle deviations from ideal: 96.21 - 103.90: 262 103.90 - 111.60: 47103 111.60 - 119.29: 11978 119.29 - 126.98: 17900 126.98 - 134.67: 185 Bond angle restraints: 77428 Sorted by residual: angle pdb=" N PRO B 463 " pdb=" CA PRO B 463 " pdb=" C PRO B 463 " ideal model delta sigma weight residual 110.70 117.36 -6.66 1.22e+00 6.72e-01 2.98e+01 angle pdb=" N PRO D 463 " pdb=" CA PRO D 463 " pdb=" C PRO D 463 " ideal model delta sigma weight residual 110.70 117.34 -6.64 1.22e+00 6.72e-01 2.96e+01 angle pdb=" N PRO A 463 " pdb=" CA PRO A 463 " pdb=" C PRO A 463 " ideal model delta sigma weight residual 110.70 117.33 -6.63 1.22e+00 6.72e-01 2.96e+01 angle pdb=" N PRO C 463 " pdb=" CA PRO C 463 " pdb=" C PRO C 463 " ideal model delta sigma weight residual 110.70 117.33 -6.63 1.22e+00 6.72e-01 2.95e+01 angle pdb=" CA TYR B 513 " pdb=" C TYR B 513 " pdb=" O TYR B 513 " ideal model delta sigma weight residual 120.82 115.91 4.91 1.05e+00 9.07e-01 2.19e+01 ... (remaining 77423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.55: 19897 30.55 - 61.09: 654 61.09 - 91.64: 81 91.64 - 122.19: 12 122.19 - 152.73: 12 Dihedral angle restraints: 20656 sinusoidal: 11404 harmonic: 9252 Sorted by residual: dihedral pdb=" CA GLY B 725 " pdb=" C GLY B 725 " pdb=" N LYS B 726 " pdb=" CA LYS B 726 " ideal model delta harmonic sigma weight residual 180.00 147.90 32.10 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA GLY D 725 " pdb=" C GLY D 725 " pdb=" N LYS D 726 " pdb=" CA LYS D 726 " ideal model delta harmonic sigma weight residual 180.00 147.92 32.08 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA GLY C 725 " pdb=" C GLY C 725 " pdb=" N LYS C 726 " pdb=" CA LYS C 726 " ideal model delta harmonic sigma weight residual 180.00 147.93 32.07 0 5.00e+00 4.00e-02 4.11e+01 ... (remaining 20653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2248 0.052 - 0.104: 821 0.104 - 0.156: 151 0.156 - 0.208: 45 0.208 - 0.261: 7 Chirality restraints: 3272 Sorted by residual: chirality pdb=" CA PHE C 431 " pdb=" N PHE C 431 " pdb=" C PHE C 431 " pdb=" CB PHE C 431 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PHE A 431 " pdb=" N PHE A 431 " pdb=" C PHE A 431 " pdb=" CB PHE A 431 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA PHE D 431 " pdb=" N PHE D 431 " pdb=" C PHE D 431 " pdb=" CB PHE D 431 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 3269 not shown) Planarity restraints: 6196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 4DY A 903 " -0.312 2.00e-02 2.50e+03 2.63e-01 8.65e+02 pdb=" C22 4DY A 903 " 0.084 2.00e-02 2.50e+03 pdb=" C24 4DY A 903 " -0.185 2.00e-02 2.50e+03 pdb=" N21 4DY A 903 " 0.454 2.00e-02 2.50e+03 pdb=" O23 4DY A 903 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 678 " 0.223 2.00e-02 2.50e+03 2.40e-01 8.64e+02 pdb=" CG ASN B 678 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN B 678 " -0.186 2.00e-02 2.50e+03 pdb=" ND2 ASN B 678 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN B 678 " -0.361 2.00e-02 2.50e+03 pdb="HD22 ASN B 678 " 0.361 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 4DY D 904 " 0.312 2.00e-02 2.50e+03 2.63e-01 8.64e+02 pdb=" C22 4DY D 904 " -0.083 2.00e-02 2.50e+03 pdb=" C24 4DY D 904 " 0.185 2.00e-02 2.50e+03 pdb=" N21 4DY D 904 " -0.454 2.00e-02 2.50e+03 pdb=" O23 4DY D 904 " 0.040 2.00e-02 2.50e+03 ... (remaining 6193 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 3681 2.23 - 2.82: 96819 2.82 - 3.42: 109263 3.42 - 4.01: 149573 4.01 - 4.60: 236635 Nonbonded interactions: 595971 Sorted by model distance: nonbonded pdb=" O MET B 549 " pdb=" H ASN B 553 " model vdw 1.638 1.850 nonbonded pdb=" O MET C 549 " pdb=" H ASN C 553 " model vdw 1.638 1.850 nonbonded pdb=" O MET D 549 " pdb=" H ASN D 553 " model vdw 1.639 1.850 nonbonded pdb=" O MET A 549 " pdb=" H ASN A 553 " model vdw 1.639 1.850 nonbonded pdb=" OE2 GLU D 418 " pdb="HH12 ARG D 422 " model vdw 1.672 1.850 ... (remaining 595966 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' and (resid 111 through 778 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211 \ or name C212 or name C213 or name C214 or name C215 or name C216 or name C217 o \ r name C218)) or resid 902 or (resid 905 and (name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29)) or (resid 906 through 907 and ( \ name C29 or name C210 or name C211 or name C212 or name C213 or name C214 or nam \ e C215 or name C216 or name C217 or name C218)))) selection = (chain 'B' and (resid 111 through 778 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211 \ or name C212 or name C213 or name C214 or name C215 or name C216 or name C217 o \ r name C218)) or resid 902 or (resid 905 and (name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29)) or (resid 906 through 907 and ( \ name C29 or name C210 or name C211 or name C212 or name C213 or name C214 or nam \ e C215 or name C216 or name C217 or name C218)))) selection = (chain 'C' and (resid 111 through 778 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211 \ or name C212 or name C213 or name C214 or name C215 or name C216 or name C217 o \ r name C218)) or resid 902 or (resid 905 and (name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29)) or (resid 906 through 907 and ( \ name C29 or name C210 or name C211 or name C212 or name C213 or name C214 or nam \ e C215 or name C216 or name C217 or name C218)))) selection = (chain 'D' and (resid 111 through 778 or resid 901 or (resid 902 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C214 or \ name C215 or name C216 or name C217 or name C218 or name C310 or name C311)) or \ (resid 905 and (name C23 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29)) or (resid 906 through 907 and (name C29 or name C210 or name \ C211 or name C212 or name C213 or name C214 or name C215 or name C216 or name C2 \ 17 or name C218)))) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.620 Extract box with map and model: 6.070 Check model and map are aligned: 0.690 Set scattering table: 0.440 Process input model: 133.760 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.190 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.013 0.090 22340 Z= 0.866 Angle : 1.332 13.675 30028 Z= 0.664 Chirality : 0.056 0.261 3272 Planarity : 0.012 0.263 3688 Dihedral : 16.166 152.731 8588 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.37 % Favored : 88.32 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.75 (0.13), residues: 2568 helix: -2.85 (0.10), residues: 1428 sheet: -4.41 (0.46), residues: 48 loop : -3.42 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 374 HIS 0.007 0.002 HIS D 291 PHE 0.023 0.003 PHE B 651 TYR 0.019 0.003 TYR D 248 ARG 0.011 0.001 ARG C 719 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 770 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 770 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8771 (pmt170) cc_final: 0.8362 (ttp-170) REVERT: A 218 LEU cc_start: 0.9393 (mm) cc_final: 0.9135 (mm) REVERT: A 225 ASN cc_start: 0.8123 (m110) cc_final: 0.7727 (m110) REVERT: A 259 CYS cc_start: 0.8800 (m) cc_final: 0.8481 (t) REVERT: A 304 THR cc_start: 0.9185 (m) cc_final: 0.8814 (p) REVERT: A 407 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7970 (tm-30) REVERT: A 495 ILE cc_start: 0.9133 (mm) cc_final: 0.8494 (mm) REVERT: A 543 MET cc_start: 0.8998 (ttp) cc_final: 0.8718 (ttt) REVERT: A 583 MET cc_start: 0.7677 (mmm) cc_final: 0.7403 (mmt) REVERT: A 591 PHE cc_start: 0.8029 (t80) cc_final: 0.7793 (t80) REVERT: A 723 ARG cc_start: 0.7036 (tpm170) cc_final: 0.6670 (tpm170) REVERT: A 750 ASN cc_start: 0.8528 (t160) cc_final: 0.8073 (t0) REVERT: B 116 ARG cc_start: 0.8836 (pmt170) cc_final: 0.8480 (ttp-170) REVERT: B 240 LYS cc_start: 0.7273 (mtpp) cc_final: 0.6986 (mmmm) REVERT: B 304 THR cc_start: 0.9343 (m) cc_final: 0.8958 (p) REVERT: B 407 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8106 (tm-30) REVERT: B 495 ILE cc_start: 0.9114 (mm) cc_final: 0.8537 (mm) REVERT: B 583 MET cc_start: 0.8068 (mmm) cc_final: 0.7802 (mmp) REVERT: B 723 ARG cc_start: 0.7127 (tpm170) cc_final: 0.6505 (tpm170) REVERT: B 750 ASN cc_start: 0.8544 (t160) cc_final: 0.8095 (t0) REVERT: C 218 LEU cc_start: 0.9275 (mm) cc_final: 0.9037 (mm) REVERT: C 240 LYS cc_start: 0.7269 (mtpp) cc_final: 0.7025 (mmmm) REVERT: C 268 PHE cc_start: 0.8074 (t80) cc_final: 0.7868 (t80) REVERT: C 304 THR cc_start: 0.9406 (m) cc_final: 0.9053 (p) REVERT: C 495 ILE cc_start: 0.9107 (mm) cc_final: 0.8496 (mm) REVERT: C 583 MET cc_start: 0.8008 (mmm) cc_final: 0.7726 (mmp) REVERT: C 723 ARG cc_start: 0.7097 (tpm170) cc_final: 0.6572 (tpm170) REVERT: D 218 LEU cc_start: 0.9291 (mm) cc_final: 0.9050 (mm) REVERT: D 240 LYS cc_start: 0.7280 (mtpp) cc_final: 0.7063 (mmmm) REVERT: D 252 LEU cc_start: 0.9211 (tm) cc_final: 0.8877 (tm) REVERT: D 268 PHE cc_start: 0.8049 (t80) cc_final: 0.7821 (t80) REVERT: D 304 THR cc_start: 0.9401 (m) cc_final: 0.9027 (p) REVERT: D 390 ASP cc_start: 0.8049 (t70) cc_final: 0.7817 (p0) REVERT: D 495 ILE cc_start: 0.9119 (mm) cc_final: 0.8510 (mm) REVERT: D 583 MET cc_start: 0.8127 (mmm) cc_final: 0.7828 (mmp) REVERT: D 723 ARG cc_start: 0.7016 (tpm170) cc_final: 0.6503 (tpm170) REVERT: D 753 THR cc_start: 0.8651 (m) cc_final: 0.8360 (p) outliers start: 0 outliers final: 0 residues processed: 770 