Starting phenix.real_space_refine on Fri Feb 23 05:32:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fid_31589/02_2024/7fid_31589_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fid_31589/02_2024/7fid_31589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fid_31589/02_2024/7fid_31589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fid_31589/02_2024/7fid_31589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fid_31589/02_2024/7fid_31589_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fid_31589/02_2024/7fid_31589_updated.pdb" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 135 5.16 5 C 23328 2.51 5 N 6490 2.21 5 O 7024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 202": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36992 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "C" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "D" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "E" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "F" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "A" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "S" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.11, per 1000 atoms: 0.52 Number of scatterers: 36992 At special positions: 0 Unit cell: (197.62, 200.08, 194.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 15 15.00 O 7024 8.00 N 6490 7.00 C 23328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.14 Conformation dependent library (CDL) restraints added in 6.7 seconds 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 35 sheets defined 40.8% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.64 Creating SS restraints... Processing helix chain 'B' and resid 28 through 38 removed outlier: 3.734A pdb=" N LYS B 31 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ARG B 32 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 36 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 138 Processing helix chain 'B' and resid 149 through 152 No H-bonds generated for 'chain 'B' and resid 149 through 152' Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 173 through 180 Processing helix chain 'B' and resid 186 through 235 Processing helix chain 'B' and resid 243 through 253 removed outlier: 3.901A pdb=" N GLU B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.984A pdb=" N ARG B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 308 through 317 removed outlier: 3.651A pdb=" N GLU B 317 " --> pdb=" O GLN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 338 Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.971A pdb=" N SER B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 479 through 484 removed outlier: 3.824A pdb=" N ARG B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 506 through 514 removed outlier: 3.801A pdb=" N SER B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 574 through 578 Processing helix chain 'B' and resid 631 through 646 removed outlier: 3.742A pdb=" N ALA B 646 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 651 No H-bonds generated for 'chain 'B' and resid 648 through 651' Processing helix chain 'B' and resid 680 through 692 Processing helix chain 'B' and resid 718 through 728 Processing helix chain 'B' and resid 737 through 745 removed outlier: 4.365A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 744 " --> pdb=" O ALA B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 751 No H-bonds generated for 'chain 'B' and resid 748 through 751' Processing helix chain 'B' and resid 762 through 769 Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.997A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 134 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 185 through 236 Processing helix chain 'C' and resid 244 through 255 Processing helix chain 'C' and resid 260 through 275 removed outlier: 3.884A pdb=" N ARG C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.937A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 317 removed outlier: 3.709A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU C 317 " --> pdb=" O GLN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 339 Processing helix chain 'C' and resid 362 through 371 removed outlier: 4.361A pdb=" N ARG C 366 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 367 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 435 through 442 removed outlier: 4.237A pdb=" N LEU C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU C 441 " --> pdb=" O SER C 437 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 479 through 484 removed outlier: 4.065A pdb=" N ARG C 484 " --> pdb=" O PRO C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 506 through 514 removed outlier: 3.624A pdb=" N SER C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'C' and resid 543 through 560 Processing helix chain 'C' and resid 574 through 578 Processing helix chain 'C' and resid 631 through 646 removed outlier: 3.633A pdb=" N ALA C 646 " --> pdb=" O THR C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 660 No H-bonds generated for 'chain 'C' and resid 657 through 660' Processing helix chain 'C' and resid 680 through 691 Processing helix chain 'C' and resid 718 through 727 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 741 through 745 removed outlier: 3.749A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 745 " --> pdb=" O GLN C 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 741 through 745' Processing helix chain 'C' and resid 748 through 753 Processing helix chain 'C' and resid 762 through 769 Processing helix chain 'D' and resid 28 through 39 removed outlier: 3.925A pdb=" N ARG D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 138 Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 159 through 168 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 185 through 237 Processing helix chain 'D' and resid 246 through 255 Processing helix chain 'D' and resid 260 through 275 Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.874A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 317 removed outlier: 3.906A pdb=" N GLU D 317 " --> pdb=" O GLN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 Processing helix chain 'D' and resid 362 through 371 Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 435 through 441 removed outlier: 4.477A pdb=" N GLU D 441 " --> pdb=" O SER D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 484 removed outlier: 4.167A pdb=" N ARG D 484 " --> pdb=" O PRO D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 506 through 513 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 541 through 560 Processing helix chain 'D' and resid 574 through 578 Processing helix chain 'D' and resid 631 through 646 removed outlier: 