Starting phenix.real_space_refine on Sat Feb 24 08:26:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4w_33608/02_2024/7y4w_33608_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4w_33608/02_2024/7y4w_33608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4w_33608/02_2024/7y4w_33608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4w_33608/02_2024/7y4w_33608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4w_33608/02_2024/7y4w_33608_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4w_33608/02_2024/7y4w_33608_updated.pdb" } resolution = 3.67 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= 0.003 sd= 0.057 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 8 5.49 5 S 230 5.16 5 C 27190 2.51 5 N 7433 2.21 5 O 7915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X GLU 44": "OE1" <-> "OE2" Residue "Z GLU 44": "OE1" <-> "OE2" Residue "Z GLU 173": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "E PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42776 Number of models: 1 Model: "" Number of chains: 14 Chain: "W" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "X" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "Y" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "Z" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "A" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5846 Classifications: {'peptide': 745} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 703} Chain: "B" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5846 Classifications: {'peptide': 745} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 703} Chain: "C" Number of atoms: 5835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5835 Classifications: {'peptide': 744} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 38, 'TRANS': 702} Chain: "D" Number of atoms: 5829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5829 Classifications: {'peptide': 743} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 701} Chain: "E" Number of atoms: 5911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5911 Classifications: {'peptide': 753} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 710} Chain: "F" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5921 Classifications: {'peptide': 755} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 712} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" 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} Time building chain proxies: 22.80, per 1000 atoms: 0.53 Number of scatterers: 42776 At special positions: 0 Unit cell: (178.2, 167.2, 193.6, 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 230 16.00 P 8 15.00 O 7915 8.00 N 7433 7.00 C 27190 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: 17.49 Conformation dependent library (CDL) restraints added in 7.8 seconds 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 251 helices and 33 sheets defined 44.8% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.50 Creating SS restraints... Processing helix chain 'W' and resid 3 through 9 Processing helix chain 'W' and resid 13 through 31 Proline residue: W 26 - end of helix Processing helix chain 'W' and resid 36 through 38 No H-bonds generated for 'chain 'W' and resid 36 through 38' Processing helix chain 'W' and resid 43 through 48 Processing helix chain 'W' and resid 57 through 59 No H-bonds generated for 'chain 'W' and resid 57 through 59' Processing helix chain 'W' and resid 69 through 88 removed outlier: 3.986A pdb=" N THR W 84 " --> pdb=" O TYR W 80 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG W 85 " --> pdb=" O GLN W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 115 Processing helix chain 'W' and resid 123 through 136 Processing helix chain 'W' and resid 155 through 165 Processing helix chain 'W' and resid 171 through 187 Processing helix chain 'W' and resid 189 through 193 Processing helix chain 'W' and resid 204 through 209 Processing helix chain 'X' and resid 3 through 10 Processing helix chain 'X' and resid 13 through 31 Proline residue: X 26 - end of helix Processing helix chain 'X' and resid 36 through 38 No H-bonds generated for 'chain 'X' and resid 36 through 38' Processing helix chain 'X' and resid 43 through 48 Processing helix chain 'X' and resid 57 through 60 No H-bonds generated for 'chain 'X' and resid 57 through 60' Processing helix chain 'X' and resid 69 through 88 removed outlier: 3.667A pdb=" N THR X 84 " --> pdb=" O TYR X 80 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG X 85 " --> pdb=" O GLN X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 95 through 115 Processing helix chain 'X' and resid 123 through 135 Processing helix chain 'X' and resid 155 through 165 Processing helix chain 'X' and resid 170 through 187 Processing helix chain 'X' and resid 189 through 193 Processing helix chain 'X' and resid 204 through 209 Processing helix chain 'Y' and resid 3 through 10 Processing helix chain 'Y' and resid 13 through 30 Proline residue: Y 26 - end of helix Processing helix chain 'Y' and resid 36 through 38 No H-bonds generated for 'chain 'Y' and resid 36 through 38' Processing helix chain 'Y' and resid 43 through 48 Processing helix chain 'Y' and resid 52 through 59 removed outlier: 4.687A pdb=" N ILE Y 56 " --> pdb=" O ILE Y 52 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR Y 59 " --> pdb=" O PRO Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 87 removed outlier: 4.283A pdb=" N THR Y 84 " --> pdb=" O TYR Y 80 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU Y 86 " --> pdb=" O TYR Y 82 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 115 Processing helix chain 'Y' and resid 123 through 136 Processing helix chain 'Y' and resid 155 through 162 Processing helix chain 'Y' and resid 170 through 187 removed outlier: 3.966A pdb=" N LEU Y 178 " --> pdb=" O LEU Y 174 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL Y 179 " --> pdb=" O ILE Y 175 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY Y 180 " --> pdb=" O GLY Y 176 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N HIS Y 181 " --> pdb=" O ASN Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 189 through 193 Processing helix chain 'Z' and resid 3 through 10 Processing helix chain 'Z' and resid 13 through 31 removed outlier: 3.883A pdb=" N ALA Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA Z 21 " --> pdb=" O TYR Z 17 " (cutoff:3.500A) Proline residue: Z 26 - end of helix Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 43 through 48 Processing helix chain 'Z' and resid 53 through 58 Processing helix chain 'Z' and resid 69 through 88 removed outlier: 4.054A pdb=" N ARG Z 85 " --> pdb=" O GLN Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 115 removed outlier: 3.528A pdb=" N LEU Z 99 " --> pdb=" O PRO Z 95 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU Z 102 " --> pdb=" O TYR Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 122 through 136 removed outlier: 3.737A pdb=" N LEU Z 136 " --> pdb=" O VAL Z 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 155 through 165 Processing helix chain 'Z' and resid 171 through 187 removed outlier: 4.872A pdb=" N GLY Z 176 " --> pdb=" O ASN Z 172 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL Z 179 " --> pdb=" O ILE Z 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 193 No H-bonds generated for 'chain 'Z' and resid 190 through 193' Processing helix chain 'Z' and resid 204 through 209 Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 135 through 138 No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 225 Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 279 through 296 removed outlier: 4.080A pdb=" N GLU A 