Starting phenix.real_space_refine on Fri Aug 9 09:57:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcg_38242/08_2024/8xcg_38242.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcg_38242/08_2024/8xcg_38242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcg_38242/08_2024/8xcg_38242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcg_38242/08_2024/8xcg_38242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcg_38242/08_2024/8xcg_38242.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcg_38242/08_2024/8xcg_38242.cif" } resolution = 3.46 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= 0.004 sd= 0.067 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 Fe 12 7.16 5 S 138 5.16 5 C 16228 2.51 5 N 4523 2.21 5 O 5040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 99": "OE1" <-> "OE2" Residue "F ASP 40": "OD1" <-> "OD2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 180": "OD1" <-> "OD2" Residue "J ASP 16": "OD1" <-> "OD2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "J TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 362": "OD1" <-> "OD2" Residue "J PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 560": "OE1" <-> "OE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "L ASP 3": "OD1" <-> "OD2" Residue "L ASP 27": "OD1" <-> "OD2" Residue "L PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 126": "OD1" <-> "OD2" Residue "L ASP 203": "OD1" <-> "OD2" Residue "M ASP 27": "OD1" <-> "OD2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "M GLU 99": "OE1" <-> "OE2" Residue "N ASP 180": "OD1" <-> "OD2" Residue "Y TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 99": "OE1" <-> "OE2" Residue "Y GLU 103": "OE1" <-> "OE2" Residue "Z ASP 16": "OD1" <-> "OD2" Residue "Z PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 278": "OD1" <-> "OD2" Residue "Z TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 314": "OD1" <-> "OD2" Residue "Z TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 463": "OD1" <-> "OD2" Residue "Z PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 59": "OE1" <-> "OE2" Residue "e GLU 103": "OE1" <-> "OE2" Residue "f TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 211": "OD1" <-> "OD2" Residue "m PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 78": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25941 Number of models: 1 Model: "" Number of chains: 18 Chain: "E" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4627 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 29, 'TRANS': 564} Chain: "I" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 412 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "J" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4657 Classifications: {'peptide': 598} Link IDs: {'PTRANS': 30, 'TRANS': 567} Chain: "K" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "M" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "N" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "P" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 436 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "Y" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "Z" Number of atoms: 4650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4650 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 29, 'TRANS': 567} Chain: "e" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "f" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "h" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 428 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "m" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12891 SG CYS L 182 91.577 90.470 69.286 1.00 27.16 S ATOM 13062 SG CYS L 205 85.408 91.943 69.478 1.00 51.17 S ATOM 12813 SG CYS L 173 86.791 86.108 68.475 1.00 33.95 S ATOM 13107 SG CYS L 212 87.012 90.562 63.982 1.00 30.13 S ATOM 15576 SG CYS N 182 19.092 62.735 71.304 1.00 53.53 S ATOM 15747 SG CYS N 205 20.398 56.107 71.928 1.00 52.32 S ATOM 15498 SG CYS N 173 24.752 60.179 70.357 1.00 53.47 S ATOM 15792 SG CYS N 212 20.597 58.204 66.112 1.00 40.06 S ATOM 24231 SG CYS f 182 79.850 13.948 75.535 1.00 68.04 S ATOM 24402 SG CYS f 205 84.408 18.820 75.651 1.00 77.47 S ATOM 24153 SG CYS f 173 78.655 20.090 73.384 1.00 75.88 S ATOM 24447 SG CYS f 212 82.450 17.327 69.805 1.00 69.39 S Time building chain proxies: 10.27, per 1000 atoms: 0.40 Number of scatterers: 25941 At special positions: 0 Unit cell: (129.978, 127.83, 166.501, 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) Fe 12 26.01 S 138 16.00 O 5040 8.00 N 4523 7.00 C 16228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 343 " - pdb=" SG CYS F 348 " distance=2.16 Simple disulfide: pdb=" SG CYS J 343 " - pdb=" SG CYS J 348 " distance=2.09 Simple disulfide: pdb=" SG CYS Z 343 " - pdb=" SG CYS Z 348 " distance=2.11 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: 9.27 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 L 301 " pdb="FE1 SF4 L 301 " - pdb=" SG CYS L 182 " pdb="FE4 SF4 L 301 " - pdb=" SG CYS L 212 " pdb="FE2 SF4 L 301 " - pdb=" SG CYS L 205 " pdb="FE3 SF4 L 301 " - pdb=" SG CYS L 173 " pdb=" SF4 N 301 " pdb="FE2 SF4 N 301 " - pdb=" SG CYS N 205 " pdb="FE3 SF4 N 301 " - pdb=" SG CYS N 173 " pdb="FE1 SF4 N 301 " - pdb=" SG CYS N 182 " pdb="FE4 SF4 N 301 " - pdb=" SG CYS N 212 " pdb=" SF4 f 301 " pdb="FE2 SF4 f 301 " - pdb=" SG CYS f 205 " pdb="FE3 SF4 f 301 " - pdb=" SG CYS f 173 " pdb="FE1 SF4 f 301 " - pdb=" SG CYS f 182 " pdb="FE4 SF4 f 301 " - pdb=" SG CYS f 212 " Number of angles added : 36 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6086 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 45 sheets defined 15.