3.587A pdb=" N ALA D 646 " --> pdb=" O THR D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 651 No H-bonds generated for 'chain 'D' and resid 648 through 651' Processing helix chain 'D' and resid 657 through 660 No H-bonds generated for 'chain 'D' and resid 657 through 660' Processing helix chain 'D' and resid 680 through 692 Processing helix chain 'D' and resid 718 through 727 Processing helix chain 'D' and resid 737 through 739 No H-bonds generated for 'chain 'D' and resid 737 through 739' Processing helix chain 'D' and resid 741 through 744 removed outlier: 3.791A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 741 through 744' Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.913A pdb=" N GLY D 753 " --> pdb=" O GLU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 769 Processing helix chain 'E' and resid 31 through 38 Processing helix chain 'E' and resid 118 through 141 removed outlier: 3.565A pdb=" N ASN E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LYS E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N SER E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 168 removed outlier: 4.328A pdb=" N HIS E 168 " --> pdb=" O THR E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'E' and resid 186 through 237 Processing helix chain 'E' and resid 247 through 250 removed outlier: 3.878A pdb=" N ARG E 250 " --> pdb=" O GLU E 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 247 through 250' Processing helix chain 'E' and resid 260 through 270 Processing helix chain 'E' and resid 283 through 294 Processing helix chain 'E' and resid 308 through 318 removed outlier: 3.702A pdb=" N GLU E 317 " --> pdb=" O GLN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 338 Processing helix chain 'E' and resid 362 through 371 Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'E' and resid 436 through 443 removed outlier: 3.793A pdb=" N VAL E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 482 No H-bonds generated for 'chain 'E' and resid 479 through 482' Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 507 through 513 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 541 through 560 Processing helix chain 'E' and resid 574 through 578 Processing helix chain 'E' and resid 631 through 651 removed outlier: 3.504A pdb=" N HIS E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR E 648 " --> pdb=" O LEU E 644 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN E 649 " --> pdb=" O ARG E 645 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASP E 650 " --> pdb=" O ALA E 646 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR E 651 " --> pdb=" O HIS E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 692 Processing helix chain 'E' and resid 718 through 727 Processing helix chain 'E' and resid 737 through 745 removed outlier: 3.526A pdb=" N GLU E 740 " --> pdb=" O LYS E 737 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 743 " --> pdb=" O GLU E 740 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU E 744 " --> pdb=" O ALA E 741 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU E 745 " --> pdb=" O GLN E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 753 Processing helix chain 'E' and resid 762 through 769 Processing helix chain 'F' and resid 28 through 37 removed outlier: 3.843A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 135 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 158 through 166 Processing helix chain 'F' and resid 173 through 180 Processing helix chain 'F' and resid 186 through 236 Processing helix chain 'F' and resid 247 through 253 Processing helix chain 'F' and resid 260 through 266 Processing helix chain 'F' and resid 285 through 293 Processing helix chain 'F' and resid 308 through 318 removed outlier: 4.337A pdb=" N GLU F 317 " --> pdb=" O GLN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 338 Processing helix chain 'F' and resid 362 through 371 Processing helix chain 'F' and resid 387 through 389 No H-bonds generated for 'chain 'F' and resid 387 through 389' Processing helix chain 'F' and resid 404 through 411 Processing helix chain 'F' and resid 424 through 426 No H-bonds generated for 'chain 'F' and resid 424 through 426' Processing helix chain 'F' and resid 436 through 443 Processing helix chain 'F' and resid 479 through 482 No H-bonds generated for 'chain 'F' and resid 479 through 482' Processing helix chain 'F' and resid 495 through 514 Proline residue: F 508 - end of helix removed outlier: 3.835A pdb=" N SER F 514 " --> pdb=" O GLN F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 534 removed outlier: 3.558A pdb=" N LEU F 528 " --> pdb=" O ASP F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 558 removed outlier: 3.531A pdb=" N ILE F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 577 No H-bonds generated for 'chain 'F' and resid 574 through 577' Processing helix chain 'F' and resid 631 through 646 Processing helix chain 'F' and resid 677 through 692 removed outlier: 3.541A pdb=" N GLY F 680 " --> pdb=" O PRO F 677 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE F 681 " --> pdb=" O SER F 678 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR F 682 " --> pdb=" O ALA F 679 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE F 687 " --> pdb=" O ALA F 684 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 691 " --> pdb=" O ALA F 688 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER F 692 " --> pdb=" O SER F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 726 Processing helix chain 'F' and resid 737 through 743 removed outlier: 4.640A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 743 " --> pdb=" O GLU F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 751 No H-bonds generated for 'chain 'F' and resid 748 through 751' Processing helix chain 'F' and resid 762 through 769 Processing helix chain 'A' and resid 31 through 39 removed outlier: 3.701A pdb=" N MET A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 118 through 135 Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 185 through 237 Processing helix chain 'A' and resid 244 through 255 Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.584A pdb=" N ASP A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 removed outlier: 4.268A pdb=" N THR A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.808A pdb=" N ARG A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 removed outlier: 4.066A pdb=" N ARG A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 4.177A pdb=" N SER A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 435 through 442 removed outlier: 3.850A pdb=" N GLU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.722A pdb=" N ASP