283 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A 284 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A 292 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 320 through 333 Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 408 through 426 removed outlier: 3.687A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.072A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 544 through 551 Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 594 through 609 Processing helix chain 'A' and resid 651 through 661 removed outlier: 3.609A pdb=" N LYS A 658 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 679 Processing helix chain 'A' and resid 684 through 714 removed outlier: 3.720A pdb=" N CYS A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 749 through 765 removed outlier: 3.519A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 225 removed outlier: 3.624A pdb=" N GLU B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.590A pdb=" N LEU B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 320 through 333 Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 408 through 426 removed outlier: 3.758A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 removed outlier: 4.349A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 524 through 535 Processing helix chain 'B' and resid 544 through 551 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 579 through 586 removed outlier: 3.711A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 609 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 650 through 660 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 713 removed outlier: 3.720A pdb=" N ALA B 694 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N CYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 749 through 765 removed outlier: 3.945A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 192 through 195 No H-bonds generated for 'chain 'C' and resid 192 through 195' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 5.469A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 279 through 296 removed outlier: 3.511A pdb=" N SER C 282 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU C 283 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU C 294 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 320 through 334 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 426 removed outlier: 3.671A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 444 No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 483 through 498 removed outlier: 4.658A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 551 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 579 through 586 removed outlier: 3.712A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG C 586 " --> pdb=" O ALA C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 3.952A pdb=" N VAL C 600 " --> pdb=" O ALA C 596 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 662 removed outlier: 3.561A pdb=" N ALA C 655 " --> pdb=" O SER C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 678 No H-bonds generated for 'chain 'C' and resid 675 through 678' Processing helix chain 'C' and resid 684 through 715 Processing helix chain 'C' and resid 727 through 729 No H-bonds generated for 'chain 'C' and resid 727 through 729' Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 749 through 761 Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 130 through 133 No H-bonds generated for 'chain 'D' and resid 130 through 133' Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 225 removed outlier: 5.088A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.601A pdb=" N LEU D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 320 through 333 Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 408 through 426 Processing helix chain 'D' and resid 437 through 442 Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 483 through 493 Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 524 through 535 Processing helix chain 'D' and resid 544 through 551 removed outlier: 3.692A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 579 through 586 removed outlier: 3.813A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 609 Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 651 through 660 Processing helix chain 'D' and resid 673 through 679 removed outlier: 3.566A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 715 removed outlier: 3.608A pdb=" N ALA D 694 " --> pdb=" O ILE D 690 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS D 695 " --> pdb=" O CYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 739 Processing helix chain 'D' and resid 750 through 762 Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' Processing helix chain 'E' and resid 130 through 133 No H-bonds generated for 'chain 'E' and resid 130 through 133' Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.835A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 282 through 294 Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 333 Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 385 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 425 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 492 Processing helix chain 'E' and resid 494 through 498 Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 524 through 535 Processing helix chain 'E' and resid 544 through 551 Processing helix chain 'E' and resid 556 through 568 Processing helix chain 'E' and resid 579 through 586 removed outlier: 3.682A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG E 586 " --> pdb=" O ALA E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 609 removed outlier: 3.840A pdb=" N VAL E 600 " --> pdb=" O ALA E 596 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 601 " --> pdb=" O ALA E 597 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 653 through 661 Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 715 removed outlier: 3.505A pdb=" N CYS E 695 " --> pdb=" O CYS E 691 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN E 714 " --> pdb=" O GLU E 710 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THR E 715 " --> pdb=" O ARG E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 Processing helix chain 'E' and resid 749 through 764 Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' Processing helix chain 'F' and resid 130 through 133 No H-bonds generated for 'chain 'F' and resid 130 through 133' Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 225 removed outlier: 4.455A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 272 through 274 No H-bonds generated for 'chain 'F' and resid 272 through 274' Processing helix chain 'F' and resid 279 through 293 Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 335 Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 428 through 430 No H-bonds generated for 'chain 'F' and resid 428 through 430' Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 removed outlier: 4.450A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 524 through 535 Processing helix chain 'F' and resid 544 through 551 Processing helix chain 'F' and resid 557 through 568 Processing helix chain 'F' and resid 579 through 586 removed outlier: 3.772A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 609 removed outlier: 3.516A pdb=" N ILE F 601 " --> pdb=" O ASP F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 663 removed outlier: 4.154A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 715 removed outlier: 3.766A pdb=" N ALA F 694 " --> pdb=" O ILE F 690 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS F 695 " --> pdb=" O CYS F 691 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 