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'E' and resid 54 through 66 removed outlier: 3.701A pdb=" N LEU E 58 " --> pdb=" O GLU E 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 45 removed outlier: 3.528A pdb=" N VAL F 45 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 227 No H-bonds generated for 'chain 'F' and resid 225 through 227' Processing helix chain 'F' and resid 271 through 282 Processing helix chain 'F' and resid 297 through 310 Processing helix chain 'F' and resid 334 through 346 removed outlier: 3.610A pdb=" N MET F 346 " --> pdb=" O PHE F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 395 removed outlier: 3.515A pdb=" N ARG F 395 " --> pdb=" O LEU F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 427 removed outlier: 3.958A pdb=" N ARG F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 458 Processing helix chain 'F' and resid 467 through 473 removed outlier: 3.636A pdb=" N LEU F 471 " --> pdb=" O ALA F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 488 Processing helix chain 'F' and resid 594 through 601 Processing helix chain 'J' and resid 40 through 43 removed outlier: 4.092A pdb=" N LYS J 43 " --> pdb=" O ASP J 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 40 through 43' Processing helix chain 'J' and resid 271 through 281 Processing helix chain 'J' and resid 297 through 309 Processing helix chain 'J' and resid 334 through 346 Processing helix chain 'J' and resid 391 through 395 Processing helix chain 'J' and resid 419 through 424 Processing helix chain 'J' and resid 440 through 458 Processing helix chain 'J' and resid 467 through 473 removed outlier: 3.834A pdb=" N LEU J 471 " --> pdb=" O ALA J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 483 through 488 Processing helix chain 'J' and resid 594 through 600 Processing helix chain 'K' and resid 54 through 64 Processing helix chain 'L' and resid 5 through 14 Processing helix chain 'L' and resid 86 through 93 removed outlier: 3.585A pdb=" N ALA L 92 " --> pdb=" O VAL L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 113 No H-bonds generated for 'chain 'L' and resid 111 through 113' Processing helix chain 'L' and resid 114 through 118 Processing helix chain 'L' and resid 208 through 215 removed outlier: 3.881A pdb=" N ARG L 215 " --> pdb=" O GLY L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 221 removed outlier: 4.495A pdb=" N GLY L 219 " --> pdb=" O ASN L 216 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE L 221 " --> pdb=" O VAL L 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 66 removed outlier: 4.323A pdb=" N THR M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL M 57 " --> pdb=" O GLU M 53 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU M 58 " --> pdb=" O GLU M 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS M 65 " --> pdb=" O PHE M 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 14 Processing helix chain 'N' and resid 29 through 32 Processing helix chain 'N' and resid 86 through 93 removed outlier: 4.185A pdb=" N ALA N 92 " --> pdb=" O VAL N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 113 No H-bonds generated for 'chain 'N' and resid 111 through 113' Processing helix chain 'N' and resid 114 through 118 Processing helix chain 'N' and resid 208 through 215 Processing helix chain 'N' and resid 217 through 221 Processing helix chain 'Y' and resid 54 through 66 removed outlier: 4.192A pdb=" N LEU Y 58 " --> pdb=" O GLU Y 54 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS Y 65 " --> pdb=" O PHE Y 61 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY Y 66 " --> pdb=" O LEU Y 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 45 Processing helix chain 'Z' and resid 271 through 281 Processing helix chain 'Z' and resid 297 through 309 Processing helix chain 'Z' and resid 334 through 346 Processing helix chain 'Z' and resid 391 through 395 Processing helix chain 'Z' and resid 419 through 426 removed outlier: 3.681A pdb=" N ARG Z 425 " --> pdb=" O GLN Z 421 " (cutoff:3.500A) Processing helix chain 'Z' and resid 440 through 458 Processing helix chain 'Z' and resid 467 through 472 removed outlier: 3.848A pdb=" N LEU Z 471 " --> pdb=" O ALA Z 468 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 487 Processing helix chain 'Z' and resid 595 through 602 removed outlier: 3.532A pdb=" N GLY Z 602 " --> pdb=" O ILE Z 598 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 66 removed outlier: 3.744A pdb=" N HIS e 65 " --> pdb=" O PHE e 61 " (cutoff:3.500A) Processing helix chain 'f' and resid 5 through 13 removed outlier: 4.049A pdb=" N THR f 13 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 32 removed outlier: 3.523A pdb=" N GLY f 32 " --> pdb=" O THR f 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 29 through 32' Processing helix chain 'f' and resid 83 through 87 removed outlier: 4.276A pdb=" N MET f 87 " --> pdb=" O LEU f 84 " (cutoff:3.500A) Processing helix chain 'f' and resid 88 through 92 removed outlier: 3.826A pdb=" N ALA f 92 " --> pdb=" O THR f 89 " (cutoff:3.500A) Processing helix chain 'f' and resid 94 through 99 removed outlier: 3.571A pdb=" N VAL f 99 " --> pdb=" O