A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 484' Processing helix chain 'A' and resid 495 through 514 removed outlier: 5.041A pdb=" N TRP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Proline residue: A 508 - end of helix removed outlier: 3.751A pdb=" N SER A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 631 through 646 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 680 through 692 Processing helix chain 'A' and resid 718 through 727 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.565A pdb=" N GLU A 740 " --> pdb=" O LYS A 737 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALA A 741 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 769 Processing sheet with id= A, first strand: chain 'B' and resid 20 through 25 removed outlier: 3.892A pdb=" N THR B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 43 through 46 Processing sheet with id= C, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.858A pdb=" N ASP B 96 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 486 through 490 removed outlier: 6.689A pdb=" N PHE B 467 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU B 353 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR B 469 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLY B 355 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA B 471 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.277A pdb=" N ARG B 567 " --> pdb=" O GLU B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 596 through 602 removed outlier: 5.902A pdb=" N LYS B 622 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL B 665 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 733 through 736 Processing sheet with id= H, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.591A pdb=" N GLU C 87 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 70 " --> pdb=" O GLU C 87 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLN C 68 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG C 91 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY C 66 " --> pdb=" O ARG C 91 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 486 through 490 removed outlier: 6.590A pdb=" N PHE C 467 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU C 353 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR C 469 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLY C 355 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 471 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 596 through 603 removed outlier: 5.965A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL C 667 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR C 626 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 700 through 702 removed outlier: 6.739A pdb=" N LYS C 732 " --> pdb=" O ALA C 701 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 7 through 9 removed outlier: 7.319A pdb=" N ILE D 8 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE D 45 " --> pdb=" O ILE D 8 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 21 through 23 removed outlier: 4.304A pdb=" N THR D 21 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 86 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU D 87 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL D 71 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 351 through 355 removed outlier: 6.245A pdb=" N GLU D 486 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL D 354 " --> pdb=" O GLU D 486 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE D 488 " --> pdb=" O VAL D 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 376 through 380 removed outlier: 6.503A pdb=" N VAL D 418 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE D 379 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU D 420 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE D 466 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU D 421 " --> pdb=" O PHE D 466 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE D 468 " --> pdb=" O LEU D 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 596 through 603 removed outlier: 6.345A pdb=" N LYS D 622 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL D 665 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.311A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 7 through 9 removed outlier: 7.916A pdb=" N ILE E 8 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N PHE E 45 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET E 85 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ALA E 74 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLN E 83 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 486 through 489 removed outlier: 4.651A pdb=" N LEU E 351 " --> pdb=" O PHE E 467 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE E 419 " --> pdb=" O PHE E 466 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.183A pdb=" N ARG E 567 " --> pdb=" O GLU E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 596 through 603 Processing sheet with id= V, first strand: chain 'E' and resid 700 through 702 removed outlier: 6.504A pdb=" N LYS E 732 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU E 755 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU E 735 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS E 757 " --> pdb=" O LEU E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 8 through 10 removed outlier: 3.903A pdb=" N ILE F 8 " --> pdb=" O PHE F 45 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL F 47 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU F 10 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA F 90 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL F 70 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ALA F 88 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 21 through 25 Processing sheet with id= Y, first strand: chain 'F' and resid 485 through 490 removed outlier: 5.680A pdb=" N ILE F 350 " --> pdb=" O GLU F 486 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE F 488 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL F 352 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE F 490 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL F 354 " --> pdb=" O ILE F 490 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU F 351 " --> pdb=" O PHE F 467 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.641A pdb=" N ARG F 567 " --> pdb=" O GLU F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 596 through 603 removed outlier: 4.993A pdb=" N THR F 611 " --> pdb=" O PRO F 668 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 733 through 736 Processing sheet with id= AC, first strand: chain 'A' and resid 4 through 6 removed outlier: 4.137A pdb=" N ARG A 104 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 106 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP A 96 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 7 through 9 removed outlier: 8.410A pdb=" N ILE A 8 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE A 45 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 22 through 25 removed outlier: 3.637A pdb=" N GLN A 73 " --> pdb=" O MET A 85 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 486 through 490 Processing sheet with id= AG, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.323A pdb=" N ARG A 567 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'A' and resid 596 through 603 removed outlier: 5.979A pdb=" N LYS A 622 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL A 665 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL A 667 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR A 626 " --> pdb=" O VAL A 667 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 733 through 736 1384 hydrogen bonds defined for protein. 