740 Processing helix chain 'F' and resid 749 through 765 removed outlier: 4.095A pdb=" N SER F 765 " --> pdb=" O THR F 761 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 27 through 29 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 41 removed outlier: 8.319A pdb=" N VAL A 39 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 70 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU A 41 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 72 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.767A pdb=" N GLU A 167 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= E, first strand: chain 'A' and resid 365 through 369 removed outlier: 3.855A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY A 245 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR A 347 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 641 through 645 removed outlier: 4.099A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 27 through 29 Processing sheet with id= H, first strand: chain 'B' and resid 39 through 41 Processing sheet with id= I, first strand: chain 'B' and resid 66 through 70 Processing sheet with id= J, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.560A pdb=" N ILE B 114 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B 113 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 167 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.598A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.861A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 81 through 83 removed outlier: 7.555A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP C 55 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.810A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= P, first strand: chain 'C' and resid 365 through 368 removed outlier: 6.565A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.690A pdb=" N GLY C 518 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 27 through 29 Processing sheet with id= S, first strand: chain 'D' and resid 38 through 41 removed outlier: 8.239A pdb=" N VAL D 39 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.636A pdb=" N ARG D 113 " --> pdb=" O ASP D 169 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.723A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 365 through 369 removed outlier: 3.744A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N GLY D 245 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR D 347 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 641 through 645 removed outlier: 4.017A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 81 through 83 removed outlier: 8.289A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.542A pdb=" N VAL E 116 " --> pdb=" O HIS E 183 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG E 113 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU E 167 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= AA, first strand: chain 'E' and resid 365 through 369 removed outlier: 3.732A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY E 245 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR E 347 " --> pdb=" O GLY E 245 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 641 through 645 removed outlier: 4.177A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.625A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 181 through 183 removed outlier: 3.532A pdb=" N GLU F 167 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AF, first strand: chain 'F' and resid 365 through 369 removed outlier: 3.701A pdb=" N GLY F 245 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.677A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) 1563 hydrogen bonds defined for protein. 4320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.86 Time building geometry restraints manager: 18.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14335 1.34 - 1.46: 8651 1.46 - 1.58: 20268 1.58 - 1.70: 12 1.70 - 1.82: 380 Bond restraints: 43646 Sorted by residual: bond pdb=" CB PRO F 298 " pdb=" CG PRO F 298 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.73e+00 bond pdb=" CA GLY F 521 " pdb=" C GLY F 521 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.48e+00 bond pdb=" N GLY F 521 " pdb=" CA GLY F 521 " ideal model delta sigma weight residual 1.464 1.448 0.017 1.12e-02 7.97e+03 2.18e+00 bond pdb=" C LYS F 543 " pdb=" N GLY F 544 " ideal model delta sigma weight residual 1.340 1.330 0.010 6.60e-03 2.30e+04 2.12e+00 bond pdb=" C ALA F 297 " pdb=" N PRO F 298 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.02e+00 ... (remaining 43641 not shown) Histogram of bond angle deviations from ideal: 97.69 - 105.37: 1081 105.37 - 113.05: 23217 113.05 - 120.73: 20149 120.73 - 128.40: 14367 128.40 - 136.08: 252 Bond angle restraints: 59066 Sorted by residual: angle pdb=" C GLN A 337 " pdb=" CA GLN A 337 " pdb=" CB GLN A 337 " ideal model delta sigma weight residual 117.23 110.38 6.85 1.36e+00 5.41e-01 2.54e+01 angle pdb=" CB ARG F 338 " pdb=" CG ARG F 338 " pdb=" CD ARG F 338 " ideal model delta sigma weight residual 111.30 122.23 -10.93 2.30e+00 1.89e-01 2.26e+01 angle pdb=" C GLU F 194 " pdb=" N GLU F 195 " pdb=" CA GLU F 195 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C GLY F 769 " pdb=" N SER F 770 " pdb=" CA SER F 770 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C GLU B 712 " pdb=" N ARG B 713 " pdb=" CA ARG B 713 " ideal model delta sigma weight residual 122.31 114.97 7.34 2.00e+00 2.50e-01 1.35e+01 ... (remaining 59061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.99: 25531 27.99 - 55.99: 1011 55.99 - 83.98: 87 83.98 - 111.98: 13 111.98 - 139.97: 3 Dihedral angle restraints: 26645 sinusoidal: 11120 harmonic: 15525 Sorted by residual: dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 79.98 -139.97 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" C2' ADP A 901 " pdb=" C1' ADP A 901 " pdb=" N9 ADP A 901 " pdb=" C4 ADP A 901 " ideal model delta sinusoidal sigma weight residual 91.55 -151.57 -116.88 1 2.00e+01 2.50e-03 3.49e+01 dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 55.18 -115.18 1 2.00e+01 2.50e-03 3.42e+01 ... (remaining 26642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 5154 0.051 - 0.102: 1090 0.102 - 0.153: 282 0.153 - 0.204: 11 0.204 - 0.255: 1 Chirality restraints: 6538 Sorted by residual: chirality pdb=" CG LEU F 335 " pdb=" CB LEU F 335 " pdb=" CD1 LEU F 335 " pdb=" CD2 LEU F 335 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PRO F 298 " pdb=" N PRO F 298 " pdb=" C PRO F 298 " pdb=" CB PRO F 298 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL X 170 " pdb=" CA VAL X 170 " pdb=" CG1 VAL X 170 " pdb=" CG2 VAL X 170 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 6535 not shown) Planarity restraints: 7734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA F 297 " 0.066 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO F 298 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO F 298 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO F 298 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 454 " -0.020 2.00e-02 2.50e+03 2.49e-02 1.55e+01 pdb=" CG TRP D 454 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP D 454 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP D 454 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 454 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP D 454 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 454 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 454 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 454 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 454 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 297 