average time/residue: 0.9219 time to fit residues: 1040.9847 Evaluate side-chains 497 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 497 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 215 ASN ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN A 291 HIS A 303 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 ASN B 172 ASN B 215 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 291 HIS B 303 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN C 172 ASN C 215 ASN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 291 HIS C 303 ASN ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN D 172 ASN D 215 ASN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 291 HIS D 303 ASN ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22340 Z= 0.242 Angle : 0.686 7.954 30028 Z= 0.361 Chirality : 0.038 0.133 3272 Planarity : 0.005 0.061 3688 Dihedral : 18.399 148.114 3644 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.90 % Favored : 91.94 % Rotamer: Outliers : 1.44 % Allowed : 10.27 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.15), residues: 2568 helix: -1.04 (0.12), residues: 1492 sheet: None (None), residues: 0 loop : -3.42 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 699 HIS 0.015 0.001 HIS A 366 PHE 0.019 0.002 PHE A 249 TYR 0.018 0.002 TYR B 248 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 579 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 546 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.9233 (mm) cc_final: 0.8960 (mm) REVERT: A 304 THR cc_start: 0.9183 (m) cc_final: 0.8805 (p) REVERT: A 380 HIS cc_start: 0.8165 (p-80) cc_final: 0.7705 (p-80) REVERT: A 723 ARG cc_start: 0.7173 (tpm170) cc_final: 0.6747 (tpm170) REVERT: A 750 ASN cc_start: 0.8597 (t0) cc_final: 0.8022 (t0) REVERT: A 773 ARG cc_start: 0.6173 (ptt90) cc_final: 0.5824 (ptm-80) REVERT: B 304 THR cc_start: 0.9338 (m) cc_final: 0.8977 (p) REVERT: B 311 TYR cc_start: 0.9200 (t80) cc_final: 0.8993 (t80) REVERT: B 583 MET cc_start: 0.8375 (mmm) cc_final: 0.7814 (mmt) REVERT: B 591 PHE cc_start: 0.8086 (t80) cc_final: 0.7827 (t80) REVERT: B 723 ARG cc_start: 0.7094 (tpm170) cc_final: 0.6647 (tpm170) REVERT: B 750 ASN cc_start: 0.8518 (t0) cc_final: 0.7963 (t0) REVERT: B 773 ARG cc_start: 0.5795 (ppt170) cc_final: 0.5443 (ptm-80) REVERT: C 304 THR cc_start: 0.9424 (m) cc_final: 0.9068 (p) REVERT: C 591 PHE cc_start: 0.8047 (t80) cc_final: 0.7831 (t80) REVERT: C 723 ARG cc_start: 0.7050 (tpm170) cc_final: 0.6656 (tpm170) REVERT: C 750 ASN cc_start: 0.8477 (t0) cc_final: 0.7911 (t0) REVERT: C 773 ARG cc_start: 0.5759 (ppt170) cc_final: 0.5413 (ptm-80) REVERT: D 304 THR cc_start: 0.9426 (m) cc_final: 0.9071 (p) REVERT: D 523 LEU cc_start: 0.9381 (mp) cc_final: 0.9177 (mm) REVERT: D 583 MET cc_start: 0.8329 (mmm) cc_final: 0.8124 (mmt) REVERT: D 591 PHE cc_start: 0.8091 (t80) cc_final: 0.7822 (t80) REVERT: D 723 ARG cc_start: 0.7044 (tpm170) cc_final: 0.6739 (tpm170) REVERT: D 750 ASN cc_start: 0.8495 (t0) cc_final: 0.7949 (t0) REVERT: D 773 ARG cc_start: 0.5737 (ppt170) cc_final: 0.5390 (ptm-80) outliers start: 33 outliers final: 19 residues processed: 568 average time/residue: 0.8397 time to fit residues: 713.1451 Evaluate side-chains 475 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 456 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 631 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 232 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 79 optimal weight: 0.4980 chunk 186 optimal weight: 9.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22340 Z= 0.351 Angle : 0.689 8.036 30028 Z= 0.366 Chirality : 0.039 0.201 3272 Planarity : 0.005 0.053 3688 Dihedral : 16.811 147.719 3644 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.05 % Favored : 89.80 % Rotamer: Outliers : 1.92 % Allowed : 13.46 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.15), residues: 2568 helix: -0.44 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -3.62 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 374 HIS 0.004 0.001 HIS A 366 PHE 0.017 0.002 PHE B 268 TYR 0.020 0.002 TYR A 376 ARG 0.005 0.000 ARG D 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 506 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 462 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 THR cc_start: 0.9168 (m) cc_final: 0.8845 (p) REVERT: A 750 ASN cc_start: 0.8644 (t0) cc_final: 0.8128 (t0) REVERT: A 773 ARG cc_start: 0.6279 (ptt90) cc_final: 0.6025 (ptm-80) REVERT: B 116 ARG cc_start: 0.8785 (pmt170) cc_final: 0.8395 (tmm-80) REVERT: B 304 THR cc_start: 0.9301 (m) cc_final: 0.8997 (p) REVERT: B 311 TYR cc_start: 0.9334 (t80) cc_final: 