4041 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: 13.10 Time building geometry restraints manager: 15.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 12595 1.35 - 1.50: 10662 1.50 - 1.65: 14145 1.65 - 1.80: 211 1.80 - 1.95: 56 Bond restraints: 37669 Sorted by residual: bond pdb=" C ILE F 113 " pdb=" N PHE F 114 " ideal model delta sigma weight residual 1.329 1.390 -0.061 1.35e-02 5.49e+03 2.05e+01 bond pdb=" C ASP A 51 " pdb=" N PRO A 52 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.21e-02 6.83e+03 1.75e+01 bond pdb=" CA GLU A 247 " pdb=" C GLU A 247 " ideal model delta sigma weight residual 1.522 1.469 0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" N SER E 380 " pdb=" CA SER E 380 " ideal model delta sigma weight residual 1.461 1.510 -0.049 1.41e-02 5.03e+03 1.22e+01 bond pdb=" C ASP B 51 " pdb=" N PRO B 52 " ideal model delta sigma weight residual 1.334 1.404 -0.071 2.34e-02 1.83e+03 9.10e+00 ... (remaining 37664 not shown) Histogram of bond angle deviations from ideal: 96.42 - 106.37: 1399 106.37 - 116.33: 24448 116.33 - 126.29: 24629 126.29 - 136.25: 628 136.25 - 146.21: 2 Bond angle restraints: 51106 Sorted by residual: angle pdb=" CA LEU D 161 " pdb=" CB LEU D 161 " pdb=" CG LEU D 161 " ideal model delta sigma weight residual 116.30 146.21 -29.91 3.50e+00 8.16e-02 7.30e+01 angle pdb=" CB ARG D 328 " pdb=" CG ARG D 328 " pdb=" CD ARG D 328 " ideal model delta sigma weight residual 111.30 126.45 -15.15 2.30e+00 1.89e-01 4.34e+01 angle pdb=" N GLY D 242 " pdb=" CA GLY D 242 " pdb=" C GLY D 242 " ideal model delta sigma weight residual 115.32 108.02 7.30 1.31e+00 5.83e-01 3.10e+01 angle pdb=" N PRO F 52 " pdb=" CA PRO F 52 " pdb=" C PRO F 52 " ideal model delta sigma weight residual 111.15 119.44 -8.29 1.58e+00 4.01e-01 2.75e+01 angle pdb=" CA ARG B 395 " pdb=" CB ARG B 395 " pdb=" CG ARG B 395 " ideal model delta sigma weight residual 114.10 124.57 -10.47 2.00e+00 2.50e-01 2.74e+01 ... (remaining 51101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.32: 22976 33.32 - 66.64: 249 66.64 - 99.96: 30 99.96 - 133.28: 7 133.28 - 166.60: 2 Dihedral angle restraints: 23264 sinusoidal: 9705 harmonic: 13559 Sorted by residual: dihedral pdb=" CA ASP D 51 " pdb=" C ASP D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta harmonic sigma weight residual -180.00 -117.34 -62.66 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA ASP C 51 " pdb=" C ASP C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta harmonic sigma weight residual -180.00 -119.70 -60.30 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA GLU D 304 " pdb=" C GLU D 304 " pdb=" N VAL D 305 " pdb=" CA VAL D 305 " ideal model delta harmonic sigma weight residual -180.00 -126.73 -53.27 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 23261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4959 0.088 - 0.176: 810 0.176 - 0.263: 56 0.263 - 0.351: 3 0.351 - 0.439: 2 Chirality restraints: 5830 Sorted by residual: chirality pdb=" CG LEU D 161 " pdb=" CB LEU D 161 " pdb=" CD1 LEU D 161 " pdb=" CD2 LEU D 161 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CG LEU E 270 " pdb=" CB LEU E 270 " pdb=" CD1 LEU E 270 " pdb=" CD2 LEU E 270 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB ILE B 398 " pdb=" CA ILE B 398 " pdb=" CG1 ILE B 398 " pdb=" CG2 ILE B 398 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 5827 not shown) Planarity restraints: 6627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 404 " 0.031 2.00e-02 2.50e+03 6.00e-02 3.60e+01 pdb=" C LYS E 404 " -0.104 2.00e-02 2.50e+03 pdb=" O LYS E 404 " 0.039 2.00e-02 2.50e+03 pdb=" N LEU E 405 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 379 " 0.027 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C ILE E 379 " -0.091 2.00e-02 2.50e+03 pdb=" O ILE E 379 " 0.034 2.00e-02 2.50e+03 pdb=" N SER E 380 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 247 " 0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C GLU A 247 " -0.076 2.00e-02 2.50e+03 pdb=" O GLU A 247 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA A 248 " 0.026 2.00e-02 2.50e+03 ... (remaining 6624 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1734 2.71 - 3.26: 33778 3.26 - 3.81: 57385 3.81 - 4.35: 70288 4.35 - 4.90: 119510 Nonbonded interactions: 282695 Sorted by model distance: nonbonded pdb=" O ASP A 422 " pdb=" OG1 THR A 470 " model vdw 2.165 2.440 nonbonded pdb=" O VAL A 359 " pdb=" O2B AGS A 901 " model vdw 2.191 2.440 nonbonded pdb=" O1B AGS A 901 " pdb=" O3G AGS A 901 " model vdw 2.220 2.440 nonbonded pdb=" O1B AGS C 901 " pdb=" O2G AGS C 901 " model vdw 2.235 2.440 nonbonded pdb=" O VAL C 359 " pdb=" O2B AGS C 901 " model vdw 2.239 2.440 ... (remaining 282690 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 2 through 780) selection = (chain 'B' and resid 2 through 780) selection = (chain 'C' and resid 2 through 780) selection = (chain 'D' and resid 2 through 780) selection = (chain 'E' and resid 2 through 780) selection = (chain 'F' and resid 2 through 780) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 0.040 Extract box with map and model: 10.350 Check model and map are aligned: 0.560 Set scattering table: 0.330 Process input model: 94.110 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.220 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:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.010 0.126 37669 Z= 0.620 Angle : 1.103 29.913 51106 Z= 0.592 Chirality : 0.063 0.439 5830 Planarity : 0.008 0.086 6627 Dihedral : 11.369 166.601 14532 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.71 % Favored : 94.12 % Rotamer: Outliers : 0.36 % Allowed : 4.20 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.20 % 