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO C 298 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 298 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 298 " -0.038 5.00e-02 4.00e+02 ... (remaining 7731 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 852 2.69 - 3.24: 42893 3.24 - 3.79: 65298 3.79 - 4.35: 81458 4.35 - 4.90: 132955 Nonbonded interactions: 323456 Sorted by model distance: nonbonded pdb=" OG SER F 748 " pdb=" OD1 ASN F 750 " model vdw 2.137 2.440 nonbonded pdb=" OG1 THR Y 202 " pdb=" OH TYR Y 207 " model vdw 2.168 2.440 nonbonded pdb=" NE1 TRP Y 7 " pdb=" OH TYR Y 80 " model vdw 2.192 2.520 nonbonded pdb=" OD1 ASP Z 193 " pdb=" NZ LYS D 109 " model vdw 2.218 2.520 nonbonded pdb=" OG1 THR B 127 " pdb=" OG1 THR B 436 " model vdw 2.227 2.440 ... (remaining 323451 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 23 through 764) selection = (chain 'B' and resid 23 through 764) selection = (chain 'C' and resid 23 through 764) selection = (chain 'D' and resid 23 through 764) selection = (chain 'E' and resid 23 through 764) selection = (chain 'F' and resid 23 through 764) } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 9.520 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 110.370 Find NCS groups from input model: 3.510 Set up NCS constraints: 0.160 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.002 0.083 43646 Z= 0.160 Angle : 0.618 12.526 59066 Z= 0.316 Chirality : 0.044 0.255 6538 Planarity : 0.005 0.099 7734 Dihedral : 14.252 139.973 16621 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.11 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.12), residues: 5365 helix: 1.10 (0.11), residues: 2406 sheet: 0.41 (0.20), residues: 669 loop : -1.32 (0.14), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP D 454 HIS 0.006 0.001 HIS F 340 PHE 0.017 0.001 PHE Z 185 TYR 0.019 0.001 TYR B 244 ARG 0.012 0.000 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 5.051 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: W 162 PHE cc_start: 0.7426 (t80) cc_final: 0.7145 (t80) REVERT: X 83 SER cc_start: 0.8472 (t) cc_final: 0.8269 (t) REVERT: Y 81 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8264 (tm-30) REVERT: Z 34 ILE cc_start: 0.7240 (mm) cc_final: 0.6896 (mm) REVERT: Z 42 TRP cc_start: 0.7998 (t-100) cc_final: 0.7678 (t-100) REVERT: A 244 TYR cc_start: 0.8240 (p90) cc_final: 0.7839 (p90) REVERT: A 674 PHE cc_start: 0.8130 (t80) cc_final: 0.7343 (t80) REVERT: A 757 MET cc_start: 0.8811 (tmm) cc_final: 0.8511 (tmm) REVERT: B 561 GLU cc_start: 0.8461 (pp20) cc_final: 0.8164 (pp20) REVERT: C 84 MET cc_start: 0.7473 (tpt) cc_final: 0.6881 (tpt) REVERT: C 720 MET cc_start: 0.3953 (pmm) cc_final: 0.3562 (pmm) REVERT: D 244 TYR cc_start: 0.7520 (p90) cc_final: 0.7210 (p90) REVERT: D 313 ARG cc_start: 0.8027 (tpt170) cc_final: 0.7470 (tpt-90) REVERT: D 349 ARG cc_start: 0.7532 (ttt90) cc_final: 0.7240 (mtp85) REVERT: D 564 ASP cc_start: 0.8578 (t70) cc_final: 0.8371 (t0) REVERT: D 720 MET cc_start: 0.1267 (ttt) cc_final: 0.0819 (ppp) REVERT: F 427 MET cc_start: 0.7492 (tpp) cc_final: 0.7225 (tpp) REVERT: F 602 ASN cc_start: 0.7944 (m110) cc_final: 0.7659 (m110) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.4907 time to fit residues: 378.6654 Evaluate side-chains 354 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 4.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 450 optimal weight: 10.0000 chunk 404 optimal weight: 4.9990 chunk 224 optimal weight: 0.0980 chunk 138 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 418 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 254 optimal weight: 7.9990 chunk 311 optimal weight: 1.9990 chunk 484 optimal weight: 0.0040 overall best weight: 2.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 105 ASN X 198 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 43646 Z= 0.241 Angle : 0.599 13.779 59066 Z= 0.299 Chirality : 0.044 0.193 6538 Planarity : 0.005 0.102 7734 Dihedral : 5.513 125.240 5943 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.41 % Favored : 91.11 % Rotamer: Outliers : 0.83 % Allowed : 7.61 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.12), residues: 5365 helix: 1.05 (0.11), residues: 2409 sheet: 0.38 (0.20), residues: 674 loop : -1.31 (0.14), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 454 HIS 0.004 0.001 HIS E 183 PHE 0.020 0.001 PHE E 152 TYR 0.016 0.001 TYR C 110 ARG 0.006 0.000 ARG D 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 361 time to evaluate : 5.241 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: X 59 THR cc_start: 0.8692 (p) cc_final: 0.8377 (t) REVERT: X 116 MET cc_start: 0.8433 (mmm) cc_final: 0.7761 (tmm) REVERT: Y 81 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8407 (tm-30) REVERT: Y 116 MET cc_start: 0.8585 (tmm) cc_final: 0.8043 (tmm) REVERT: Y 118 MET cc_start: 0.8367 (ptp) cc_final: 0.7642 (ptp) REVERT: Y 163 ASN cc_start: 0.8963 (t0) cc_final: 0.8721 (t0) REVERT: Z 34 ILE cc_start: 0.7286 (mm) cc_final: 0.6915 (mm) REVERT: Z 42 TRP cc_start: 0.8107 (t-100) cc_final: 0.7621 (t-100) REVERT: Z 82 TYR cc_start: 0.8336 (m-80) cc_final: 0.8119 (m-80) REVERT: Z 99 LEU cc_start: 0.9202 (tt) cc_final: 0.8992 (tt) REVERT: Z 117 ASP cc_start: 0.8534 (t70) cc_final: 0.8204 (t0) REVERT: Z 185 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8144 (t80) REVERT: Z 187 MET cc_start: 0.7852 (tpp) cc_final: 0.7645 (tpp) REVERT: A 244 TYR cc_start: 0.8282 (p90) cc_final: 0.7876 (p90) REVERT: A 577 ASP cc_start: 0.8203 (t0) cc_final: 0.7792 (t0) REVERT: A 678 MET cc_start: 0.7213 (ptm) cc_final: 0.6931 (ptm) REVERT: A 757 MET cc_start: 0.8861 (tmm) cc_final: 0.8527 (tmm) REVERT: B 304 ASP cc_start: 0.8204 (t0) cc_final: 0.7905 (t0) REVERT: B 561 GLU cc_start: 0.8533 (pp20) cc_final: 0.8209 (pp20) REVERT: C 720 MET cc_start: 0.4418 (pmm) cc_final: 0.4050 (pmm) REVERT: D 244 TYR cc_start: 0.7442 (p90) cc_final: 0.7052 (p90) REVERT: D 564 ASP cc_start: 0.8645 (t70) cc_final: 0.8442 (t0) REVERT: D 720 MET cc_start: 0.1574 (ttt) cc_final: 0.0330 (ppp) REVERT: E 173 TYR cc_start: 0.7865 (p90) cc_final: 0.7374 (p90) REVERT: F 292 GLU cc_start: 0.8245 (tp30) cc_final: 0.7921 (tm-30) outliers start: 38 outliers final: 29 residues processed: 385 average time/residue: 0.5006 time to fit residues: 329.5376 Evaluate side-chains 365 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 335 time to evaluate : 5.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 139 ASP Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain Y residue 174 LEU Chi-restraints excluded: chain Y residue 192 MET Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 185 PHE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain F residue 562 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 269 optimal weight: 0.4980 chunk 150 optimal weight: 0.2980 chunk 403 optimal weight: 0.9980 chunk 330 optimal weight: 0.3980 chunk 133 optimal weight: 7.9990 chunk 485 optimal weight: 0.7980 chunk 524 optimal weight: 10.0000 chunk 432 optimal weight: 8.9990 chunk 481 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 chunk 389 optimal weight: 50.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 692 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 589 ASN ** F 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 43646 Z= 0.142 Angle : 0.561 14.875 59066 Z= 0.274 Chirality : 0.043 0.200 6538 Planarity : 0.004 0.097 7734 Dihedral : 5.354 119.634 5943 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.74 % Favored : 91.82 % Rotamer: Outliers : 1.04 % Allowed : 9.77 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 5365 helix: 1.07 (0.11), residues: 2424 sheet: 0.56 (0.20), residues: 680 loop : -1.29 (0.14), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 454 HIS 0.003 0.000 HIS A 183 PHE 0.033 0.001 PHE D 52 TYR 0.022 0.001 TYR C 110 ARG 0.006 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 376 time to evaluate : 5.