GLN f 96 " (cutoff:3.500A) Processing helix chain 'f' and resid 111 through 113 No H-bonds generated for 'chain 'f' and resid 111 through 113' Processing helix chain 'f' and resid 114 through 118 Processing helix chain 'f' and resid 199 through 203 removed outlier: 3.794A pdb=" N ASP f 203 " --> pdb=" O ILE f 200 " (cutoff:3.500A) Processing helix chain 'f' and resid 208 through 216 Processing helix chain 'f' and resid 217 through 221 removed outlier: 3.674A pdb=" N PHE f 221 " --> pdb=" O VAL f 218 " (cutoff:3.500A) Processing helix chain 'm' and resid 52 through 66 removed outlier: 4.077A pdb=" N THR m 56 " --> pdb=" O ARG m 52 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL m 57 " --> pdb=" O GLU m 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 13 through 15 removed outlier: 3.732A pdb=" N ASP E 13 " --> pdb=" O SER E 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 43 through 51 current: chain 'E' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 82 through 86 current: chain 'E' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 97 through 106 current: chain 'K' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 43 through 51 current: chain 'K' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 82 through 86 current: chain 'K' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 97 through 106 current: chain 'M' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 43 through 51 current: chain 'M' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 82 through 86 current: chain 'M' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 97 through 106 current: chain 'Y' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 43 through 51 current: chain 'Y' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 82 through 86 current: chain 'Y' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 97 through 106 current: chain 'e' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 43 through 51 current: chain 'e' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 82 through 86 current: chain 'e' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 97 through 106 current: chain 'm' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 43 through 51 current: chain 'm' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 82 through 86 current: chain 'm' and resid 97 through 106 Processing sheet with id=AA2, first strand: chain 'E' and resid 21 through 24 Processing sheet with id=AA3, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'F' and resid 29 through 30 Processing sheet with id=AA5, first strand: chain 'F' and resid 35 through 38 removed outlier: 7.172A pdb=" N GLY F 240 " --> pdb=" O GLU F 36 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU F 238 " --> pdb=" O PRO F 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 85 through 94 removed outlier: 5.838A pdb=" N SER F 200 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR F 92 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU F 198 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR F 115 " --> pdb=" O SER F 200 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR F 202 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG F 113 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU F 204 " --> pdb=" O ARG F 111 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG F 111 " --> pdb=" O GLU F 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 179 through 183 removed outlier: 6.337A pdb=" N ILE F 141 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N THR F 149 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 244 through 246 Processing sheet with id=AA9, first strand: chain 'F' and resid 249 through 250 removed outlier: 3.554A pdb=" N GLN F 255 " --> pdb=" O ASN F 250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 311 through 313 Processing sheet with id=AB2, first strand: chain 'F' and resid 328 through 329 Processing sheet with id=AB3, first strand: chain 'F' and resid 350 through 353 Processing sheet with id=AB4, first strand: chain 'F' and resid 368 through 372 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 368 through 372 current: chain 'F' and resid 460 through 463 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 460 through 463 current: chain 'F' and resid 570 through 578 removed outlier: 6.865A pdb=" N THR F 587 " --> pdb=" O VAL F 574 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE F 576 " --> pdb=" O ALA F 585 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA F 585 " --> pdb=" O ILE F 576 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 411 through 418 removed outlier: 3.821A pdb=" N GLU F 411 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 493 through 499 removed outlier: 6.834A pdb=" N THR F 506 " --> pdb=" O LEU F 496 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL F 498 " --> pdb=" O THR F 504 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR F 504 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS F 543 " --> pdb=" O VAL F 538 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL F 538 " --> pdb=" O LYS F 543 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS F 545 " --> pdb=" O GLN F 536 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL F 524 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL F 558 " --> pdb=" O VAL F 524 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 191 through 193 