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: -3.56 (0.10), residues: 4662 helix: -2.36 (0.09), residues: 1984 sheet: -0.54 (0.21), residues: 582 loop : -2.87 (0.11), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 602 HIS 0.022 0.002 HIS D 168 PHE 0.032 0.003 PHE D 132 TYR 0.041 0.003 TYR F 135 ARG 0.024 0.001 ARG E 519 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 348 time to evaluate : 4.461 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: B 85 MET cc_start: 0.1062 (tpp) cc_final: -0.0136 (ppp) REVERT: D 38 MET cc_start: 0.3760 (mtt) cc_final: 0.3355 (mpm) REVERT: D 160 MET cc_start: 0.4155 (tpt) cc_final: 0.2581 (ptm) REVERT: E 75 MET cc_start: 0.0959 (ttp) cc_final: 0.0111 (ttp) REVERT: E 373 ASN cc_start: 0.8498 (m110) cc_final: 0.8229 (m110) REVERT: F 342 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6724 (tm) outliers start: 14 outliers final: 4 residues processed: 361 average time/residue: 1.9105 time to fit residues: 800.6411 Evaluate side-chains 232 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 227 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 50.0000 chunk 351 optimal weight: 20.0000 chunk 195 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 237 optimal weight: 50.0000 chunk 187 optimal weight: 1.9990 chunk 363 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 421 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 HIS B 220 ASN B 229 GLN B 495 ASN B 727 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN D 139 HIS D 168 HIS D 211 GLN D 220 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN D 393 HIS D 407 HIS E 18 HIS E 216 GLN E 220 ASN E 234 GLN E 277 GLN E 411 GLN E 499 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN F 340 GLN ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN A 68 GLN A 319 HIS A 447 GLN A 472 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 37669 Z= 0.162 Angle : 0.639 15.256 51106 Z= 0.317 Chirality : 0.043 0.171 5830 Planarity : 0.006 0.069 6627 Dihedral : 8.645 162.446 5262 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.80 % Rotamer: Outliers : 1.63 % Allowed : 7.86 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.11 % 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: -2.01 (0.11), residues: 4662 helix: -0.64 (0.11), residues: 1991 sheet: -0.37 (0.20), residues: 605 loop : -2.33 (0.12), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 292 HIS 0.006 0.001 HIS D 168 PHE 0.029 0.001 PHE B 203 TYR 0.032 0.001 TYR A 332 ARG 0.010 0.000 ARG F 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 249 time to evaluate : 4.098 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: B 85 MET cc_start: 0.1057 (tpp) cc_final: -0.0075 (ppp) REVERT: B 479 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7027 (mpt180) REVERT: D 38 MET cc_start: 0.3391 (mtt) cc_final: 0.3158 (mpm) REVERT: D 160 MET cc_start: 0.4183 (tpt) cc_final: 0.2463 (ptm) REVERT: E 75 MET cc_start: 0.1033 (ttp) cc_final: 0.0108 (ttp) REVERT: F 50 ARG cc_start: 0.2346 (OUTLIER) cc_final: 0.1616 (mmt-90) REVERT: F 75 MET cc_start: 0.2635 (ptp) cc_final: 0.2138 (ppp) REVERT: F 455 TYR cc_start: 0.7600 (t80) cc_final: 0.7340 (t80) REVERT: A 188 ARG cc_start: 0.0728 (OUTLIER) cc_final: 0.0030 (ptt90) outliers start: 64 outliers final: 16 residues processed: 295 average time/residue: 1.7045 time to fit residues: 596.0493 Evaluate side-chains 250 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 231 time to evaluate : 4.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 40.0000 chunk 130 optimal weight: 7.9990 chunk 350 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 422 optimal weight: 5.9990 chunk 456 optimal weight: 7.9990 chunk 375 optimal weight: 0.0570 chunk 418 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 338 optimal weight: 4.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN B 319 HIS B 727 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN C 659 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 373 ASN E 447 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 GLN ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 647 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 37669 Z= 0.407 Angle : 0.709 13.070 51106 Z= 0.351 Chirality : 0.047 0.233 5830 Planarity : 0.005 0.072 6627 Dihedral : 8.404 160.209 5262 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.00 % Rotamer: Outliers : 2.14 % Allowed : 9.06 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.07 % 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: -1.43 (0.12), residues: 4662 helix: -0.01 (0.12), residues: 2029 sheet: -0.24 (0.20), residues: 639 loop : -2.19 (0.12), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 292 HIS 0.009 0.001 HIS C 454 PHE 0.034 0.002 PHE B 466 TYR 0.037 0.002 TYR A 332 ARG 0.011 0.001 ARG F 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 228 time to evaluate : 4.029 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: B 85 MET cc_start: 0.1087 (tpp) cc_final: -0.0154 (ppp) REVERT: B 479 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7241 (mpt180) REVERT: B 713 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7653 (mtt) REVERT: C 85 MET cc_start: -0.1072 (tpp) cc_final: -0.1819 (tpp) REVERT: D 38 MET cc_start: 0.3304 (mtt) cc_final: 0.3092 (mpm) REVERT: D 160 MET cc_start: 0.4049 (tpt) cc_final: 0.2455 (ptm) REVERT: E 75 MET cc_start: 0.1207 (ttp) cc_final: 0.0234 (ttp) REVERT: E 476 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8427 (p) REVERT: F 50 ARG cc_start: 0.2576 (OUTLIER) cc_final: 0.1829 (mpt90) REVERT: F 75 MET cc_start: 0.2690 (ptp) cc_final: 0.2341 (ppp) REVERT: F 455 TYR cc_start: 0.7625 (t80) cc_final: 0.7415 (t80) REVERT: F 713 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6538 (mpp) REVERT: A 188 ARG cc_start: 0.0699 (OUTLIER) cc_final: -0.0037 (ptt90) outliers start: 84 outliers final: 33 residues processed: 291 average time/residue: 1.6501 time to fit residues: 571.9565 Evaluate side-chains 258 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 219 time to evaluate : 4.