0.9128 (t80) REVERT: B 523 LEU cc_start: 0.9555 (mp) cc_final: 0.9296 (mm) REVERT: B 583 MET cc_start: 0.8554 (mmm) cc_final: 0.8276 (mmp) REVERT: B 591 PHE cc_start: 0.8435 (t80) cc_final: 0.8184 (t80) REVERT: B 723 ARG cc_start: 0.7061 (tpm170) cc_final: 0.6742 (tpm170) REVERT: B 750 ASN cc_start: 0.8517 (t0) cc_final: 0.7934 (t0) REVERT: B 763 GLU cc_start: 0.8183 (tt0) cc_final: 0.7778 (tt0) REVERT: B 773 ARG cc_start: 0.5910 (ppt170) cc_final: 0.5628 (ptm-80) REVERT: C 262 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.6960 (mt0) REVERT: C 304 THR cc_start: 0.9317 (m) cc_final: 0.9026 (p) REVERT: C 723 ARG cc_start: 0.7064 (tpm170) cc_final: 0.6799 (tpm170) REVERT: C 750 ASN cc_start: 0.8516 (t0) cc_final: 0.7929 (t0) REVERT: C 773 ARG cc_start: 0.5930 (ppt170) cc_final: 0.5493 (ptm-80) REVERT: D 116 ARG cc_start: 0.8771 (pmt170) cc_final: 0.8373 (tmm-80) REVERT: D 262 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.6909 (mt0) REVERT: D 304 THR cc_start: 0.9319 (m) cc_final: 0.9003 (p) REVERT: D 523 LEU cc_start: 0.9421 (mp) cc_final: 0.9180 (mm) REVERT: D 583 MET cc_start: 0.8564 (mmm) cc_final: 0.8271 (mmp) REVERT: D 723 ARG cc_start: 0.7216 (tpm170) cc_final: 0.7004 (tpm170) REVERT: D 750 ASN cc_start: 0.8552 (t0) cc_final: 0.7975 (t0) REVERT: D 773 ARG cc_start: 0.5795 (ppt170) cc_final: 0.5535 (ptm-80) outliers start: 44 outliers final: 37 residues processed: 481 average time/residue: 0.8039 time to fit residues: 601.4299 Evaluate side-chains 454 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 415 time to evaluate : 4.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 221 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22340 Z= 0.218 Angle : 0.581 7.922 30028 Z= 0.306 Chirality : 0.036 0.130 3272 Planarity : 0.004 0.052 3688 Dihedral : 15.801 139.869 3644 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.80 % Favored : 91.04 % Rotamer: Outliers : 1.75 % Allowed : 14.29 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.16), residues: 2568 helix: 0.02 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -3.56 (0.16), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 374 HIS 0.007 0.001 HIS C 380 PHE 0.028 0.002 PHE A 268 TYR 0.018 0.002 TYR C 248 ARG 0.007 0.000 ARG A 411 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 499 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 459 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 THR cc_start: 0.9175 (m) cc_final: 0.8811 (p) REVERT: A 750 ASN cc_start: 0.8652 (t0) cc_final: 0.8110 (t0) REVERT: A 773 ARG cc_start: 0.6347 (ptt90) cc_final: 0.6089 (ptm-80) REVERT: B 116 ARG cc_start: 0.8760 (pmt170) cc_final: 0.8364 (tmm-80) REVERT: B 304 THR cc_start: 0.9305 (m) cc_final: 0.8982 (p) REVERT: B 311 TYR cc_start: 0.9282 (t80) cc_final: 0.9067 (t80) REVERT: B 500 GLN cc_start: 0.7665 (mp10) cc_final: 0.7126 (mp10) REVERT: B 523 LEU cc_start: 0.9528 (mp) cc_final: 0.9258 (mm) REVERT: B 583 MET cc_start: 0.8505 (mmm) cc_final: 0.8216 (mmp) REVERT: B 750 ASN cc_start: 0.8546 (t0) cc_final: 0.7962 (t0) REVERT: B 773 ARG cc_start: 0.6010 (ppt170) cc_final: 0.5697 (ptm-80) REVERT: C 116 ARG cc_start: 0.8755 (pmt170) cc_final: 0.8303 (tmm-80) REVERT: C 304 THR cc_start: 0.9291 (m) cc_final: 0.8995 (p) REVERT: C 523 LEU cc_start: 0.9456 (mp) cc_final: 0.9190 (mm) REVERT: C 750 ASN cc_start: 0.8601 (t0) cc_final: 0.8004 (t0) REVERT: C 773 ARG cc_start: 0.6031 (ppt170) cc_final: 0.5709 (ptm-80) REVERT: D 116 ARG cc_start: 0.8744 (pmt170) cc_final: 0.8332 (tmm-80) REVERT: D 304 THR cc_start: 0.9274 (m) cc_final: 0.8979 (p) REVERT: D 523 LEU cc_start: 0.9362 (mp) cc_final: 0.9094 (mm) REVERT: D 583 MET cc_start: 0.8543 (mmm) cc_final: 0.8230 (mmp) REVERT: D 653 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6911 (tm-30) REVERT: D 750 ASN cc_start: 0.8572 (t0) cc_final: 0.7973 (t0) REVERT: D 773 ARG cc_start: 0.5855 (ppt170) cc_final: 0.5585 (ptm-80) outliers start: 40 outliers final: 36 residues processed: 481 average time/residue: 0.7394 time to fit residues: 545.9949 Evaluate side-chains 462 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 426 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 312 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 312 ASN B 678 ASN C 312 ASN D 312 ASN D 678 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22340 Z= 0.338 Angle : 0.632 8.159 30028 Z= 0.337 Chirality : 0.038 0.141 3272 Planarity : 0.004 0.049 3688 Dihedral : 15.563 135.323 3644 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.01 % Favored : 89.84 % Rotamer: Outliers : 2.36 % Allowed : 14.99 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.16), residues: 2568 helix: 0.05 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -3.52 (0.16), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 374 HIS 0.005 0.001 HIS B 380 PHE 0.025 0.002 PHE A 582 TYR 0.016 0.002 TYR A 673 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 488 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 434 time to evaluate : 3.