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 59 THR cc_start: 0.8622 (p) cc_final: 0.8311 (t) REVERT: X 116 MET cc_start: 0.8355 (mmm) cc_final: 0.7894 (tmm) REVERT: Y 1 MET cc_start: 0.5083 (tpt) cc_final: 0.2625 (pmm) REVERT: Y 81 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8320 (tm-30) REVERT: Y 116 MET cc_start: 0.8662 (tmm) cc_final: 0.8014 (tmm) REVERT: Y 118 MET cc_start: 0.8289 (ptp) cc_final: 0.7400 (ptt) REVERT: Y 140 MET cc_start: 0.8204 (mtp) cc_final: 0.7939 (mtt) REVERT: Y 163 ASN cc_start: 0.8948 (t0) cc_final: 0.8617 (t0) REVERT: Z 42 TRP cc_start: 0.8132 (t-100) cc_final: 0.7630 (t-100) REVERT: Z 82 TYR cc_start: 0.8307 (m-80) cc_final: 0.8098 (m-80) REVERT: Z 99 LEU cc_start: 0.9211 (tt) cc_final: 0.8974 (tt) REVERT: Z 185 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8340 (t80) REVERT: A 244 TYR cc_start: 0.8172 (p90) cc_final: 0.7826 (p90) REVERT: A 577 ASP cc_start: 0.8165 (t0) cc_final: 0.7777 (t0) REVERT: A 757 MET cc_start: 0.8910 (tmm) cc_final: 0.8614 (tmm) REVERT: B 561 GLU cc_start: 0.8476 (pp20) cc_final: 0.8169 (pp20) REVERT: B 577 ASP cc_start: 0.7945 (t0) cc_final: 0.7742 (t0) REVERT: C 46 MET cc_start: 0.7387 (tpt) cc_final: 0.7177 (mmt) REVERT: C 720 MET cc_start: 0.3979 (pmm) cc_final: 0.3597 (pmm) REVERT: C 757 MET cc_start: 0.8680 (ptp) cc_final: 0.8470 (ptp) REVERT: D 198 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8655 (pp) REVERT: D 244 TYR cc_start: 0.7305 (p90) cc_final: 0.6915 (p90) REVERT: D 564 ASP cc_start: 0.8601 (t70) cc_final: 0.8395 (t0) REVERT: D 720 MET cc_start: 0.1278 (ttt) cc_final: 0.0287 (ppp) REVERT: E 46 MET cc_start: 0.5531 (tmm) cc_final: 0.4729 (ptp) REVERT: E 173 TYR cc_start: 0.7880 (p90) cc_final: 0.7374 (p90) REVERT: F 292 GLU cc_start: 0.8231 (tp30) cc_final: 0.7973 (tm-30) REVERT: F 740 MET cc_start: 0.8585 (tmm) cc_final: 0.7943 (tmm) outliers start: 48 outliers final: 30 residues processed: 404 average time/residue: 0.4819 time to fit residues: 333.1844 Evaluate side-chains 381 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 349 time to evaluate : 4.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 139 ASP Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 101 MET Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 185 PHE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 469 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 479 optimal weight: 3.9990 chunk 365 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 326 optimal weight: 20.0000 chunk 487 optimal weight: 0.9980 chunk 516 optimal weight: 6.9990 chunk 254 optimal weight: 9.9990 chunk 462 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 HIS ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS D 536 GLN ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 GLN F 50 GLN F 199 ASN F 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 43646 Z= 0.384 Angle : 0.681 14.644 59066 Z= 0.340 Chirality : 0.046 0.268 6538 Planarity : 0.005 0.106 7734 Dihedral : 5.620 123.207 5943 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.97 % Favored : 90.55 % Rotamer: Outliers : 1.89 % Allowed : 12.03 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 5365 helix: 0.85 (0.11), residues: 2419 sheet: 0.27 (0.20), residues: 668 loop : -1.36 (0.14), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 551 HIS 0.005 0.001 HIS C 340 PHE 0.024 0.002 PHE F 563 TYR 0.018 0.002 TYR Z 77 ARG 0.007 0.001 ARG E 599 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 330 time to evaluate : 4.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 59 THR cc_start: 0.8790 (p) cc_final: 0.8559 (t) REVERT: X 116 MET cc_start: 0.8397 (mmm) cc_final: 0.7829 (tmm) REVERT: X 192 MET cc_start: 0.5958 (tmm) cc_final: 0.5696 (tmm) REVERT: Y 81 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8418 (tm-30) REVERT: Y 116 MET cc_start: 0.8603 (tmm) cc_final: 0.7908 (tmm) REVERT: Y 118 MET cc_start: 0.8656 (ptp) cc_final: 0.7688 (ptt) REVERT: Y 140 MET cc_start: 0.8333 (mtp) cc_final: 0.8069 (mtt) REVERT: Y 163 ASN cc_start: 0.9111 (t0) cc_final: 0.8699 (t0) REVERT: Z 42 TRP cc_start: 0.8243 (t-100) cc_final: 0.7592 (t-100) REVERT: Z 82 TYR cc_start: 0.8452 (m-80) cc_final: 0.7964 (m-10) REVERT: Z 116 MET cc_start: 0.7650 (tpt) cc_final: 0.7410 (tpt) REVERT: Z 185 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8377 (t80) REVERT: A 244 TYR cc_start: 0.8462 (p90) cc_final: 0.7974 (p90) REVERT: A 508 MET cc_start: 0.7708 (tpp) cc_final: 0.6821 (tpt) REVERT: A 577 ASP cc_start: 0.8296 (t0) cc_final: 0.7918 (t0) REVERT: A 751 ASP cc_start: 0.8856 (m-30) cc_final: 0.8646 (m-30) REVERT: A 757 MET cc_start: 0.8886 (tmm) cc_final: 0.8524 (tmm) REVERT: B 561 GLU cc_start: 0.8539 (pp20) cc_final: 0.8225 (pp20) REVERT: B 577 ASP cc_start: 0.8186 (t0) cc_final: 0.7969 (t0) REVERT: C 278 LEU cc_start: 0.7828 (tp) cc_final: 0.7562 (tt) REVERT: C 720 MET cc_start: 0.4486 (pmm) cc_final: 0.4153 (pmm) REVERT: C 757 MET cc_start: 0.8693 (ptp) cc_final: 0.8385 (ptp) REVERT: D 52 PHE cc_start: 0.8322 (t80) cc_final: 0.8070 (t80) REVERT: D 109 LYS cc_start: 0.7756 (tptt) cc_final: 0.7532 (tptt) REVERT: D 313 ARG cc_start: 0.8058 (tpt170) cc_final: 0.7512 (tpt-90) REVERT: D 349 ARG cc_start: 0.8526 (mmm160) cc_final: 0.7948 (tpp-160) REVERT: D 427 MET cc_start: 0.8751 (mmm) cc_final: 0.7901 (tpp) REVERT: D 720 MET cc_start: 0.1637 (ttt) cc_final: 0.0145 (ppp) REVERT: D 757 MET cc_start: 0.8331 (ppp) cc_final: 0.8066 (ppp) REVERT: E 46 MET cc_start: 0.5705 (tmm) cc_final: 0.4999 (ptp) REVERT: E 432 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8045 (mp) REVERT: F 292 GLU cc_start: 0.8500 (tp30) cc_final: 0.8290 (tm-30) outliers start: 87 outliers final: 52 residues processed: 399 average time/residue: 0.4695 time to fit residues: 324.5035 Evaluate side-chains 369 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 315 time to evaluate : 4.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 83 SER Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain W residue 139 ASP Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 139 ASP Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 182 LEU Chi-restraints excluded: chain Z residue 185 PHE Chi-restraints excluded: chain Z residue 202 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 589 ASN Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 429 optimal weight: 0.0470 chunk 293 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 384 optimal weight: 0.0570 chunk 212 optimal weight: 0.9990 chunk 440 optimal weight: 0.4980 chunk 356 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 chunk 463 optimal weight: 7.9990 chunk 130 optimal weight: 0.0370 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 43646 Z= 0.147 Angle : 0.576 16.609 59066 Z= 0.282 Chirality : 0.043 0.197 6538 Planarity : 0.004 0.098 7734 Dihedral : 5.357 118.060 5943 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.59 % Favored : 91.95 % Rotamer: Outliers : 1.37 % Allowed : 13.57 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.12), residues: 5365 helix: 1.09 (0.11), residues: 2412 sheet: 0.50 (0.20), residues: 678 loop : -1.33 (0.14), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 454 HIS 0.003 0.001 HIS A 115 PHE 0.015 0.001 PHE E 773 TYR 0.021 0.001 TYR D 244 ARG 0.007 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 363 time to evaluate : 5.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 59 THR cc_start: 0.8675 (p) cc_final: 0.8371 (t) REVERT: X 116 MET cc_start: 0.8191 (mmm) cc_final: 0.7656 (tmm) REVERT: X 192 MET cc_start: 0.5895 (tmm) cc_final: 0.5610 (tmm) REVERT: Y 81 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8325 (tm-30) REVERT: Y 116 MET cc_start: 0.8681 (tmm) cc_final: 0.8001 (tmm) REVERT: Y 118 MET cc_start: 0.8495 (ptp) cc_final: 0.7580 (ptt) REVERT: Y 140 MET cc_start: 0.8272 (mtp) cc_final: 0.8015 (mtt) REVERT: Y 163 ASN cc_start: 0.8968 (t0) cc_final: 0.8630 (t0) REVERT: Y 192 MET cc_start: 0.7813 (ptt) cc_final: 0.7218 (ptt) REVERT: Z 42 TRP cc_start: 0.8231 (t-100) cc_final: 0.7592 (t-100) REVERT: Z 99 LEU cc_start: 0.9222 (tt) cc_final: 0.8983 (tt) REVERT: Z 185 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8413 (t80) REVERT: A 244 TYR cc_start: 0.8251 (p90) cc_final: 0.7810 (p90) REVERT: A 288 LYS cc_start: 0.9313 (tppt) cc_final: 0.8876 (tppt) REVERT: A 577 ASP cc_start: 0.8206 (t0) cc_final: 0.7826 (t0) REVERT: A 757 MET cc_start: 0.8907 (tmm) cc_final: 0.8579 (tmm) REVERT: B 561 GLU cc_start: 0.8541 (pp20) cc_final: 0.8217 (pp20) REVERT: B 577 ASP cc_start: 0.8122 (t0) cc_final: 0.7866 (t0) REVERT: C 230 PHE cc_start: 0.7991 (t80) cc_final: 0.7769 (t80) REVERT: C 278 LEU cc_start: 0.7598 (tp) cc_final: 0.7300 (tt) REVERT: C 720 MET cc_start: 0.4416 (pmm) cc_final: 0.4063 (pmm) REVERT: C 757 MET cc_start: 0.8700 (ptp) cc_final: 0.8382 (ptp) REVERT: D 52 PHE cc_start: 0.8399 (t80) cc_final: 0.8123 (t80) REVERT: D 109 LYS cc_start: 0.7797 (tptt) cc_final: 0.7447 (tptt) REVERT: D 313 ARG cc_start: 0.8120 (tpt170) cc_final: 0.7551 (tpt-90) REVERT: D 427 MET cc_start: 0.8703 (mmm) cc_final: 0.7830 (tpp) REVERT: D 720 MET cc_start: 0.1421 (ttt) cc_final: 0.0336 (ppp) REVERT: D 751 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8626 (p0) REVERT: E 46 MET cc_start: 0.5779 (tmm) cc_final: 0.5096 (ptp) REVERT: E 432 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7996 (mp) REVERT: F 292 GLU cc_start: 0.8472 (tp30) cc_final: 0.8230 (tm-30) outliers start: 63 outliers final: 42 residues processed: 399 average time/residue: 0.4933 time to fit residues: 342.3441 Evaluate side-chains 391 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 346 time to evaluate : 5.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain W residue 250 ASP Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 139 ASP Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 101 MET Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 185 PHE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 173 optimal weight: 0.4980 chunk 464 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 303 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 516 optimal weight: 3.9990 chunk 428 optimal weight: 9.9990 chunk 239 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 51 GLN ** W 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 198 ASN A 340 HIS B 692 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 43646 Z= 0.279 Angle : 0.621 16.975 59066 Z= 0.307 Chirality : 0.044 0.187 6538 Planarity : 0.005 0.101 7734 Dihedral : 5.426 121.599 5943 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.56 % Favored : 91.00 % Rotamer: Outliers : 1.85 % Allowed : 14.46 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.12), residues: 5365 helix: 1.01 (0.11), residues: 2414 sheet: 0.34 (0.20), residues: 681 loop : -1.33 (0.14), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 551 HIS 0.003 0.001 HIS C 340 PHE 0.024 0.001 PHE W 184 TYR 0.013 0.001 TYR Z 183 ARG 0.008 0.000 ARG F 713 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 329 time to evaluate : 5.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 59 THR cc_start: 0.8775 (p) cc_final: 0.8523 (t) REVERT: X 116 MET cc_start: 0.8139 (mmm) cc_final: 0.7580 (tmm) REVERT: X 130 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9154 (tt) REVERT: X 192 MET cc_start: 0.5775 (tmm) cc_final: 0.5445 (tmm) REVERT: Y 81 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8352 (tm-30) REVERT: Y 116 MET cc_start: 0.8673 (tmm) cc_final: 0.7952 (tmm) REVERT: Y 118 MET cc_start: 0.8663 (ptp) cc_final: 0.7735 (ptm) REVERT: Y 140 MET cc_start: 0.8341 (mtp) cc_final: 0.8108 (mtt) REVERT: Y 163 ASN cc_start: 0.9046 (t0) cc_final: 0.8719 (t0) REVERT: Y 192 MET cc_start: 0.7947 (ptt) cc_final: 0.7298 (ptt) REVERT: Z 42 TRP cc_start: 0.8334 (t-100) cc_final: 0.7555 (t-100) REVERT: Z 82 TYR cc_start: 0.8443 (m-80) cc_final: 0.8221 (m-80) REVERT: A 244 TYR cc_start: 0.8421 (p90) cc_final: 0.7882 (p90) REVERT: A 577 ASP cc_start: 0.8278 (t0) cc_final: 0.7907 (t0) REVERT: A 647 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7248 (pp) REVERT: A 757 MET cc_start: 0.8895 (tmm) cc_final: 0.8560 (tmm) REVERT: B 561 GLU cc_start: 0.8523 (pp20) cc_final: 0.8196 (pp20) REVERT: B 577 ASP cc_start: 0.8168 (t0) cc_final: 0.7902 (t0) REVERT: C 230 PHE cc_start: 0.8012 (t80) cc_final: 0.7769 (t80) REVERT: C 278 LEU cc_start: 0.7714 (tp) cc_final: 0.7427 (tt) REVERT: C 720 MET cc_start: 0.4629 (pmm) cc_final: 0.4289 (pmm) REVERT: D 52 PHE cc_start: 0.8355 (t80) cc_final: 0.8149 (t80) REVERT: D 109 LYS cc_start: 0.7898 (tptt) cc_final: 0.7546 (tptp) REVERT: D 304 ASP cc_start: 0.8824 (t0) cc_final: 0.8576 (p0) REVERT: D 313 ARG cc_start: 0.8151 (tpt170) cc_final: 0.7580 (tpt-90) REVERT: D 427 MET cc_start: 0.8668 (mmm) cc_final: 0.7706 (tpp) REVERT: D 720 MET cc_start: 0.1712 (ttt) cc_final: 0.0159 (ppp) REVERT: D 751 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8600 (p0) REVERT: D 757 MET cc_start: 0.8398 (ppp) cc_final: 0.8154 (ppp) REVERT: E 432 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8013 (mp) outliers start: 85 outliers final: 56 residues processed: 395 average time/residue: 0.4811 time to fit residues: 331.5741 Evaluate side-chains 384 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 324 time to evaluate : 5.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 130 LEU Chi-restraints excluded: chain X residue 139 ASP Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 172 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 498 optimal weight: 6.9990 chunk 58 optimal weight: 0.0870 chunk 294 optimal weight: 5.9990 chunk 377 optimal weight: 9.9990 chunk 292 optimal weight: 10.0000 chunk 434 optimal weight: 7.9990 chunk 288 optimal weight: 8.9990 chunk 514 optimal weight: 0.1980 chunk 322 optimal weight: 1.9990 chunk 313 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 overall best weight: 3.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 43646 Z= 0.263 Angle : 0.621 17.285 59066 Z= 0.308 Chirality : 0.044 0.189 6538 Planarity : 0.005 0.102 7734 Dihedral : 5.467 121.993 5943 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.65 % Favored : 90.89 % Rotamer: Outliers : 2.00 % Allowed : 15.40 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.12), residues: 5365 helix: 0.97 (0.11), residues: 2413 sheet: 0.22 (0.20), residues: 691 loop : -1.36 (0.14), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 551 HIS 0.004 0.001 HIS A 340 PHE 0.022 0.001 PHE E 773 TYR 0.015 0.001 TYR B 755 ARG 0.016 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 326 time to evaluate : 5.179 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: X 59 THR cc_start: 0.8747 (p) cc_final: 0.8500 (t) REVERT: X 116 MET cc_start: 0.8075 (mmm) cc_final: 0.7492 (tmm) REVERT: X 192 MET cc_start: 0.5866 (tmm) cc_final: 0.5508 (tmm) REVERT: Y 81 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8357 (tm-30) REVERT: Y 116 MET cc_start: 0.8687 (tmm) cc_final: 0.7949 (tmm) REVERT: Y 118 MET cc_start: 0.8660 (ptp) cc_final: 0.7754 (ptm) REVERT: Y 127 MET cc_start: 0.7762 (ppp) cc_final: 0.7503 (ppp) REVERT: Y 140 MET cc_start: 0.8356 (mtp) cc_final: 0.8122 (mtt) REVERT: Y 163 ASN cc_start: 0.9040 (t0) cc_final: 0.8742 (t0) REVERT: Y 192 MET cc_start: 0.7863 (ptt) cc_final: 0.7443 (ptt) REVERT: Z 99 LEU cc_start: 0.9263 (tt) cc_final: 0.9038 (tt) REVERT: A 244 TYR cc_start: 0.8438 (p90) cc_final: 0.7992 (p90) REVERT: A 577 ASP cc_start: 0.8212 (t0) cc_final: 0.7846 (t0) REVERT: A 647 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7251 (pp) REVERT: A 757 MET cc_start: 0.8890 (tmm) cc_final: 0.8541 (tmm) REVERT: B 561 GLU cc_start: 0.8529 (pp20) cc_final: 0.8196 (pp20) REVERT: B 577 ASP cc_start: 0.8173 (t0) cc_final: 0.7906 (t0) REVERT: C 84 MET cc_start: 0.7187 (tpt) cc_final: 0.6745 (tpt) REVERT: C 230 PHE cc_start: 0.8048 (t80) cc_final: 0.7782 (t80) REVERT: C 278 LEU cc_start: 0.7743 (tp) cc_final: 0.7447 (tt) REVERT: C 720 MET cc_start: 0.4584 (pmm) cc_final: 0.4260 (pmm) REVERT: D 52 PHE cc_start: 0.8401 (t80) cc_final: 0.8189 (t80) REVERT: D 102 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8124 (mp) REVERT: D 109 LYS cc_start: 0.7978 (tptt) cc_final: 0.7269 (tppt) REVERT: D 313 ARG cc_start: 0.8144 (tpt170) cc_final: 0.7571 (tpt-90) REVERT: D 427 MET cc_start: 0.8685 (mmm) cc_final: 0.7707 (tpp) REVERT: D 508 MET cc_start: 0.8341 (tpt) cc_final: 0.7962 (tpt) REVERT: D 720 MET cc_start: 0.1635 (ttt) cc_final: 0.0141 (ppp) REVERT: D 751 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8579 (p0) REVERT: D 757 MET cc_start: 0.8390 (ppp) cc_final: 0.8154 (ppp) REVERT: E 275 MET cc_start: 0.8378 (tpp) cc_final: 0.8174 (tpp) REVERT: E 432 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7979 (mp) REVERT: F 244 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7371 (p90) outliers start: 92 outliers final: 68 residues processed: 400 average time/residue: 0.4904 time to fit residues: 341.0204 Evaluate side-chains 395 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 322 time to evaluate : 5.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 139 ASP Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Y residue 101 MET Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Z residue 28 VAL Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 172 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 318 optimal weight: 10.0000 chunk 205 optimal weight: 0.4980 chunk 307 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 327 optimal weight: 9.9990 chunk 350 optimal weight: 0.9990 chunk 254 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 404 optimal weight: 0.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 135 GLN A 340 HIS ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 43646 Z= 0.169 Angle : 0.592 18.340 59066 Z= 0.289 Chirality : 0.043 0.194 6538 Planarity : 0.004 0.099 7734 Dihedral : 5.335 120.190 5943 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.24 % Favored : 91.30 % Rotamer: Outliers : 1.50 % Allowed : 16.20 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.12), residues: 5365 helix: 1.08 (0.11), residues: 2407 sheet: 0.37 (0.20), residues: 686 loop : -1.34 (0.14), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 454 HIS 0.002 0.000 HIS A 115 PHE 0.037 0.001 PHE Y 8 TYR 0.012 0.001 TYR F 244 ARG 0.007 0.000 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 345 time to evaluate : 5.450 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: W 150 PHE cc_start: 0.8261 (m-80) cc_final: 0.8054 (m-80) REVERT: X 59 THR cc_start: 0.8693 (p) cc_final: 0.8393 (t) REVERT: X 116 MET cc_start: 0.8064 (mmm) cc_final: 0.7464 (tmm) REVERT: X 130 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9135 (tt) REVERT: X 192 MET cc_start: 0.6045 (tmm) cc_final: 0.5689 (tmm) REVERT: Y 81 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8281 (tm-30) REVERT: Y 116 MET cc_start: 0.8732 (tmm) cc_final: 0.8030 (tmm) REVERT: Y 118 MET cc_start: 0.8612 (ptp) cc_final: 0.7634 (ptm) REVERT: Y 140 MET cc_start: 0.8334 (mtp) cc_final: 0.8092 (mtt) REVERT: Y 163 ASN cc_start: 0.9007 (t0) cc_final: 0.8716 (t0) REVERT: Y 192 MET cc_start: 0.7858 (ptt) cc_final: 0.7446 (ptt) REVERT: Z 44 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7661 (mm-30) REVERT: Z 99 LEU cc_start: 0.9227 (tt) cc_final: 0.9017 (tt) REVERT: A 244 TYR cc_start: 0.8358 (p90) cc_final: 0.7851 (p90) REVERT: A 577 ASP cc_start: 0.8176 (t0) cc_final: 0.7804 (t0) REVERT: A 757 MET cc_start: 0.8890 (tmm) cc_final: 0.8563 (tmm) REVERT: B 550 MET cc_start: 0.8776 (ptp) cc_final: 0.8284 (ptp) REVERT: B 561 GLU cc_start: 0.8559 (pp20) cc_final: 0.8291 (pp20) REVERT: B 577 ASP cc_start: 0.8092 (t0) cc_final: 0.7824 (t0) REVERT: C 230 PHE cc_start: 0.8042 (t80) cc_final: 0.7772 (t80) REVERT: C 278 LEU cc_start: 0.7544 (tp) cc_final: 0.7237 (tt) REVERT: C 720 MET cc_start: 0.4395 (pmm) cc_final: 0.4051 (pmm) REVERT: C 757 MET cc_start: 0.8774 (ptt) cc_final: 0.8566 (ptt) REVERT: D 52 PHE cc_start: 0.8411 (t80) cc_final: 0.8192 (t80) REVERT: D 109 LYS cc_start: 0.8005 (tptt) cc_final: 0.7257 (tppt) REVERT: D 313 ARG cc_start: 0.8095 (tpt170) cc_final: 0.7513 (tpt-90) REVERT: D 427 MET cc_start: 0.8664 (mmm) cc_final: 0.7648 (tpp) REVERT: D 720 MET cc_start: 0.1539 (ttt) cc_final: 0.1031 (mmm) REVERT: D 751 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8565 (p0) REVERT: D 757 MET cc_start: 0.8386 (ppp) cc_final: 0.8143 (ppp) REVERT: E 432 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7977 (mp) REVERT: F 195 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5904 (mp0) outliers start: 69 outliers final: 57 residues processed: 393 average time/residue: 0.5039 time to fit residues: 345.4013 Evaluate side-chains 392 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 331 time to evaluate : 4.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 130 LEU Chi-restraints excluded: chain X residue 139 ASP Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain X residue 174 LEU Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 101 MET Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 468 optimal weight: 10.0000 chunk 493 optimal weight: 4.9990 chunk 449 optimal weight: 9.9990 chunk 479 optimal weight: 0.2980 chunk 492 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 376 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 433 optimal weight: 0.2980 chunk 453 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 43646 Z= 0.224 Angle : 0.615 18.443 59066 Z= 0.301 Chirality : 0.043 0.192 6538 Planarity : 0.004 0.099 7734 Dihedral : 5.355 121.508 5943 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.74 % Favored : 90.81 % Rotamer: Outliers : 1.61 % Allowed : 16.20 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.12), residues: 5365 helix: 1.06 (0.11), residues: 2405 sheet: 0.31 (0.21), residues: 679 loop : -1.33 (0.14), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 551 HIS 0.002 0.001 HIS Z 181 PHE 0.036 0.001 PHE Y 8 TYR 0.011 0.001 TYR Z 183 ARG 0.006 0.000 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 329 time to evaluate : 5.054 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: X 59 THR cc_start: 0.8724 (p) cc_final: 0.8455 (t) REVERT: X 116 MET cc_start: 0.8075 (mmm) cc_final: 0.7406 (tmm) REVERT: X 130 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9145 (tt) REVERT: X 192 MET cc_start: 0.6078 (tmm) cc_final: 0.5708 (tmm) REVERT: Y 81 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8296 (tm-30) REVERT: Y 116 MET cc_start: 0.8717 (tmm) cc_final: 0.8010 (tmm) REVERT: Y 118 MET cc_start: 0.8651 (ptp) cc_final: 0.7754 (ptm) REVERT: Y 127 MET cc_start: 0.7800 (ppp) cc_final: 0.7488 (ppp) REVERT: Y 140 MET cc_start: 0.8348 (mtp) cc_final: 0.8113 (mtt) REVERT: Y 163 ASN cc_start: 0.9040 (t0) cc_final: 0.8762 (t0) REVERT: Z 44 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7667 (mm-30) REVERT: Z 99 LEU cc_start: 0.9257 (tt) cc_final: 0.9042 (tt) REVERT: A 244 TYR cc_start: 0.8430 (p90) cc_final: 0.7997 (p90) REVERT: A 577 ASP cc_start: 0.8125 (t0) cc_final: 0.7775 (t0) REVERT: A 757 MET cc_start: 0.8885 (tmm) cc_final: 0.8553 (tmm) REVERT: B 561 GLU cc_start: 0.8526 (pp20) cc_final: 0.8178 (pp20) REVERT: B 577 ASP cc_start: 0.8142 (t0) cc_final: 0.7871 (t0) REVERT: C 84 MET cc_start: 0.7270 (tpt) cc_final: 0.6870 (tpt) REVERT: C 110 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7556 (t80) REVERT: C 230 PHE cc_start: 0.8008 (t80) cc_final: 0.7726 (t80) REVERT: C 278 LEU cc_start: 0.7603 (tp) cc_final: 0.7311 (tt) REVERT: C 720 MET cc_start: 0.4559 (pmm) cc_final: 0.4209 (pmm) REVERT: C 757 MET cc_start: 0.8760 (ptt) cc_final: 0.8549 (ptt) REVERT: D 52 PHE cc_start: 0.8399 (t80) cc_final: 0.8173 (t80) REVERT: D 109 LYS cc_start: 0.8037 (tptt) cc_final: 0.7269 (tppt) REVERT: D 313 ARG cc_start: 0.8183 (tpt170) cc_final: 0.7609 (tpt-90) REVERT: D 427 MET cc_start: 0.8691 (mmm) cc_final: 0.7691 (tpp) REVERT: D 508 MET cc_start: 0.8324 (tpt) cc_final: 0.7987 (tpt) REVERT: D 720 MET cc_start: 0.1477 (ttt) cc_final: 0.0033 (ppp) REVERT: D 751 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8563 (p0) REVERT: D 757 MET cc_start: 0.8408 (ppp) cc_final: 0.8177 (ppp) REVERT: E 173 TYR cc_start: 0.7436 (p90) cc_final: 0.7029 (p90) REVERT: E 432 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7961 (mp) REVERT: F 195 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5911 (mp0) outliers start: 74 outliers final: 59 residues processed: 385 average time/residue: 0.4896 time to fit residues: 330.4685 Evaluate side-chains 389 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 325 time to evaluate : 4.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 130 LEU Chi-restraints excluded: chain X residue 139 ASP Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 101 MET Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Z residue 28 VAL Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 172 ASN Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 477 optimal weight: 6.9990 chunk 314 optimal weight: 20.0000 chunk 507 optimal weight: 0.0070 chunk 309 optimal weight: 0.7980 chunk 240 optimal weight: 6.9990 chunk 352 optimal weight: 0.0470 chunk 532 optimal weight: 9.9990 chunk 489 optimal weight: 1.9990 chunk 423 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 327 optimal weight: 5.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 43646 Z= 0.158 Angle : 0.600 18.822 59066 Z= 0.293 Chirality : 0.043 0.195 6538 Planarity : 0.004 0.096 7734 Dihedral : 5.276 119.570 5943 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.15 % Favored : 91.43 % Rotamer: Outliers : 1.30 % Allowed : 16.64 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.12), residues: 5365 helix: 1.12 (0.11), residues: 2403 sheet: 0.38 (0.20), residues: 699 loop : -1.33 (0.14), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 551 HIS 0.003 0.000 HIS A 115 PHE 0.016 0.001 PHE E 773 TYR 0.012 0.001 TYR A 203 ARG 0.006 0.000 ARG C 711 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 345 time to evaluate : 5.064 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: W 150 PHE cc_start: 0.8253 (m-80) cc_final: 0.8045 (m-80) REVERT: W 192 MET cc_start: 0.7243 (ppp) cc_final: 0.6798 (ppp) REVERT: X 116 MET cc_start: 0.8078 (mmm) cc_final: 0.7434 (tmm) REVERT: X 122 MET cc_start: 0.8533 (ttm) cc_final: 0.8152 (ttm) REVERT: X 130 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9140 (tt) REVERT: X 192 MET cc_start: 0.6038 (tmm) cc_final: 0.5677 (tmm) REVERT: Y 81 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8279 (tm-30) REVERT: Y 116 MET cc_start: 0.8723 (tmm) cc_final: 0.8030 (tmm) REVERT: Y 118 MET cc_start: 0.8596 (ptp) cc_final: 0.7720 (ptm) REVERT: Y 127 MET cc_start: 0.7812 (ppp) cc_final: 0.7538 (ppp) REVERT: Y 140 MET cc_start: 0.8312 (mtp) cc_final: 0.8084 (mtt) REVERT: Y 163 ASN cc_start: 0.8999 (t0) cc_final: 0.8707 (t0) REVERT: Z 44 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7629 (mm-30) REVERT: Z 99 LEU cc_start: 0.9233 (tt) cc_final: 0.9015 (tt) REVERT: Z 122 MET cc_start: 0.7682 (pmm) cc_final: 0.7448 (ptt) REVERT: A 244 TYR cc_start: 0.8347 (p90) cc_final: 0.7857 (p90) REVERT: A 577 ASP cc_start: 0.8161 (t0) cc_final: 0.7794 (t0) REVERT: A 757 MET cc_start: 0.8888 (tmm) cc_final: 0.8565 (tmm) REVERT: B 550 MET cc_start: 0.8772 (ptp) cc_final: 0.8564 (ptp) REVERT: B 561 GLU cc_start: 0.8579 (pp20) cc_final: 0.8311 (pp20) REVERT: B 577 ASP cc_start: 0.8039 (t0) cc_final: 0.7764 (t0) REVERT: C 84 MET cc_start: 0.7234 (tpt) cc_final: 0.6822 (tpt) REVERT: C 230 PHE cc_start: 0.8088 (t80) cc_final: 0.7814 (t80) REVERT: C 278 LEU cc_start: 0.7448 (tp) cc_final: 0.7147 (tt) REVERT: C 720 MET cc_start: 0.4329 (pmm) cc_final: 0.3950 (pmm) REVERT: C 757 MET cc_start: 0.8755 (ptt) cc_final: 0.8538 (ptt) REVERT: D 52 PHE cc_start: 0.8411 (t80) cc_final: 0.8146 (t80) REVERT: D 109 LYS cc_start: 0.8063 (tptt) cc_final: 0.7358 (tppt) REVERT: D 313 ARG cc_start: 0.8145 (tpt170) cc_final: 0.7574 (tpt-90) REVERT: D 427 MET cc_start: 0.8666 (mmm) cc_final: 0.7657 (tpp) REVERT: D 508 MET cc_start: 0.8240 (tpt) cc_final: 0.7793 (tpt) REVERT: D 751 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8555 (p0) REVERT: D 757 MET cc_start: 0.8411 (ppp) cc_final: 0.8157 (ppp) REVERT: E 432 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7967 (mp) REVERT: F 195 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6058 (mp0) outliers start: 60 outliers final: 53 residues processed: 388 average time/residue: 0.5019 time to fit residues: 338.2441 Evaluate side-chains 391 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 334 time to evaluate : 4.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 130 LEU Chi-restraints excluded: chain X residue 139 ASP Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 3 ASP Chi-restraints excluded: chain Y residue 101 MET Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 172 ASN Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 259 optimal weight: 0.9990 chunk 336 optimal weight: 0.9980 chunk 451 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 390 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 424 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 435 optimal weight: 0.3980 chunk 53 optimal weight: 0.0040 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.106279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.081303 restraints weight = 134138.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.081233 restraints weight = 81333.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.081935 restraints weight = 69124.412| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 43646 Z= 0.155 Angle : 0.601 18.906 59066 Z= 0.292 Chirality : 0.043 0.210 6538 Planarity : 0.004 0.092 7734 Dihedral : 5.177 118.488 5943 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.79 % Favored : 91.80 % Rotamer: Outliers : 1.33 % Allowed : 16.88 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.12), residues: 5365 helix: 1.16 (0.11), residues: 2409 sheet: 0.45 (0.20), residues: 706 loop : -1.34 (0.14), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 551 HIS 0.003 0.000 HIS A 115 PHE 0.016 0.001 PHE E 773 TYR 0.011 0.001 TYR F 244 ARG 0.007 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7611.56 seconds wall clock time: 139 minutes 57.88 seconds (8397.88 seconds total)