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 713 MET Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 1.9990 chunk 317 optimal weight: 0.0170 chunk 219 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 283 optimal weight: 5.9990 chunk 423 optimal weight: 3.9990 chunk 448 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 401 optimal weight: 50.0000 chunk 120 optimal weight: 0.5980 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 GLN ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 37669 Z= 0.165 Angle : 0.612 10.924 51106 Z= 0.298 Chirality : 0.043 0.177 5830 Planarity : 0.005 0.066 6627 Dihedral : 8.140 159.263 5262 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.92 % Rotamer: Outliers : 1.98 % Allowed : 9.64 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4662 helix: 0.57 (0.12), residues: 1986 sheet: -0.03 (0.21), residues: 626 loop : -1.95 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 292 HIS 0.005 0.001 HIS E 407 PHE 0.027 0.001 PHE B 203 TYR 0.024 0.001 TYR F 460 ARG 0.008 0.000 ARG F 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 239 time to evaluate : 4.674 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: B 38 MET cc_start: 0.2613 (pmm) cc_final: 0.2401 (pmm) REVERT: B 85 MET cc_start: 0.1075 (tpp) cc_final: -0.0098 (ppp) REVERT: B 230 MET cc_start: 0.5690 (OUTLIER) cc_final: 0.5333 (mpm) REVERT: B 479 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7324 (mpt180) REVERT: B 713 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7414 (mtt) REVERT: C 385 ARG cc_start: 0.7657 (ttt90) cc_final: 0.7454 (ttt90) REVERT: D 38 MET cc_start: 0.3246 (mtt) cc_final: 0.3009 (mpm) REVERT: D 85 MET cc_start: 0.4275 (tpt) cc_final: 0.3393 (pmm) REVERT: D 160 MET cc_start: 0.3806 (tpt) cc_final: 0.2405 (ptt) REVERT: D 258 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7750 (mtt) REVERT: D 432 ARG cc_start: 0.7943 (ttt-90) cc_final: 0.7706 (ttt180) REVERT: E 75 MET cc_start: 0.1201 (ttp) cc_final: 0.0216 (ttp) REVERT: E 476 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8353 (p) REVERT: F 50 ARG cc_start: 0.2639 (OUTLIER) cc_final: 0.2120 (mpt90) REVERT: F 713 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.6445 (mpp) REVERT: A 188 ARG cc_start: 0.0555 (OUTLIER) cc_final: -0.0206 (ptt90) outliers start: 78 outliers final: 27 residues processed: 295 average time/residue: 1.6665 time to fit residues: 586.6596 Evaluate side-chains 257 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 222 time to evaluate : 3.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 713 MET Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 271 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 0.0770 chunk 254 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 333 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 382 optimal weight: 3.9990 chunk 310 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 229 optimal weight: 0.9990 chunk 402 optimal weight: 40.0000 chunk 113 optimal weight: 4.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 GLN C 659 ASN D 229 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 HIS E 411 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37669 Z= 0.267 Angle : 0.630 12.647 51106 Z= 0.306 Chirality : 0.044 0.165 5830 Planarity : 0.005 0.066 6627 Dihedral : 7.988 157.659 5261 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.24 % Rotamer: Outliers : 2.26 % Allowed : 10.25 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.81 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 4662 helix: 0.82 (0.12), residues: 1990 sheet: 0.10 (0.21), residues: 634 loop : -1.86 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 292 HIS 0.005 0.001 HIS E 407 PHE 0.026 0.001 PHE B 203 TYR 0.023 0.001 TYR D 167 ARG 0.010 0.000 ARG D 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 232 time to evaluate : 4.515 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: B 85 MET cc_start: 0.1128 (tpp) cc_final: -0.0112 (ppp) REVERT: B 176 LYS cc_start: 0.0286 (OUTLIER) cc_final: -0.0204 (mmmt) REVERT: B 230 MET cc_start: 0.5649 (OUTLIER) cc_final: 0.5299 (mpm) REVERT: B 479 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7320 (mpt180) REVERT: B 713 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7589 (mtt) REVERT: C 713 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7052 (mtm) REVERT: D 38 MET cc_start: 0.3328 (mtt) cc_final: 0.3070 (mpm) REVERT: D 85 MET cc_start: 0.4338 (tpt) cc_final: 0.3383 (pmm) REVERT: D 160 MET cc_start: 0.3662 (tpt) cc_final: 0.2395 (ptt) REVERT: D 258 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7862 (mtt) REVERT: E 75 MET cc_start: 0.1213 (ttp) cc_final: 0.0214 (ttp) REVERT: E 406 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7367 (mm) REVERT: E 427 MET cc_start: 0.6485 (mmm) cc_final: 0.6225 (tpp) REVERT: E 476 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8383 (p) REVERT: F 38 MET cc_start: 0.4660 (pmt) cc_final: 0.3351 (tpt) REVERT: F 50 ARG cc_start: 0.2557 (OUTLIER) cc_final: 0.2164 (mpt90) REVERT: F 182 LEU cc_start: 0.3468 (OUTLIER) cc_final: 0.3223 (mt) REVERT: F 217 MET cc_start: 0.7937 (mmp) cc_final: 0.7697 (mmp) REVERT: F 713 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6493 (mpp) REVERT: A 85 MET cc_start: 0.2742 (mpp) cc_final: 0.1519 (mpp) REVERT: A 188 ARG cc_start: 0.0477 (OUTLIER) cc_final: -0.0300 (ptt90) outliers start: 89 outliers final: 41 residues processed: 295 average time/residue: 1.6522 time to fit residues: 580.3033 Evaluate side-chains 274 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 221 time to evaluate : 3.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain F residue 713 MET Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 0.9990 chunk 403 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 263 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 448 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 235 optimal weight: 50.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 37669 Z= 0.177 Angle : 0.603 15.423 51106 Z= 0.291 Chirality : 0.043 0.167 5830 Planarity : 0.004 0.063 6627 Dihedral : 7.851 157.124 5261 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.96 % Allowed : 11.20 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.81 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.12), residues: 4662 helix: 1.06 (0.12), residues: 1985 sheet: 0.15 (0.21), residues: 629 loop : -1.79 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 292 HIS 0.005 0.001 HIS E 407 PHE 0.026 0.001 PHE B 203 TYR 0.022 0.001 TYR D 167 ARG 0.008 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 228 time to evaluate : 4.519 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: B 85 MET cc_start: 0.1112 (tpp) cc_final: -0.0161 (ppp) REVERT: B 176 LYS cc_start: 0.0108 (OUTLIER) cc_final: -0.0348 (mmmt) REVERT: B 479 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7291 (mpt180) REVERT: B 713 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7485 (mtt) REVERT: C 439 MET cc_start: 0.7982 (mmm) cc_final: 0.7756 (tpt) REVERT: D 38 MET cc_start: 0.3223 (mtt) cc_final: 0.3013 (mpm) REVERT: D 85 MET cc_start: 0.4330 (tpt) cc_final: 0.3366 (pmm) REVERT: D 160 MET cc_start: 0.3678 (tpt) cc_final: 0.2423 (ptt) REVERT: D 258 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7676 (mtt) REVERT: E 