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.7726 (tt0) cc_final: 0.7236 (tt0) REVERT: A 304 THR cc_start: 0.9222 (m) cc_final: 0.8863 (p) REVERT: A 441 PHE cc_start: 0.8465 (t80) cc_final: 0.8110 (t80) REVERT: A 750 ASN cc_start: 0.8758 (t0) cc_final: 0.8040 (t0) REVERT: A 773 ARG cc_start: 0.6347 (ptt90) cc_final: 0.6061 (ptm-80) REVERT: B 116 ARG cc_start: 0.8786 (pmt170) cc_final: 0.8347 (tmm-80) REVERT: B 262 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: B 304 THR cc_start: 0.9349 (m) cc_final: 0.9049 (p) REVERT: B 311 TYR cc_start: 0.9388 (t80) cc_final: 0.9157 (t80) REVERT: B 500 GLN cc_start: 0.7701 (mp10) cc_final: 0.7120 (mp10) REVERT: B 523 LEU cc_start: 0.9557 (mp) cc_final: 0.9295 (mm) REVERT: B 567 TYR cc_start: 0.8752 (t80) cc_final: 0.8545 (t80) REVERT: B 583 MET cc_start: 0.8583 (mmm) cc_final: 0.8281 (mmp) REVERT: B 750 ASN cc_start: 0.8564 (t0) cc_final: 0.8022 (t0) REVERT: B 773 ARG cc_start: 0.6076 (ppt170) cc_final: 0.5745 (ptm-80) REVERT: C 116 ARG cc_start: 0.8767 (pmt170) cc_final: 0.8291 (tmm-80) REVERT: C 237 PHE cc_start: 0.8615 (t80) cc_final: 0.8326 (t80) REVERT: C 304 THR cc_start: 0.9327 (m) cc_final: 0.9030 (p) REVERT: C 441 PHE cc_start: 0.8342 (t80) cc_final: 0.7979 (t80) REVERT: C 523 LEU cc_start: 0.9484 (mp) cc_final: 0.9219 (mm) REVERT: C 653 GLU cc_start: 0.7238 (mt-10) cc_final: 0.7000 (tm-30) REVERT: C 750 ASN cc_start: 0.8634 (t0) cc_final: 0.8073 (t0) REVERT: C 773 ARG cc_start: 0.6161 (ppt170) cc_final: 0.5833 (ptm-80) REVERT: D 116 ARG cc_start: 0.8758 (pmt170) cc_final: 0.8319 (tmm-80) REVERT: D 304 THR cc_start: 0.9314 (m) cc_final: 0.9024 (p) REVERT: D 441 PHE cc_start: 0.8135 (t80) cc_final: 0.7780 (t80) REVERT: D 523 LEU cc_start: 0.9391 (mp) cc_final: 0.9123 (mm) REVERT: D 583 MET cc_start: 0.8575 (mmm) cc_final: 0.8265 (mmp) REVERT: D 653 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6984 (tm-30) REVERT: D 750 ASN cc_start: 0.8668 (t0) cc_final: 0.8128 (t0) REVERT: D 773 ARG cc_start: 0.5903 (ppt170) cc_final: 0.5621 (ptm-80) outliers start: 54 outliers final: 47 residues processed: 467 average time/residue: 0.7551 time to fit residues: 545.0672 Evaluate side-chains 459 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 411 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 561 PHE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 561 PHE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 764 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 247 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22340 Z= 0.211 Angle : 0.570 8.910 30028 Z= 0.299 Chirality : 0.036 0.130 3272 Planarity : 0.004 0.044 3688 Dihedral : 15.113 127.054 3644 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.19 % Favored : 90.65 % Rotamer: Outliers : 2.10 % Allowed : 16.30 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2568 helix: 0.39 (0.14), residues: 1460 sheet: None (None), residues: 0 loop : -3.41 (0.16), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 374 HIS 0.006 0.001 HIS C 380 PHE 0.019 0.001 PHE A 582 TYR 0.014 0.001 TYR C 248 ARG 0.003 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 468 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 420 time to evaluate : 3.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 THR cc_start: 0.9186 (m) cc_final: 0.8820 (p) REVERT: A 750 ASN cc_start: 0.8759 (t0) cc_final: 0.8020 (t0) REVERT: A 773 ARG cc_start: 0.6359 (ptt90) cc_final: 0.6092 (ptm-80) REVERT: B 116 ARG cc_start: 0.8778 (pmt170) cc_final: 0.8335 (tmm-80) REVERT: B 304 THR cc_start: 0.9290 (m) cc_final: 0.8960 (p) REVERT: B 495 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8760 (tp) REVERT: B 500 GLN cc_start: 0.7631 (mp10) cc_final: 0.7149 (mp10) REVERT: B 523 LEU cc_start: 0.9538 (mp) cc_final: 0.9280 (mm) REVERT: B 583 MET cc_start: 0.8547 (mmm) cc_final: 0.8241 (mmp) REVERT: B 750 ASN cc_start: 0.8548 (t0) cc_final: 0.7986 (t0) REVERT: B 773 ARG cc_start: 0.6117 (ppt170) cc_final: 0.5763 (ptm-80) REVERT: C 116 ARG cc_start: 0.8769 (pmt170) cc_final: 0.8285 (tmm-80) REVERT: C 237 PHE cc_start: 0.8546 (t80) cc_final: 0.8254 (t80) REVERT: C 304 THR cc_start: 0.9259 (m) cc_final: 0.8973 (p) REVERT: C 523 LEU cc_start: 0.9466 (mp) cc_final: 0.9189 (mm) REVERT: C 750 ASN cc_start: 0.8584 (t0) cc_final: 0.8033 (t0) REVERT: C 773 ARG cc_start: 0.6175 (ppt170) cc_final: 0.5846 (ptm-80) REVERT: D 116 ARG cc_start: 0.8743 (pmt170) cc_final: 0.8293 (tmm-80) REVERT: D 304 THR cc_start: 0.9266 (m) cc_final: 0.8972 (p) REVERT: D 523 LEU cc_start: 0.9344 (mp) cc_final: 0.9063 (mm) REVERT: D 750 ASN cc_start: 0.8620 (t0) cc_final: 0.8033 (t0) REVERT: D 773 ARG cc_start: 0.5939 (ppt170) cc_final: 0.5641 (ptm-80) outliers start: 48 outliers final: 42 residues processed: 449 average time/residue: 0.7564 time to fit residues: 526.3161 Evaluate side-chains 438 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 395 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 141 optimal weight: 0.3980 chunk 180 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 208 optimal weight: 0.8980 chunk 138 optimal weight: 0.0000 chunk 246 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22340 Z= 0.148 Angle : 0.536 8.198 30028 Z= 0.279 Chirality : 0.035 0.128 3272 Planarity : 0.003 0.042 3688 Dihedral : 14.319 113.035 3644 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.33 % Favored : 91.59 % Rotamer: Outliers : 2.14 % Allowed : 16.22 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.17), residues: 2568 helix: 0.68 (0.14), residues: 1472 sheet: -3.48 (0.54), residues: 48 loop : -3.30 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 374 HIS 0.006 0.000 HIS C 380 PHE 0.023 0.001 PHE A 582 TYR 0.012 0.001 TYR C 248 ARG 0.003 0.000 ARG A 411 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 442 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 THR cc_start: 0.9167 (m) cc_final: 0.8820 (p) REVERT: A 513 TYR cc_start: 0.8422 (t80) cc_final: 0.8183 (t80) REVERT: A 549 MET cc_start: 0.8721 (mtm) cc_final: 0.8502 (mtm) REVERT: A 750 ASN cc_start: 0.8703 (t0) cc_final: 0.8132 (t0) REVERT: A 773 ARG cc_start: 0.6364 (ptt90) cc_final: 0.6052 (ptm-80) REVERT: B 116 ARG cc_start: 0.8785 (pmt170) cc_final: 0.8335 (tmm-80) REVERT: B 304 THR cc_start: 0.9275 (m) cc_final: 0.8945 (p) REVERT: B 523 LEU cc_start: 0.9511 (mp) cc_final: 0.9216 (mm) REVERT: B 750 ASN cc_start: 0.8535 (t0) cc_final: 0.7982 (t0) REVERT: B 761 ILE cc_start: 0.9070 (mp) cc_final: 0.8827 (mp) REVERT: B 773 ARG cc_start: 0.6138 (ppt170) cc_final: 0.5816 (ptm-80) REVERT: C 116 ARG cc_start: 0.8764 (pmt170) cc_final: 0.8275 (tmm-80) REVERT: C 237 PHE cc_start: 0.8436 (t80) cc_final: 0.8148 (t80) REVERT: C 304 THR cc_start: 0.9225 (m) cc_final: 0.8951 (p) REVERT: C 500 GLN cc_start: 0.7579 (mp10) cc_final: 0.7171 (mp10) REVERT: C 523 LEU cc_start: 0.9433 (mp) cc_final: 0.9092 (mm) REVERT: C 750 ASN cc_start: 0.8539 (t0) cc_final: 0.7932 (t0) REVERT: C 761 ILE cc_start: 0.9069 (mp) cc_final: 0.8844 (mp) REVERT: C 773 ARG cc_start: 0.6191 (ppt170) cc_final: 0.5869 (ptm-80) REVERT: D 116 ARG cc_start: 0.8736 (pmt170) cc_final: 0.8284 (tmm-80) REVERT: D 304 THR cc_start: 0.9215 (m) cc_final: 0.8944 (p) REVERT: D 500 GLN cc_start: 0.7638 (mp10) cc_final: 0.7245 (mp10) REVERT: D 501 ARG cc_start: 0.7590 (mmp-170) cc_final: 0.6876 (ptt180) REVERT: D 570 MET cc_start: 0.8758 (mtp) cc_final: 0.8514 (mtp) REVERT: D 750 ASN cc_start: 0.8593 (t0) cc_final: 0.7977 (t0) REVERT: D 773 ARG cc_start: 0.5899 (ppt170) cc_final: 0.5640 (ptm-80) outliers start: 49 outliers final: 40 residues processed: 468 average time/residue: 0.7581 time to fit residues: 553.7695 Evaluate side-chains 450 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 410 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN B 678 ASN ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22340 Z= 0.196 Angle : 0.548 8.270 30028 Z= 0.288 Chirality : 0.035 0.146 3272 Planarity : 0.003 0.038 3688 Dihedral : 13.884 103.105 3644 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.61 % Favored : 91.24 % Rotamer: Outliers : 2.23 % Allowed : 16.65 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2568 helix: 0.72 (0.14), residues: 1476 sheet: -3.25 (0.54), residues: 48 loop : -3.25 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 374 HIS 0.005 0.001 HIS C 380 PHE 0.024 0.001 PHE A 582 TYR 0.012 0.001 TYR C 248 ARG 0.002 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 471 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 420 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 THR cc_start: 0.9193 (m) cc_final: 0.8840 (p) REVERT: A 426 ASP cc_start: 0.8850 (t0) cc_final: 0.8128 (t0) REVERT: A 501 ARG cc_start: 0.7595 (mmp-170) cc_final: 0.7271 (mmp80) REVERT: A 549 MET cc_start: 0.8723 (mtm) cc_final: 0.8507 (mtm) REVERT: A 750 ASN cc_start: 0.8745 (t0) cc_final: 0.8181 (t0) REVERT: A 773 ARG cc_start: 0.6305 (ptt90) cc_final: 