Processing sheet with id=AB8, first strand: chain 'I' and resid 202 through 207 removed outlier: 6.324A pdb=" N VAL I 202 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA J 29 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER I 204 " --> pdb=" O ILE J 27 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 218 through 221 removed outlier: 5.643A pdb=" N THR J 149 " --> pdb=" O ILE J 141 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE J 141 " --> pdb=" O THR J 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 45 through 46 Processing sheet with id=AC2, first strand: chain 'J' and resid 86 through 94 removed outlier: 7.203A pdb=" N SER J 86 " --> pdb=" O ILE J 205 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE J 205 " --> pdb=" O SER J 86 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR J 88 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR J 203 " --> pdb=" O THR J 88 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU J 90 " --> pdb=" O SER J 201 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N SER J 201 " --> pdb=" O LEU J 90 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR J 197 " --> pdb=" O VAL J 94 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR J 115 " --> pdb=" O SER J 200 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR J 202 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG J 113 " --> pdb=" O TYR J 202 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU J 204 " --> pdb=" O ARG J 111 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ARG J 111 " --> pdb=" O GLU J 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 249 through 250 Processing sheet with id=AC4, first strand: chain 'J' and resid 311 through 313 Processing sheet with id=AC5, first strand: chain 'J' and resid 348 through 352 Processing sheet with id=AC6, first strand: chain 'J' and resid 369 through 371 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 369 through 371 current: chain 'J' and resid 460 through 463 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 460 through 463 current: chain 'J' and resid 570 through 577 removed outlier: 6.939A pdb=" N THR J 587 " --> pdb=" O VAL J 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 411 through 418 removed outlier: 3.848A pdb=" N GLU J 411 " --> pdb=" O ASP J 405 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 492 through 494 removed outlier: 6.624A pdb=" N VAL J 558 " --> pdb=" O VAL J 524 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL J 524 " --> pdb=" O VAL J 558 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER J 537 " --> pdb=" O LYS J 545 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS J 543 " --> pdb=" O THR J 539 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 21 through 23 Processing sheet with id=AD1, first strand: chain 'L' and resid 49 through 51 removed outlier: 6.958A pdb=" N PHE L 37 " --> pdb=" O GLN L 57 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU L 138 " --> pdb=" O SER L 153 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER L 153 " --> pdb=" O GLU L 138 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS L 140 " --> pdb=" O VAL L 151 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL L 151 " --> pdb=" O CYS L 140 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 21 through 24 Processing sheet with id=AD3, first strand: chain 'N' and resid 49 through 51 removed outlier: 10.314A pdb=" N GLN N 55 " --> pdb=" O ARG N 35 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE N 37 " --> pdb=" O GLN N 55 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 61 through 63 removed outlier: 6.690A pdb=" N SER N 147 " --> pdb=" O LEU N 143 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU N 143 " --> pdb=" O SER N 147 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER N 149 " --> pdb=" O SER N 141 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN N 139 " --> pdb=" O VAL N 151 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 21 through 24 Processing sheet with id=AD6, first strand: chain 'Z' and resid 64 through 69 removed outlier: 6.520A pdb=" N LEU Z 23 " --> pdb=" O ILE h 207 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE h 207 " --> pdb=" O LEU Z 23 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER Z 25 " --> pdb=" O GLN h 205 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN h 205 " --> pdb=" O SER Z 25 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE Z 27 " --> pdb=" O VAL h 203 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 84 through 94 removed outlier: 7.173A pdb=" N SER Z 86 " --> pdb=" O ILE Z 205 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ILE Z 205 " --> pdb=" O SER Z 86 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR Z 88 " --> pdb=" O THR Z 203 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR Z 203 " --> pdb=" O THR Z 88 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU Z 90 " --> pdb=" O SER Z 201 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER Z 201 " --> pdb=" O LEU Z 90 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR Z 197 " --> pdb=" O VAL Z 94 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR Z 115 " --> pdb=" O SER Z 200 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR Z 202 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG Z 113 " --> pdb=" O TYR Z 202 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU Z 204 " --> pdb=" O ARG Z 111 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG Z 111 " --> pdb=" O GLU Z 204 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Z' and resid 179 through 183 removed outlier: 6.234A pdb=" N ILE Z 141 " --> pdb=" O THR Z 149 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR Z 149 " --> pdb=" O ILE Z 141 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG Z 143 " --> pdb=" O TRP Z 147 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP Z 147 " --> pdb=" O ARG Z 143 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP Z 152 " --> pdb=" O ILE h 221 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE h 221 " --> pdb=" O ASP Z 152 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 243 through 246 Processing sheet with id=AE1, first strand: chain 'Z' and resid 249 through 250 Processing sheet with id=AE2, first strand: chain 'Z' and resid 311 through 313 Processing sheet with id=AE3, first strand: chain 'Z' and resid 327 through 329 Processing sheet with id=AE4, first strand: chain 'Z' and resid 349 through 352 Processing sheet with id=AE5, first strand: chain 'Z' and resid 369 through 371 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 369 through 371 current: chain 'Z' and resid 460 through 463 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 460 through 463 current: chain 'Z' and resid 570 through 578 removed outlier: 6.987A pdb=" N THR Z 587 " --> pdb=" O VAL Z 574 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE Z 576 " --> pdb=" O ALA Z 585 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA Z 585 " --> pdb=" O ILE Z 576 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 411 through 418 removed outlier: 3.604A pdb=" N GLU Z 411 " --> pdb=" O ASP Z 405 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 492 through 499 removed outlier: 3.881A pdb=" N SER Z 537 " --> pdb=" O LYS Z 545 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'e' and resid 21 through 23 Processing sheet with id=AE9, first strand: chain 'f' and resid 49 through 51 removed outlier: 11.622A pdb=" N ARG f 35 " --> pdb=" O GLN f 55 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N GLN f 57 " --> pdb=" O ARG f 35 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE f 37 " --> pdb=" O GLN f 57 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL f 151 " --> pdb=" O GLU f 138 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N CYS f 140 " --> pdb=" O SER f 149 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER f 149 " --> pdb=" O CYS f 140 " (cutoff:3.500A) 626 hydrogen bonds defined for protein. 1608 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: 7.30 Time building geometry restraints manager: 10.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.41: 10936 1.41 - 1.67: 15337 1.67 - 1.93: 195 1.93 - 2.19: 6 2.19 - 2.45: 30 Bond restraints: 26504 Sorted by residual: bond pdb=" C PRO F 475 " pdb=" O PRO F 475 " ideal model delta sigma weight residual 1.233 1.154 0.079 1.21e-02 6.83e+03 4.24e+01 bond pdb=" C ALA F 293 " pdb=" O ALA F 293 " ideal model delta sigma weight residual 1.233 1.309 -0.077 1.21e-02 6.83e+03 4.00e+01 bond pdb=" C LEU F 357 " pdb=" O LEU F 357 " ideal model delta sigma weight residual 1.235 1.159 0.076 1.22e-02 6.72e+03 3.93e+01 bond pdb=" C ILE J 205 " pdb=" O ILE J 205 " ideal model delta sigma weight residual 1.238 1.170 0.067 1.10e-02 8.26e+03 3.73e+01 bond pdb=" C PRO N 77 " pdb=" O PRO N 77 " ideal model delta sigma weight residual 1.235 1.157 0.079 1.30e-02 5.92e+03 3.65e+01 ... (remaining 26499 not shown) Histogram of bond angle deviations from ideal: 67.38 - 80.85: 36 80.85 - 94.31: 1 94.31 - 107.77: 1911 107.77 - 121.24: 25697 121.24 - 134.70: 8377 Bond angle restraints: 36022 Sorted by residual: angle pdb=" C PHE J 177 " pdb=" CA PHE J 177 " pdb=" CB PHE J 177 " ideal model delta sigma weight residual 110.42 87.21 23.21 1.99e+00 2.53e-01 1.36e+02 angle pdb=" CA TYR F 268 " pdb=" C TYR F 268 " pdb=" O TYR F 268 " ideal model delta sigma weight residual 120.69 110.12 10.57 1.14e+00 7.69e-01 8.60e+01 angle pdb=" CA TRP N 175 " pdb=" C TRP N 175 " pdb=" O TRP N 175 " ideal model delta sigma weight residual 121.44 112.22 9.22 1.08e+00 8.57e-01 7.29e+01 angle pdb=" CA ARG F 241 " pdb=" C ARG F 241 " pdb=" O ARG F 241 " ideal model delta sigma weight residual 121.87 112.57 9.30 1.10e+00 8.26e-01 7.15e+01 angle pdb=" C ASN J 235 " pdb=" CA ASN J 235 " pdb=" CB ASN J 235 " ideal model delta sigma weight residual 110.79 99.11 11.68 1.39e+00 5.18e-01 7.06e+01 ... (remaining 36017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 13334 17.56 - 35.12: 1760 35.12 - 52.68: 557 52.68 - 70.24: 113 70.24 - 87.80: 37 Dihedral angle restraints: 15801 sinusoidal: 6313 harmonic: 9488 Sorted by residual: dihedral pdb=" CA PHE f 163 " pdb=" C PHE f 163 " pdb=" N PRO f 164 " pdb=" CA PRO f 164 " ideal model delta harmonic sigma weight residual -180.00 -99.50 -80.50 0 5.00e+00 4.00e-02 2.59e+02 dihedral pdb=" CA PHE L 163 " pdb=" C PHE L 163 " pdb=" N PRO L 164 " pdb=" CA PRO L 164 " ideal model delta harmonic sigma weight residual -180.00 -115.46 -64.54 0 5.00e+00 4.00e-02 1.67e+02 dihedral pdb=" CA ARG J 175 " pdb=" C ARG J 175 " pdb=" N PRO J 176 " pdb=" CA PRO J 176 " ideal model delta harmonic sigma weight residual 180.00 121.74 58.26 0 5.00e+00 4.00e-02 1.36e+02 ... (remaining 