75 MET cc_start: 0.1248 (ttp) cc_final: 0.0234 (ttp) REVERT: E 406 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7369 (mm) REVERT: E 427 MET cc_start: 0.6514 (mmm) cc_final: 0.6205 (tpp) REVERT: E 476 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8370 (p) REVERT: F 38 MET cc_start: 0.4551 (OUTLIER) cc_final: 0.3163 (tpt) REVERT: F 50 ARG cc_start: 0.2744 (OUTLIER) cc_final: 0.2061 (mpt90) REVERT: F 182 LEU cc_start: 0.3722 (OUTLIER) cc_final: 0.3506 (mt) REVERT: F 265 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7697 (mtmm) REVERT: F 289 TYR cc_start: 0.6269 (t80) cc_final: 0.5217 (t80) REVERT: F 713 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.6776 (mpp) REVERT: A 188 ARG cc_start: 0.0301 (OUTLIER) cc_final: -0.0492 (ptt90) REVERT: A 432 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7919 (tpm170) outliers start: 77 outliers final: 41 residues processed: 285 average time/residue: 1.6562 time to fit residues: 566.7531 Evaluate side-chains 275 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 222 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 587 LYS Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain F residue 713 MET Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 255 optimal weight: 30.0000 chunk 327 optimal weight: 50.0000 chunk 254 optimal weight: 40.0000 chunk 377 optimal weight: 7.9990 chunk 250 optimal weight: 50.0000 chunk 447 optimal weight: 7.9990 chunk 279 optimal weight: 10.0000 chunk 272 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 GLN F 68 GLN F 221 GLN ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 37669 Z= 0.567 Angle : 0.760 16.771 51106 Z= 0.371 Chirality : 0.050 0.238 5830 Planarity : 0.005 0.069 6627 Dihedral : 8.071 158.791 5261 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.30 % Favored : 94.66 % Rotamer: Outliers : 2.39 % Allowed : 11.30 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.81 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.12), residues: 4662 helix: 0.78 (0.12), residues: 2014 sheet: 0.16 (0.21), residues: 638 loop : -1.84 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 292 HIS 0.009 0.001 HIS C 454 PHE 0.032 0.002 PHE B 466 TYR 0.023 0.002 TYR D 167 ARG 0.008 0.001 ARG F 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 226 time to evaluate : 3.995 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: B 85 MET cc_start: 0.1034 (tpp) cc_final: -0.0193 (ppp) REVERT: B 230 MET cc_start: 0.5829 (OUTLIER) cc_final: 0.5417 (mpm) REVERT: B 713 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7716 (mtt) REVERT: D 85 MET cc_start: 0.4363 (tpt) cc_final: 0.3285 (pmm) REVERT: D 160 MET cc_start: 0.3594 (tpt) cc_final: 0.2481 (ptt) REVERT: E 75 MET cc_start: 0.1264 (ttp) cc_final: 0.0240 (ttp) REVERT: E 406 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7438 (mm) REVERT: E 427 MET cc_start: 0.6549 (mmm) cc_final: 0.6291 (tpp) REVERT: E 476 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8492 (p) REVERT: F 50 ARG cc_start: 0.2766 (OUTLIER) cc_final: 0.2137 (mpt90) REVERT: F 182 LEU cc_start: 0.3673 (OUTLIER) cc_final: 0.3413 (mt) REVERT: F 289 TYR cc_start: 0.6400 (t80) cc_final: 0.4857 (t80) REVERT: F 460 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.6595 (m-80) REVERT: A 188 ARG cc_start: 0.0388 (OUTLIER) cc_final: -0.0379 (ptt90) outliers start: 94 outliers final: 49 residues processed: 292 average time/residue: 1.6117 time to fit residues: 563.2541 Evaluate side-chains 276 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 219 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 298 TRP Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 460 TYR Chi-restraints excluded: chain F residue 489 GLU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 20.0000 chunk 178 optimal weight: 0.8980 chunk 267 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 284 optimal weight: 7.9990 chunk 304 optimal weight: 0.0060 chunk 221 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 351 optimal weight: 9.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 ASN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN F 449 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.128 37669 Z= 0.162 Angle : 0.617 15.943 51106 Z= 0.298 Chirality : 0.042 0.176 5830 Planarity : 0.004 0.064 6627 Dihedral : 7.834 158.845 5261 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.16 % Favored : 95.82 % Rotamer: Outliers : 1.83 % Allowed : 12.09 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.81 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.12), residues: 4662 helix: 1.14 (0.12), residues: 1996 sheet: 0.27 (0.21), residues: 624 loop : -1.70 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 292 HIS 0.017 0.001 HIS E 454 PHE 0.025 0.001 PHE B 203 TYR 0.043 0.001 TYR D 135 ARG 0.010 0.000 ARG F 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 236 time to evaluate : 4.274 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: B 85 MET cc_start: 0.1125 (tpp) cc_final: -0.0153 (ppp) REVERT: B 132 PHE cc_start: -0.1511 (OUTLIER) cc_final: -0.2031 (t80) REVERT: B 176 LYS cc_start: -0.0012 (OUTLIER) cc_final: -0.0383 (mmmt) REVERT: B 230 MET cc_start: 0.5725 (OUTLIER) cc_final: 0.5334 (mpm) REVERT: B 713 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7448 (mtt) REVERT: D 85 MET cc_start: 0.4456 (tpt) cc_final: 0.3368 (pmm) REVERT: D 160 MET cc_start: 0.3536 (tpt) cc_final: 0.2593 (ptt) REVERT: E 75 MET cc_start: 0.1235 (ttp) cc_final: 0.0241 (ttp) REVERT: E 427 MET cc_start: 0.6612 (mmm) cc_final: 0.6366 (tpp) REVERT: E 476 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8394 (p) REVERT: F 38 MET cc_start: 0.4653 (pmt) cc_final: 0.3295 (tpt) REVERT: F 50 ARG cc_start: 0.2667 (OUTLIER) cc_final: 0.2140 (mpt90) REVERT: F 182 LEU cc_start: 0.3594 (OUTLIER) cc_final: 0.3339 (mt) REVERT: F 289 TYR cc_start: 0.6140 (t80) cc_final: 0.5392 (t80) REVERT: F 455 TYR cc_start: 0.7627 (t80) cc_final: 0.7068 (t80) REVERT: F 461 ASP cc_start: 0.6482 (p0) cc_final: 0.6263 (p0) REVERT: A 188 ARG cc_start: 0.0314 (OUTLIER) cc_final: -0.0501 (ptt90) outliers start: 72 outliers final: 38 residues processed: 290 average time/residue: 1.6041 time to fit residues: 558.9135 Evaluate side-chains 266 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 220 time to evaluate : 4.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 397 TYR Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 8.9990 chunk 428 optimal weight: 0.9980 chunk 390 optimal weight: 20.0000 chunk 416 optimal weight: 6.9990 chunk 250 optimal weight: 50.0000 chunk 181 optimal weight: 0.0870 chunk 327 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 376 optimal weight: 2.9990 chunk 394 optimal weight: 10.0000 chunk 415 optimal weight: 2.