0.6091 (ptm-80) REVERT: B 116 ARG cc_start: 0.8784 (pmt170) cc_final: 0.8336 (tmm-80) REVERT: B 304 THR cc_start: 0.9290 (m) cc_final: 0.8965 (p) REVERT: B 495 ILE cc_start: 0.9050 (tp) cc_final: 0.8711 (tp) REVERT: B 500 GLN cc_start: 0.7608 (mp10) cc_final: 0.7020 (mp10) REVERT: B 523 LEU cc_start: 0.9522 (mp) cc_final: 0.9235 (mm) REVERT: B 750 ASN cc_start: 0.8589 (t0) cc_final: 0.8010 (t0) REVERT: B 761 ILE cc_start: 0.9076 (mp) cc_final: 0.8850 (mp) REVERT: B 773 ARG cc_start: 0.6161 (ppt170) cc_final: 0.5811 (ptm-80) REVERT: C 116 ARG cc_start: 0.8772 (pmt170) cc_final: 0.8286 (tmm-80) REVERT: C 237 PHE cc_start: 0.8514 (t80) cc_final: 0.8193 (t80) REVERT: C 304 THR cc_start: 0.9247 (m) cc_final: 0.8978 (p) REVERT: C 500 GLN cc_start: 0.7609 (mp10) cc_final: 0.7174 (mp10) REVERT: C 501 ARG cc_start: 0.7538 (mmp-170) cc_final: 0.7245 (mmp80) REVERT: C 523 LEU cc_start: 0.9468 (mp) cc_final: 0.9128 (mm) REVERT: C 570 MET cc_start: 0.8764 (mtp) cc_final: 0.8548 (mtp) REVERT: C 750 ASN cc_start: 0.8544 (t0) cc_final: 0.7966 (t0) REVERT: C 773 ARG cc_start: 0.6182 (ppt170) cc_final: 0.5869 (ptm-80) REVERT: D 116 ARG cc_start: 0.8747 (pmt170) cc_final: 0.8291 (tmm-80) REVERT: D 304 THR cc_start: 0.9234 (m) cc_final: 0.8960 (p) REVERT: D 500 GLN cc_start: 0.7636 (mp10) cc_final: 0.7217 (mp10) REVERT: D 501 ARG cc_start: 0.7510 (mmp-170) cc_final: 0.6785 (ptt180) REVERT: D 750 ASN cc_start: 0.8619 (t0) cc_final: 0.8011 (t0) REVERT: D 773 ARG cc_start: 0.5941 (ppt170) cc_final: 0.5655 (ptm-80) outliers start: 51 outliers final: 45 residues processed: 446 average time/residue: 0.7739 time to fit residues: 536.2241 Evaluate side-chains 444 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 399 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22340 Z= 0.259 Angle : 0.569 8.153 30028 Z= 0.302 Chirality : 0.036 0.151 3272 Planarity : 0.003 0.034 3688 Dihedral : 13.847 92.660 3644 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.27 % Favored : 90.58 % Rotamer: Outliers : 2.10 % Allowed : 16.74 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2568 helix: 0.68 (0.14), residues: 1476 sheet: -3.25 (0.53), residues: 48 loop : -3.17 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 374 HIS 0.005 0.001 HIS C 380 PHE 0.026 0.001 PHE A 582 TYR 0.013 0.002 TYR C 673 ARG 0.003 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 471 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 423 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 THR cc_start: 0.9222 (m) cc_final: 0.8881 (p) REVERT: A 426 ASP cc_start: 0.8878 (t0) cc_final: 0.8240 (t0) REVERT: A 441 PHE cc_start: 0.8458 (t80) cc_final: 0.8145 (t80) REVERT: A 501 ARG cc_start: 0.7623 (mmp-170) cc_final: 0.7311 (mmp80) REVERT: A 549 MET cc_start: 0.8771 (mtm) cc_final: 0.8568 (mtm) REVERT: A 750 ASN cc_start: 0.8768 (t0) cc_final: 0.8022 (t0) REVERT: A 773 ARG cc_start: 0.6376 (ptt90) cc_final: 0.6101 (ptm-80) REVERT: B 116 ARG cc_start: 0.8828 (pmt170) cc_final: 0.8373 (tmm-80) REVERT: B 304 THR cc_start: 0.9325 (m) cc_final: 0.8995 (p) REVERT: B 500 GLN cc_start: 0.7655 (mp10) cc_final: 0.7014 (mp10) REVERT: B 523 LEU cc_start: 0.9548 (mp) cc_final: 0.9271 (mm) REVERT: B 750 ASN cc_start: 0.8666 (t0) cc_final: 0.8115 (t0) REVERT: B 773 ARG cc_start: 0.6166 (ppt170) cc_final: 0.5809 (ptm-80) REVERT: C 116 ARG cc_start: 0.8757 (pmt170) cc_final: 0.8295 (tmm-80) REVERT: C 237 PHE cc_start: 0.8590 (t80) cc_final: 0.8317 (t80) REVERT: C 304 THR cc_start: 0.9254 (m) cc_final: 0.8972 (p) REVERT: C 441 PHE cc_start: 0.8350 (t80) cc_final: 0.8014 (t80) REVERT: C 500 GLN cc_start: 0.7637 (mp10) cc_final: 0.7192 (mp10) REVERT: C 501 ARG cc_start: 0.7563 (mmp-170) cc_final: 0.7274 (mmp80) REVERT: C 523 LEU cc_start: 0.9500 (mp) cc_final: 0.9153 (mm) REVERT: C 750 ASN cc_start: 0.8624 (t0) cc_final: 0.8076 (t0) REVERT: C 773 ARG cc_start: 0.6222 (ppt170) cc_final: 0.5891 (ptm-80) REVERT: D 116 ARG cc_start: 0.8739 (pmt170) cc_final: 0.8304 (tmm-80) REVERT: D 304 THR cc_start: 0.9257 (m) cc_final: 0.8977 (p) REVERT: D 441 PHE cc_start: 0.8160 (t80) cc_final: 0.7817 (t80) REVERT: D 500 GLN cc_start: 0.7650 (mp10) cc_final: 0.7234 (mp10) REVERT: D 501 ARG cc_start: 0.7511 (mmp-170) cc_final: 0.7182 (mmp80) REVERT: D 523 LEU cc_start: 0.9373 (mp) cc_final: 0.9044 (mm) REVERT: D 570 MET cc_start: 0.8729 (mtp) cc_final: 0.8475 (mtp) REVERT: D 750 ASN cc_start: 0.8687 (t0) cc_final: 0.8107 (t0) REVERT: D 773 ARG cc_start: 0.5962 (ppt170) cc_final: 0.5666 (ptm-80) outliers start: 48 outliers final: 40 residues processed: 447 average time/residue: 0.7298 time to fit residues: 503.5785 Evaluate side-chains 