15798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2304 0.092 - 0.184: 1448 0.184 - 0.277: 213 0.277 - 0.369: 18 0.369 - 0.461: 3 Chirality restraints: 3986 Sorted by residual: chirality pdb="FE1 SF4 L 301 " pdb=" S2 SF4 L 301 " pdb=" S3 SF4 L 301 " pdb=" S4 SF4 L 301 " both_signs ideal model delta sigma weight residual False -10.55 -11.02 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA CYS F 348 " pdb=" N CYS F 348 " pdb=" C CYS F 348 " pdb=" CB CYS F 348 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CA PHE N 163 " pdb=" N PHE N 163 " pdb=" C PHE N 163 " pdb=" CB PHE N 163 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 3983 not shown) Planarity restraints: 4690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 274 " -0.050 2.00e-02 2.50e+03 2.94e-02 2.17e+01 pdb=" CG TRP J 274 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP J 274 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP J 274 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP J 274 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP J 274 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP J 274 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 274 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 274 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP J 274 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Z 274 " 0.045 2.00e-02 2.50e+03 2.82e-02 1.98e+01 pdb=" CG TRP Z 274 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP Z 274 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP Z 274 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP Z 274 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP Z 274 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP Z 274 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP Z 274 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP Z 274 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP Z 274 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 163 " -0.046 2.00e-02 2.50e+03 3.06e-02 1.64e+01 pdb=" CG PHE N 163 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE N 163 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE N 163 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE N 163 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE N 163 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE N 163 " -0.029 2.00e-02 2.50e+03 ... (remaining 4687 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 72 2.40 - 3.03: 15379 3.03 - 3.65: 36849 3.65 - 4.28: 58485 4.28 - 4.90: 97468 Nonbonded interactions: 208253 Sorted by model distance: nonbonded pdb=" O THR J 105 " pdb=" OG1 THR J 105 " model vdw 1.777 3.040 nonbonded pdb=" OG SER F 31 " pdb=" N GLU F 32 " model vdw 1.895 3.120 nonbonded pdb=" OG SER Z 224 " pdb=" O THR h 174 " model vdw 1.989 3.040 nonbonded pdb=" O ASP L 203 " pdb=" OD1 ASP L 203 " model vdw 2.082 3.040 nonbonded pdb=" O GLU Z 32 " pdb=" O GLY Z 33 " model vdw 2.095 3.040 ... (remaining 208248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'M' selection = chain 'Y' selection = chain 'e' selection = chain 'm' } ncs_group { reference = chain 'F' selection = (chain 'J' and resid 11 through 604) selection = (chain 'Z' and resid 11 through 604) } ncs_group { reference = chain 'I' selection = (chain 'P' and resid 167 through 222) selection = (chain 'h' and resid 167 through 222) } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.720 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: 0.030 Extract box with map and model: 0.780 Check model and map are aligned: 0.120 Set scattering table: 0.200 Process input model: 59.440 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.179 26504 Z= 1.019 Angle : 1.991 23.213 36022 Z= 1.402 Chirality : 0.105 0.461 3986 Planarity : 0.007 0.070 4690 Dihedral : 18.167 87.803 9706 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 2.71 % Allowed : 13.56 % Favored : 83.73 % Rotamer: Outliers : 8.53 % Allowed : 21.19 % Favored : 70.28 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.38 % 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: -3.83 (0.12), residues: 3282 helix: -1.91 (0.22), residues: 381 sheet: -1.94 (0.16), residues: 894 loop : -3.11 (0.12), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.006 TRP J 274 HIS 0.019 0.004 HIS J 396 PHE 0.055 0.007 PHE J 177 TYR 0.051 0.007 TYR F 328 ARG 0.013 0.001 ARG F 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 380 time to evaluate : 3.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8782 (tm-30) REVERT: E 78 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8669 (mt-10) REVERT: E 99 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7777 (mm-30) REVERT: F 17 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8265 (p0) REVERT: F 144 ASN cc_start: 0.9370 (t0) cc_final: 0.8400 (m110) REVERT: F 162 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8610 (tp40) REVERT: F 221 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: F 261 ASP cc_start: 0.9624 (OUTLIER) cc_final: 0.9187 (p0) REVERT: F 489 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7768 (tt) REVERT: F 496 LEU cc_start: 0.8000 (mt) cc_final: 0.7638 (mt) REVERT: I 171 LYS cc_start: 0.5495 (OUTLIER) cc_final: 0.5185 (tptm) REVERT: I 172 GLN cc_start: 0.7009 (tp-100) cc_final: 0.6627 (tp40) REVERT: J 32 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.8786 (tt0) REVERT: J 47 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8564 (mt) REVERT: J 134 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7961 (tm-30) REVERT: J 175 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8033 (mtm-85) REVERT: J 187 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7441 (t70) REVERT: J 272 MET cc_start: 0.8987 (ttm) cc_final: 0.8594 (ttt) REVERT: J 483 ASP cc_start: 0.8637 (t70) cc_final: 0.8351 (t0) REVERT: J 523 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8253 (mt) REVERT: J 568 GLN cc_start: 0.7536 (tp40) cc_final: 0.7215 (tp40) REVERT: J 601 ASN cc_start: 0.6967 (OUTLIER) cc_final: 0.6599 (m110) REVERT: K 9 LYS cc_start: 0.7809 (mmtp) cc_final: 0.7309 (mmtp) REVERT: K 31 GLN cc_start: 0.8879 (mt0) cc_final: 0.8050 (mt0) REVERT: K 40 ASN cc_start: 0.7315 (OUTLIER) cc_final: 0.7017 (t0) REVERT: K 63 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8130 (mm-30) REVERT: K 64 GLU cc_start: 0.8877 (mp0) cc_final: 0.8417 (mp0) REVERT: K 97 ARG cc_start: 0.7241 (mmp-170) cc_final: 0.6517 (mmp-170) REVERT: L 1 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7905 (mmm) REVERT: L 59 TYR cc_start: 0.9202 (t80) cc_final: 0.8855 (t80) REVERT: L 69 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8854 (m-40) REVERT: M 9 LYS cc_start: 0.2275 (OUTLIER) cc_final: 0.0769 (mmmm) REVERT: M 52 ARG cc_start: 0.8109 (mtp180) cc_final: 0.7881 (mtp-110) REVERT: M 63 GLU cc_start: 0.8281 (tp30) cc_final: 0.8045 (tp30) REVERT: M 79 TRP cc_start: 0.8075 (m100) cc_final: 0.7788 (m100) REVERT: P 180 ASP cc_start: 0.8942 (t0) cc_final: 0.8672 (t0) REVERT: Y 2 LYS cc_start: 0.6322 (tptt) cc_final: 0.6027 (tptp) REVERT: Y 24 ARG cc_start: 0.9343 (ttp-110) cc_final: 0.8954 (ttp80) REVERT: Y 40 ASN cc_start: 0.7577 (p0) cc_final: 0.7308 (p0) REVERT: Y 63 GLU cc_start: 0.8666 (pp20) cc_final: 0.8406 (pp20) REVERT: Y 69 LYS cc_start: 0.7857 (tmtt) cc_final: 0.7266 (tmtt) REVERT: Y 72 LEU cc_start: 0.8995 (mp) cc_final: 0.8771 (mp) REVERT: Z 346 MET cc_start: 0.9385 (ptm) cc_final: 0.9177 (ptt) REVERT: Z 425 ARG cc_start: 0.9181 (ptt-90) cc_final: 0.8821 (ptm160) REVERT: e 12 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7484 (ttt) REVERT: e 95 MET cc_start: 0.7282 (tpp) cc_final: 0.6785 (tpp) REVERT: e 103 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8536 (mm-30) REVERT: f 2 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8702 (tm-30) REVERT: f 111 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7877 (ptp-170) REVERT: f 149 SER cc_start: 0.9334 (OUTLIER) cc_final: 0.9027 (p) REVERT: f 213 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8530 (mtpp) REVERT: h 182 MET cc_start: 0.9150 (mmm) cc_final: 0.8832 (mmm) REVERT: h 196 MET cc_start: 0.9060 (tpp) cc_final: 0.8689 (tpp) REVERT: m 9 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7499 (mtmm) REVERT: m 59 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7697 (tm-30) outliers start: 244 outliers final: 126 residues processed: 579 average time/residue: 0.4205 time to fit residues: 367.3457 Evaluate side-chains 475 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 328 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 MET Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 162 GLN Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 211 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 599 VAL Chi-restraints excluded: chain F residue 604 HIS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain J residue 207 ASP Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 268 TYR Chi-restraints excluded: chain J residue 279 MET Chi-restraints excluded: chain J residue 280 LEU Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 407 ASN Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 463 ASP Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 601 ASN Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 12 CYS Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 133 SER Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain N residue 162 VAL Chi-restraints excluded: chain P residue 173 ASN Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain Z residue 27 ILE Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 97 ASP Chi-restraints excluded: chain Z residue 103 THR Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 181 MET Chi-restraints excluded: chain Z residue 197 THR Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 215 THR Chi-restraints excluded: chain Z residue 222 VAL Chi-restraints excluded: chain Z residue 248 ASN Chi-restraints excluded: chain Z residue 339 LEU Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 452 ILE Chi-restraints excluded: chain Z residue 461 THR Chi-restraints excluded: chain Z residue 606 ASP Chi-restraints excluded: chain e residue 12 MET Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain f residue 2 GLN Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 74 SER Chi-restraints excluded: chain f residue 111 ARG Chi-restraints excluded: chain f residue 149 SER Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 213 LYS Chi-restraints excluded: chain f residue 226 SER Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 181 ASN Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 205 GLN Chi-restraints excluded: chain h residue 214 ASP Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 91 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 129 optimal weight: 0.0770 chunk 251 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 291 optimal weight: 7.