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS F 221 GLN A 449 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 37669 Z= 0.257 Angle : 0.636 16.521 51106 Z= 0.306 Chirality : 0.044 0.203 5830 Planarity : 0.004 0.065 6627 Dihedral : 7.711 156.851 5261 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.57 % Favored : 95.41 % Rotamer: Outliers : 1.76 % Allowed : 12.44 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.81 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.12), residues: 4662 helix: 1.19 (0.12), residues: 2005 sheet: 0.32 (0.21), residues: 630 loop : -1.65 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 292 HIS 0.006 0.001 HIS E 407 PHE 0.028 0.001 PHE F 451 TYR 0.026 0.001 TYR D 135 ARG 0.010 0.000 ARG F 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 226 time to evaluate : 4.605 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: B 85 MET cc_start: 0.1140 (tpp) cc_final: -0.0225 (ppp) REVERT: B 132 PHE cc_start: -0.1354 (OUTLIER) cc_final: -0.1884 (t80) REVERT: B 176 LYS cc_start: -0.0001 (OUTLIER) cc_final: -0.0416 (mmmt) REVERT: B 230 MET cc_start: 0.5759 (OUTLIER) cc_final: 0.5356 (mpm) REVERT: B 245 ASP cc_start: 0.7402 (p0) cc_final: 0.7190 (p0) REVERT: B 713 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7561 (mtt) REVERT: C 490 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8316 (mm) REVERT: D 85 MET cc_start: 0.4398 (tpt) cc_final: 0.3313 (pmm) REVERT: D 160 MET cc_start: 0.3512 (tpt) cc_final: 0.2599 (ptt) REVERT: E 75 MET cc_start: 0.1221 (ttp) cc_final: 0.0271 (ttp) REVERT: E 406 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7497 (mm) REVERT: E 427 MET cc_start: 0.6659 (mmm) cc_final: 0.6342 (mmm) REVERT: E 476 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8420 (p) REVERT: F 38 MET cc_start: 0.4613 (OUTLIER) cc_final: 0.3222 (tpt) REVERT: F 50 ARG cc_start: 0.2723 (OUTLIER) cc_final: 0.2164 (mpt90) REVERT: F 160 MET cc_start: 0.2822 (OUTLIER) cc_final: 0.2525 (pmt) REVERT: F 182 LEU cc_start: 0.3773 (OUTLIER) cc_final: 0.3514 (mt) REVERT: A 188 ARG cc_start: 0.0342 (OUTLIER) cc_final: -0.0478 (ptt90) outliers start: 69 outliers final: 44 residues processed: 279 average time/residue: 1.6944 time to fit residues: 564.4052 Evaluate side-chains 274 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 218 time to evaluate : 4.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 397 TYR Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 10.0000 chunk 440 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 chunk 462 optimal weight: 40.0000 chunk 425 optimal weight: 0.0020 chunk 368 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 284 optimal weight: 6.9990 chunk 225 optimal weight: 0.7980 overall best weight: 2.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 ASN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN E 220 ASN E 454 HIS F 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 37669 Z= 0.256 Angle : 0.640 15.970 51106 Z= 0.309 Chirality : 0.044 0.181 5830 Planarity : 0.005 0.092 6627 Dihedral : 7.688 156.653 5261 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.53 % Favored : 95.45 % Rotamer: Outliers : 1.63 % Allowed : 12.49 % Favored : 85.88 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.81 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.12), residues: 4662 helix: 1.24 (0.12), residues: 1999 sheet: 0.36 (0.21), residues: 613 loop : -1.61 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 292 HIS 0.006 0.001 HIS E 407 PHE 0.025 0.001 PHE B 203 TYR 0.029 0.001 TYR A 332 ARG 0.020 0.000 ARG F 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 221 time to evaluate : 4.001 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: B 85 MET cc_start: 0.0966 (tpp) cc_final: -0.0044 (ppp) REVERT: B 132 PHE cc_start: -0.1467 (OUTLIER) cc_final: -0.1989 (t80) REVERT: B 176 LYS cc_start: -0.0005 (OUTLIER) cc_final: -0.0400 (mmmt) REVERT: B 230 MET cc_start: 0.5685 (OUTLIER) cc_final: 0.5285 (mpm) REVERT: B 245 ASP cc_start: 0.7365 (p0) cc_final: 0.7126 (p0) REVERT: B 479 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7349 (mpt180) REVERT: B 683 MET cc_start: 0.8109 (mtt) cc_final: 0.7886 (mtt) REVERT: B 713 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7552 (mtt) REVERT: C 490 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8331 (mm) REVERT: D 38 MET cc_start: 0.3002 (mpm) cc_final: 0.0032 (mmt) REVERT: D 85 MET cc_start: 0.4373 (tpt) cc_final: 0.3276 (pmm) REVERT: D 160 MET cc_start: 0.3586 (tpt) cc_final: 0.2704 (ptt) REVERT: E 75 MET cc_start: 0.1344 (ttp) cc_final: 0.0390 (ttp) REVERT: E 476 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8416 (p) REVERT: F 50 ARG cc_start: 0.2686 (OUTLIER) cc_final: 0.2192 (mpt90) REVERT: F 160 MET cc_start: 0.2852 (OUTLIER) cc_final: 0.1497 (mmm) REVERT: F 182 LEU cc_start: 0.3698 (OUTLIER) cc_final: 0.3414 (mt) REVERT: A 188 ARG cc_start: 0.0336 (OUTLIER) cc_final: -0.0502 (ptt90) outliers start: 64 outliers final: 45 residues processed: 270 average time/residue: 1.5865 time to fit residues: 514.4344 Evaluate side-chains 274 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 218 time to evaluate : 4.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 463 SER Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 397 TYR Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 0.8980 chunk 392 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 339 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 368 optimal weight: 4.9990 chunk 154 optimal weight: 50.0000 chunk 378 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 30.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 ASN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.183103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104418 restraints weight = 66142.769| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.81 r_work: 0.2844 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 37669 Z= 0.300 Angle : 0.656 15.509 51106 Z= 0.318 Chirality : 0.045 0.180 5830 Planarity : 0.005 0.082 6627 Dihedral : 7.678 156.719 5261 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.76 % Favored : 95.22 % Rotamer: Outliers : 1.58 % Allowed : 12.65 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.12), residues: 4662 helix: 1.26 (0.12), residues: 1990 sheet: 0.39 (0.21), residues: 617 loop : -1.56 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 292 HIS 0.006 0.001 HIS E 407 PHE 0.027 0.001 PHE F 451 TYR 0.027 0.001 TYR A 332 ARG 0.019 0.000 ARG F 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13655.61 seconds wall clock time: 244 minutes 1.67 seconds (14641.67 seconds total)