448 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 408 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 709 ASP Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 255 optimal weight: 0.0870 chunk 234 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 678 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22340 Z= 0.245 Angle : 0.563 8.088 30028 Z= 0.297 Chirality : 0.036 0.140 3272 Planarity : 0.003 0.033 3688 Dihedral : 13.760 87.203 3644 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.79 % Allowed : 17.48 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.16), residues: 2568 helix: 0.71 (0.14), residues: 1476 sheet: -3.19 (0.54), residues: 48 loop : -3.08 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 374 HIS 0.005 0.001 HIS C 380 PHE 0.026 0.001 PHE A 582 TYR 0.012 0.001 TYR D 673 ARG 0.003 0.000 ARG B 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Residue TYR 201 is missing expected H atoms. Skipping. Residue THR 752 is missing expected H atoms. Skipping. Evaluate side-chains 456 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 415 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 THR cc_start: 0.9246 (m) cc_final: 0.8902 (p) REVERT: A 426 ASP cc_start: 0.8881 (t0) cc_final: 0.8233 (t0) REVERT: A 441 PHE cc_start: 0.8432 (t80) cc_final: 0.8096 (t80) REVERT: A 501 ARG cc_start: 0.7622 (mmp-170) cc_final: 0.7312 (mmp80) REVERT: A 549 MET cc_start: 0.8749 (mtm) cc_final: 0.8538 (mtm) REVERT: A 750 ASN cc_start: 0.8782 (t0) cc_final: 0.8099 (t0) REVERT: A 773 ARG cc_start: 0.6374 (ptt90) cc_final: 0.6132 (ptm-80) REVERT: B 116 ARG cc_start: 0.8821 (pmt170) cc_final: 0.8350 (tmm-80) REVERT: B 164 MET cc_start: 0.8744 (mmm) cc_final: 0.8513 (mmm) REVERT: B 304 THR cc_start: 0.9321 (m) cc_final: 0.9002 (p) REVERT: B 500 GLN cc_start: 0.7691 (mp10) cc_final: 0.7097 (mp10) REVERT: B 523 LEU cc_start: 0.9547 (mp) cc_final: 0.9264 (mm) REVERT: B 750 ASN cc_start: 0.8686 (t0) cc_final: 0.8175 (t0) REVERT: B 773 ARG cc_start: 0.6184 (ppt170) cc_final: 0.5824 (ptm-80) REVERT: C 116 ARG cc_start: 0.8769 (pmt170) cc_final: 0.8297 (tmm-80) REVERT: C 237 PHE cc_start: 0.8651 (t80) cc_final: 0.8414 (t80) REVERT: C 304 THR cc_start: 0.9209 (m) cc_final: 0.8921 (p) REVERT: C 500 GLN cc_start: 0.7632 (mp10) cc_final: 0.7154 (mp10) REVERT: C 501 ARG cc_start: 0.7555 (mmp-170) cc_final: 0.6871 (ptt180) REVERT: C 523 LEU cc_start: 0.9496 (mp) cc_final: 0.9172 (mm) REVERT: C 750 ASN cc_start: 0.8660 (t0) cc_final: 0.8110 (t0) REVERT: C 773 ARG cc_start: 0.6249 (ppt170) cc_final: 0.5921 (ptm-80) REVERT: D 116 ARG cc_start: 0.8750 (pmt170) cc_final: 0.8305 (tmm-80) REVERT: D 304 THR cc_start: 0.9241 (m) cc_final: 0.8969 (p) REVERT: D 441 PHE cc_start: 0.8118 (t80) cc_final: 0.7773 (t80) REVERT: D 500 GLN cc_start: 0.7661 (mp10) cc_final: 0.7223 (mp10) REVERT: D 501 ARG cc_start: 0.7524 (mmp-170) cc_final: 0.7183 (mmp80) REVERT: D 523 LEU cc_start: 0.9345 (mp) cc_final: 0.9004 (mm) REVERT: D 750 ASN cc_start: 0.8721 (t0) cc_final: 0.8174 (t0) REVERT: D 761 ILE cc_start: 0.9146 (mp) cc_final: 0.8884 (mp) REVERT: D 773 ARG cc_start: 0.5942 (ppt170) cc_final: 0.5631 (ptm-80) outliers start: 41 outliers final: 39 residues processed: 432 average time/residue: 0.7443 time to fit residues: 495.6912 Evaluate side-chains 449 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 410 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 709 ASP Chi-restraints excluded: chain D residue 722 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 203 optimal weight: 0.3980 chunk 85 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.156919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115588 restraints weight = 88681.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122054 restraints weight = 46122.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123476 restraints weight = 24157.103| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.6425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22340 Z= 0.209 Angle : 0.543 7.912 30028 Z= 0.285 Chirality : 0.035 0.129 3272 Planarity : 0.003 0.032 3688 Dihedral : 13.450 86.587 3644 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 1.79 % Allowed : 17.83 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2568 helix: 0.82 (0.14), residues: 1472 sheet: -3.07 (0.55), residues: 48 loop : -3.01 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 374 HIS 0.005 0.001 HIS C 380 PHE 0.032 0.001 PHE D 237 TYR 0.010 0.001 TYR A 248 ARG 0.003 0.000 ARG A 723 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10389.25 seconds wall clock time: 185 minutes 13.19 seconds (11113.19 seconds total)