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 250 ASN F 443 GLN F 460 GLN I 172 GLN I 185 GLN I 205 GLN J 22 GLN ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 GLN K 65 HIS L 2 GLN M 31 GLN N 6 GLN N 42 GLN Z 22 GLN ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 332 GLN e 40 ASN e 106 GLN f 6 GLN ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26504 Z= 0.208 Angle : 0.705 10.777 36022 Z= 0.375 Chirality : 0.047 0.205 3986 Planarity : 0.005 0.094 4690 Dihedral : 9.277 81.082 3858 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 1.01 % Allowed : 9.32 % Favored : 89.67 % Rotamer: Outliers : 5.21 % Allowed : 23.22 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.14), residues: 3282 helix: 0.05 (0.26), residues: 382 sheet: -1.41 (0.16), residues: 1024 loop : -2.46 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 89 HIS 0.006 0.001 HIS F 445 PHE 0.021 0.001 PHE N 163 TYR 0.020 0.001 TYR Z 212 ARG 0.006 0.001 ARG e 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 368 time to evaluate : 3.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 72 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8736 (mm-30) REVERT: F 144 ASN cc_start: 0.9318 (t0) cc_final: 0.8591 (m110) REVERT: F 182 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7987 (ptm160) REVERT: F 264 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: F 287 MET cc_start: 0.9150 (tpp) cc_final: 0.8771 (tpp) REVERT: F 484 ASP cc_start: 0.8820 (p0) cc_final: 0.8535 (m-30) REVERT: F 489 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7428 (tt) REVERT: F 507 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8133 (pp) REVERT: F 516 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8106 (p) REVERT: J 27 ILE cc_start: 0.9154 (mt) cc_final: 0.8792 (tt) REVERT: J 28 ASP cc_start: 0.8791 (m-30) cc_final: 0.8557 (m-30) REVERT: J 96 TYR cc_start: 0.7899 (t80) cc_final: 0.7367 (t80) REVERT: J 134 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7871 (tm-30) REVERT: J 503 ARG cc_start: 0.7737 (ptt-90) cc_final: 0.7309 (ptt-90) REVERT: J 568 GLN cc_start: 0.7526 (tp40) cc_final: 0.7294 (tp40) REVERT: K 9 LYS cc_start: 0.7760 (mmtp) cc_final: 0.7299 (mmtp) REVERT: K 22 LYS cc_start: 0.9045 (ttpp) cc_final: 0.8812 (ptmt) REVERT: K 31 GLN cc_start: 0.8571 (mt0) cc_final: 0.8010 (mt0) REVERT: K 40 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6952 (t0) REVERT: K 64 GLU cc_start: 0.8676 (mp0) cc_final: 0.8311 (pt0) REVERT: L 1 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7457 (tpt) REVERT: L 59 TYR cc_start: 0.9015 (t80) cc_final: 0.8588 (t80) REVERT: L 69 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8223 (m-40) REVERT: L 214 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8328 (t80) REVERT: M 13 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8203 (t0) REVERT: M 27 ASP cc_start: 0.8316 (p0) cc_final: 0.8110 (p0) REVERT: M 64 GLU cc_start: 0.9032 (tp30) cc_final: 0.8509 (tm-30) REVERT: M 78 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7986 (tm-30) REVERT: M 92 ARG cc_start: 0.8250 (tpp80) cc_final: 0.8013 (tpp80) REVERT: N 3 ASP cc_start: 0.8280 (p0) cc_final: 0.8060 (p0) REVERT: N 181 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8809 (mp0) REVERT: P 172 GLN cc_start: 0.7733 (mp10) cc_final: 0.7053 (tp40) REVERT: P 180 ASP cc_start: 0.8890 (t0) cc_final: 0.8551 (t0) REVERT: Y 24 ARG cc_start: 0.9323 (ttp-110) cc_final: 0.9047 (ttp80) REVERT: Y 27 ASP cc_start: 0.8638 (m-30) cc_final: 0.8053 (m-30) REVERT: Y 69 LYS cc_start: 0.7995 (tmtt) cc_final: 0.7613 (tmtt) REVERT: Z 93 GLU cc_start: 0.8949 (pm20) cc_final: 0.8707 (pt0) REVERT: Z 179 ILE cc_start: 0.9093 (pp) cc_final: 0.8632 (pt) REVERT: Z 272 MET cc_start: 0.8919 (tpp) cc_final: 0.8574 (tpt) REVERT: Z 373 ARG cc_start: 0.8674 (ttt90) cc_final: 0.8378 (mtp85) REVERT: Z 425 ARG cc_start: 0.9118 (ptt-90) cc_final: 0.8698 (ptm160) REVERT: e 12 MET cc_start: 0.7699 (ttt) cc_final: 0.7169 (ttt) REVERT: e 95 MET cc_start: 0.7257 (tpp) cc_final: 0.6949 (tpp) REVERT: f 159 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8619 (m-30) REVERT: h 171 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7474 (mptt) REVERT: h 182 MET cc_start: 0.8420 (mmm) cc_final: 0.7984 (mmm) REVERT: m 5 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6832 (mtm110) outliers start: 149 outliers final: 82 residues processed: 483 average time/residue: 0.3622 time to fit residues: 269.0926 Evaluate side-chains 435 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 340 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 211 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 264 PHE Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 507 LEU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 604 HIS Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 280 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 132 ILE Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain N residue 181 GLU Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain Z residue 27 ILE Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 215 THR Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 463 ASP Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 292 optimal weight: 1.9990 chunk 315 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: