Starting phenix.real_space_refine on Fri Mar 22 23:52:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl7_24519/03_2024/7rl7_24519_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl7_24519/03_2024/7rl7_24519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl7_24519/03_2024/7rl7_24519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl7_24519/03_2024/7rl7_24519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl7_24519/03_2024/7rl7_24519_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl7_24519/03_2024/7rl7_24519_updated.pdb" } resolution = 3.0 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= 0.001 sd= 0.027 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 21882 2.51 5 N 6138 2.21 5 O 6690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 564": "OD1" <-> "OD2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 564": "OD1" <-> "OD2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 564": "OD1" <-> "OD2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D GLU 498": "OE1" <-> "OE2" Residue "D PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 564": "OD1" <-> "OD2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 470": "OE1" <-> "OE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "E PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 564": "OD1" <-> "OD2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F GLU 466": "OE1" <-> "OE2" Residue "F GLU 470": "OE1" <-> "OE2" Residue "F GLU 483": "OE1" <-> "OE2" Residue "F GLU 498": "OE1" <-> "OE2" Residue "F PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 564": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34950 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5761 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5761 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5761 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5761 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5761 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5761 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 18.57, per 1000 atoms: 0.53 Number of scatterers: 34950 At special positions: 0 Unit cell: (163.013, 175.163, 118.463, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 36 15.00 Mg 12 11.99 O 6690 8.00 N 6138 7.00 C 21882 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: 12.89 Conformation dependent library (CDL) restraints added in 7.3 seconds 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 12 sheets defined 39.3% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.32 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 43 through 46 No H-bonds generated for 'chain 'A' and resid 43 through 46' Processing helix chain 'A' and resid 86 through 89 Processing helix chain 'A' and resid 192 through 198 removed outlier: 3.514A pdb=" N GLU A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 198' 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 219 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.868A pdb=" N ASN A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 426 removed outlier: 3.582A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 458 removed outlier: 3.791A pdb=" N GLN A 458 " --> pdb=" O TRP A 454 " (cutoff:3.500A) 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: 4.544A 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 removed outlier: 3.851A pdb=" N LEU A 504 " --> pdb=" O ASP A 501 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS A 505 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 551 removed outlier: 3.564A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.569A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.153A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 660 removed outlier: 3.985A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 706 Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.588A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 removed outlier: 3.806A pdb=" N GLN A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 43 through 46 No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 86 through 89 Processing helix chain 'B' and resid 192 through 198 removed outlier: 3.514A pdb=" N GLU B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 198' 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 219 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 251 through 261 removed outlier: 3.868A pdb=" N ASN B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 319 through 334 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 426 removed outlier: 3.581A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 449 through 458 removed outlier: 3.791A pdb=" N GLN B 458 " --> pdb=" O TRP B 454 " (cutoff:3.500A) 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: 4.544A 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 removed outlier: 3.850A pdb=" N LEU B 504 " --> pdb=" O ASP B 501 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS B 505 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 551 removed outlier: 3.563A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 579 through 585 removed outlier: 3.568A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 610 removed outlier: 4.153A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 660 removed outlier: 3.986A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 706 Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.588A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 removed outlier: 3.806A pdb=" N GLN B 760 " --> pdb=" O GLU B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 43 through 46 No H-bonds generated for 'chain 'C' and resid 43 through 46' Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.515A pdb=" N GLU C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 192 through 198' 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 219 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 251 through 261 removed outlier: 3.868A pdb=" N ASN C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 295 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 319 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 374 through 385 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 426 removed outlier: 3.581A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 449 through 458 removed outlier: 3.791A pdb=" N GLN C 458 " --> pdb=" O TRP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 removed outlier: 4.544A 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 removed outlier: 3.850A pdb=" N LEU C 504 " --> pdb=" O ASP C 501 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS C 505 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 551 removed outlier: 3.564A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 568 Processing helix chain 'C' and resid 579 through 585 removed outlier: 3.569A pdb=" N ALA C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 610 removed outlier: 4.152A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 660 removed outlier: 3.986A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 706 Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.588A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 760 removed outlier: 3.805A pdb=" N GLN C 760 " --> pdb=" O GLU C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 765 No H-bonds generated for 'chain 'C' and resid 763 through 765' Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 43 through 46 No H-bonds generated for 'chain 'D' and resid 43 through 46' Processing helix chain 'D' and resid 86 through 89 Processing helix chain 'D' and resid 192 through 198 removed outlier: 3.514A pdb=" N GLU D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 192 through 198' 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 219 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 251 through 261 removed outlier: 3.869A pdb=" N ASN D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 295 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 319 through 334 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 374 through 385 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 426 removed outlier: 3.581A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.791A pdb=" N GLN D 458 " --> pdb=" O TRP D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 498 removed outlier: 4.544A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 506 removed outlier: 3.850A pdb=" N LEU D 504 " --> pdb=" O ASP D 501 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS D 505 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 551 removed outlier: 3.563A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 568 Processing helix chain 'D' and resid 579 through 585 removed outlier: 3.569A pdb=" N ALA D 585 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 610 removed outlier: 4.153A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 660 removed outlier: 3.986A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 706 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.588A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 760 removed outlier: 3.806A pdb=" N GLN D 760 " --> pdb=" O GLU D 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 765 No H-bonds generated for 'chain 'D' and resid 763 through 765' Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 43 through 46 No H-bonds generated for 'chain 'E' and resid 43 through 46' Processing helix chain 'E' and resid 86 through 89 Processing helix chain 'E' and resid 192 through 198 removed outlier: 3.514A pdb=" N GLU E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 192 through 198' 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 219 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 251 through 261 removed outlier: 3.868A pdb=" N ASN E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' 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 426 removed outlier: 3.581A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 442 No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'E' and resid 449 through 458 removed outlier: 3.791A pdb=" N GLN E 458 " --> pdb=" O TRP E 454 " (cutoff:3.500A) 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 498 removed outlier: 4.544A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 506 removed outlier: 3.851A pdb=" N LEU E 504 " --> pdb=" O ASP E 501 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS E 505 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 551 removed outlier: 3.563A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 568 Processing helix chain 'E' and resid 579 through 585 removed outlier: 3.569A pdb=" N ALA E 585 " --> pdb=" O SER E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 610 removed outlier: 4.153A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 660 removed outlier: 3.987A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 706 Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.588A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 760 removed outlier: 3.805A pdb=" N GLN E 760 " --> pdb=" O GLU E 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 765 No H-bonds generated for 'chain 'E' and resid 763 through 765' Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 43 through 46 No H-bonds generated for 'chain 'F' and resid 43 through 46' Processing helix chain 'F' and resid 86 through 89 Processing helix chain 'F' and resid 192 through 198 removed outlier: 3.514A pdb=" N GLU F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 192 through 198' 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 219 Processing helix chain 'F' and resid 221 through 225 Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 251 through 261 removed outlier: 3.868A pdb=" N ASN F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 374 through 385 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 426 removed outlier: 3.581A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 449 through 458 removed outlier: 3.791A pdb=" N GLN F 458 " --> pdb=" O TRP F 454 " (cutoff:3.500A) 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: 4.544A 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 removed outlier: 3.850A pdb=" N LEU F 504 " --> pdb=" O ASP F 501 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS F 505 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 551 removed outlier: 3.563A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 568 Processing helix chain 'F' and resid 579 through 585 removed outlier: 3.569A pdb=" N ALA F 585 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 610 removed outlier: 4.152A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 removed outlier: 3.986A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 706 Processing helix chain 'F' and resid 733 through 741 removed outlier: 3.588A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 760 removed outlier: 3.805A pdb=" N GLN F 760 " --> pdb=" O GLU F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 763 through 765 No H-bonds generated for 'chain 'F' and resid 763 through 765' Processing sheet with id= A, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.397A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.602A pdb=" N GLY A 518 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 365 through 368 removed outlier: 8.396A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.600A pdb=" N GLY B 518 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.396A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.602A pdb=" N GLY C 518 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.397A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.601A pdb=" N GLY D 518 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.396A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.601A pdb=" N GLY E 518 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 365 through 368 removed outlier: 8.396A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.601A pdb=" N GLY F 518 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) 930 hydrogen bonds defined for protein. 2682 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: 11.20 Time building geometry restraints manager: 14.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 12100 1.37 - 1.52: 9725 1.52 - 1.66: 13401 1.66 - 1.80: 191 1.80 - 1.95: 109 Bond restraints: 35526 Sorted by residual: bond pdb=" CA PHE F 163 " pdb=" CB PHE F 163 " ideal model delta sigma weight residual 1.533 1.562 -0.029 1.72e-02 3.38e+03 2.77e+00 bond pdb=" CA PHE A 163 " pdb=" CB PHE A 163 " ideal model delta sigma weight residual 1.533 1.562 -0.028 1.72e-02 3.38e+03 2.72e+00 bond pdb=" CA PHE E 163 " pdb=" CB PHE E 163 " ideal model delta sigma weight residual 1.533 1.562 -0.028 1.72e-02 3.38e+03 2.71e+00 bond pdb=" CA PHE D 163 " pdb=" CB PHE D 163 " ideal model delta sigma weight residual 1.533 1.561 -0.028 1.72e-02 3.38e+03 2.66e+00 bond pdb=" CA PHE B 163 " pdb=" CB PHE B 163 " ideal model delta sigma weight residual 1.533 1.561 -0.028 1.72e-02 3.38e+03 2.65e+00 ... (remaining 35521 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.78: 851 105.78 - 112.87: 19270 112.87 - 119.95: 12814 119.95 - 127.03: 14753 127.03 - 134.12: 372 Bond angle restraints: 48060 Sorted by residual: angle pdb=" N VAL B 94 " pdb=" CA VAL B 94 " pdb=" C VAL B 94 " ideal model delta sigma weight residual 113.71 109.77 3.94 9.50e-01 1.11e+00 1.72e+01 angle pdb=" CB MET F 678 " pdb=" CG MET F 678 " pdb=" SD MET F 678 " ideal model delta sigma weight residual 112.70 123.95 -11.25 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CB MET D 678 " pdb=" CG MET D 678 " pdb=" SD MET D 678 " ideal model delta sigma weight residual 112.70 123.94 -11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CB MET E 678 " pdb=" CG MET E 678 " pdb=" SD MET E 678 " ideal model delta sigma weight residual 112.70 123.94 -11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CB MET C 678 " pdb=" CG MET C 678 " pdb=" SD MET C 678 " ideal model delta sigma weight residual 112.70 123.92 -11.22 3.00e+00 1.11e-01 1.40e+01 ... (remaining 48055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 18948 16.04 - 32.09: 2178 32.09 - 48.13: 726 48.13 - 64.17: 156 64.17 - 80.22: 42 Dihedral angle restraints: 22050 sinusoidal: 9330 harmonic: 12720 Sorted by residual: dihedral pdb=" CA ARG B 599 " pdb=" C ARG B 599 " pdb=" N VAL B 600 " pdb=" CA VAL B 600 " ideal model delta harmonic sigma weight residual -180.00 -164.48 -15.52 0 5.00e+00 4.00e-02 9.64e+00 dihedral pdb=" CA ARG D 599 " pdb=" C ARG D 599 " pdb=" N VAL D 600 " pdb=" CA VAL D 600 " ideal model delta harmonic sigma weight residual -180.00 -164.50 -15.50 0 5.00e+00 4.00e-02 9.61e+00 dihedral pdb=" CA ARG E 599 " pdb=" C ARG E 599 " pdb=" N VAL E 600 " pdb=" CA VAL E 600 " ideal model delta harmonic sigma weight residual -180.00 -164.50 -15.50 0 5.00e+00 4.00e-02 9.61e+00 ... (remaining 22047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3739 0.040 - 0.081: 1228 0.081 - 0.121: 421 0.121 - 0.162: 42 0.162 - 0.202: 6 Chirality restraints: 5436 Sorted by residual: chirality pdb=" CB ILE A 590 " pdb=" CA ILE A 590 " pdb=" CG1 ILE A 590 " pdb=" CG2 ILE A 590 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE F 590 " pdb=" CA ILE F 590 " pdb=" CG1 ILE F 590 " pdb=" CG2 ILE F 590 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE E 590 " pdb=" CA ILE E 590 " pdb=" CG1 ILE E 590 " pdb=" CG2 ILE E 590 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 5433 not shown) Planarity restraints: 6288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 297 " -0.044 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PRO D 298 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 298 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 298 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 297 " 0.044 5.00e-02 4.00e+02 6.79e-02 7.39e+00 pdb=" N PRO B 298 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 298 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 298 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 297 " -0.044 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO E 298 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 298 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 298 " -0.038 5.00e-02 4.00e+02 ... (remaining 6285 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 527 2.63 - 3.19: 31017 3.19 - 3.76: 54671 3.76 - 4.33: 74000 4.33 - 4.90: 118654 Nonbonded interactions: 278869 Sorted by model distance: nonbonded pdb=" OG1 THR F 252 " pdb="MG MG F 903 " model vdw 2.057 2.170 nonbonded pdb=" OG1 THR C 252 " pdb="MG MG C 903 " model vdw 2.058 2.170 nonbonded pdb=" OG1 THR B 252 " pdb="MG MG B 903 " model vdw 2.058 2.170 nonbonded pdb=" OG1 THR A 252 " pdb="MG MG A 903 " model vdw 2.058 2.170 nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 903 " model vdw 2.059 2.170 ... (remaining 278864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.620 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 90.540 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.003 0.035 35526 Z= 0.194 Angle : 0.683 11.251 48060 Z= 0.378 Chirality : 0.044 0.202 5436 Planarity : 0.003 0.068 6288 Dihedral : 15.608 80.215 13806 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 21.35 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 4398 helix: 0.34 (0.13), residues: 1746 sheet: 0.29 (0.27), residues: 372 loop : -1.84 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP E 551 HIS 0.003 0.001 HIS F 317 PHE 0.014 0.001 PHE D 758 TYR 0.008 0.001 TYR F 755 ARG 0.006 0.000 ARG C 424 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 4.249 Fit side-chains REVERT: A 508 MET cc_start: 0.8280 (mmt) cc_final: 0.8008 (mmt) REVERT: D 163 PHE cc_start: 0.7301 (t80) cc_final: 0.7074 (t80) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 1.3863 time to fit residues: 350.6680 Evaluate side-chains 184 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 6.9990 chunk 331 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 343 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 chunk 255 optimal weight: 3.9990 chunk 397 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 406 HIS D 406 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN F 327 GLN F 406 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 35526 Z= 0.297 Angle : 0.572 7.640 48060 Z= 0.279 Chirality : 0.045 0.170 5436 Planarity : 0.003 0.027 6288 Dihedral : 6.798 53.394 5022 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.09 % Allowed : 19.12 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 4398 helix: 0.66 (0.13), residues: 1722 sheet: 0.04 (0.26), residues: 390 loop : -1.63 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 551 HIS 0.003 0.001 HIS E 384 PHE 0.018 0.001 PHE F 163 TYR 0.008 0.001 TYR B 755 ARG 0.004 0.000 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 183 time to evaluate : 3.927 Fit side-chains REVERT: A 158 MET cc_start: 0.5038 (pmm) cc_final: 0.4783 (pmm) REVERT: A 508 MET cc_start: 0.8284 (mmt) cc_final: 0.7987 (mmt) REVERT: B 158 MET cc_start: 0.5783 (OUTLIER) cc_final: 0.5311 (ppp) REVERT: B 437 ILE cc_start: 0.5826 (OUTLIER) cc_final: 0.5544 (mp) REVERT: C 158 MET cc_start: 0.4404 (pmm) cc_final: 0.4132 (pmm) REVERT: C 437 ILE cc_start: 0.6202 (OUTLIER) cc_final: 0.5980 (mp) REVERT: D 163 PHE cc_start: 0.7363 (t80) cc_final: 0.6870 (t80) REVERT: E 158 MET cc_start: 0.5777 (OUTLIER) cc_final: 0.5292 (ppp) REVERT: F 46 MET cc_start: 0.6180 (tpt) cc_final: 0.5953 (tpt) REVERT: F 158 MET cc_start: 0.4806 (pmm) cc_final: 0.4551 (pmm) REVERT: F 219 MET cc_start: 0.8939 (ptp) cc_final: 0.8527 (ptp) outliers start: 116 outliers final: 25 residues processed: 284 average time/residue: 1.2135 time to fit residues: 428.5767 Evaluate side-chains 201 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 468 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 270 optimal weight: 6.9990 chunk 109 optimal weight: 0.1980 chunk 398 optimal weight: 0.9990 chunk 430 optimal weight: 0.9990 chunk 354 optimal weight: 0.8980 chunk 395 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 319 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 296 ASN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN C 296 ASN D 296 ASN E 296 ASN E 406 HIS F 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35526 Z= 0.152 Angle : 0.498 7.953 48060 Z= 0.241 Chirality : 0.043 0.142 5436 Planarity : 0.003 0.028 6288 Dihedral : 6.475 55.417 5022 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.18 % Allowed : 20.05 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 4398 helix: 0.78 (0.13), residues: 1752 sheet: 0.10 (0.26), residues: 390 loop : -1.62 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 551 HIS 0.002 0.000 HIS F 317 PHE 0.014 0.001 PHE D 742 TYR 0.005 0.001 TYR D 173 ARG 0.002 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 174 time to evaluate : 4.233 Fit side-chains REVERT: A 59 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7994 (tm) REVERT: A 158 MET cc_start: 0.5155 (pmm) cc_final: 0.4864 (pmm) REVERT: A 163 PHE cc_start: 0.7189 (t80) cc_final: 0.6973 (t80) REVERT: A 173 TYR cc_start: 0.4736 (OUTLIER) cc_final: 0.3133 (p90) REVERT: A 508 MET cc_start: 0.8208 (mmt) cc_final: 0.7967 (mmt) REVERT: B 158 MET cc_start: 0.5641 (OUTLIER) cc_final: 0.5364 (ppp) REVERT: C 437 ILE cc_start: 0.6323 (OUTLIER) cc_final: 0.6119 (mp) REVERT: D 59 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8069 (tm) REVERT: D 163 PHE cc_start: 0.7294 (t80) cc_final: 0.6834 (t80) REVERT: D 173 TYR cc_start: 0.4815 (OUTLIER) cc_final: 0.3056 (p90) REVERT: D 437 ILE cc_start: 0.5955 (OUTLIER) cc_final: 0.5708 (mp) REVERT: D 758 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8053 (t80) REVERT: E 158 MET cc_start: 0.5584 (OUTLIER) cc_final: 0.5288 (ppp) REVERT: F 46 MET cc_start: 0.6175 (tpt) cc_final: 0.5918 (tpt) REVERT: F 158 MET cc_start: 0.4766 (pmm) cc_final: 0.4412 (pmm) REVERT: F 163 PHE cc_start: 0.7231 (t80) cc_final: 0.6994 (t80) REVERT: F 437 ILE cc_start: 0.6119 (OUTLIER) cc_final: 0.5892 (mp) outliers start: 82 outliers final: 30 residues processed: 240 average time/residue: 1.2923 time to fit residues: 382.3560 Evaluate side-chains 209 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 758 PHE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 0.0870 chunk 299 optimal weight: 8.9990 chunk 206 optimal weight: 0.1980 chunk 44 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 267 optimal weight: 0.9990 chunk 399 optimal weight: 1.9990 chunk 423 optimal weight: 9.9990 chunk 208 optimal weight: 0.6980 chunk 379 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN B 43 GLN B 406 HIS E 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35526 Z= 0.147 Angle : 0.490 8.680 48060 Z= 0.232 Chirality : 0.042 0.136 5436 Planarity : 0.002 0.033 6288 Dihedral : 6.262 57.335 5022 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.33 % Allowed : 19.52 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.13), residues: 4398 helix: 0.96 (0.13), residues: 1758 sheet: 0.26 (0.25), residues: 396 loop : -1.60 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 551 HIS 0.002 0.000 HIS E 406 PHE 0.011 0.001 PHE C 302 TYR 0.004 0.001 TYR D 517 ARG 0.002 0.000 ARG D 638 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 173 time to evaluate : 4.117 Fit side-chains REVERT: A 59 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8120 (tm) REVERT: A 158 MET cc_start: 0.5213 (pmm) cc_final: 0.4760 (pmm) REVERT: A 163 PHE cc_start: 0.7149 (t80) cc_final: 0.6861 (t80) REVERT: A 173 TYR cc_start: 0.4518 (OUTLIER) cc_final: 0.2866 (p90) REVERT: A 281 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7463 (tp30) REVERT: A 508 MET cc_start: 0.8152 (mmt) cc_final: 0.7916 (mmt) REVERT: A 758 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.7956 (t80) REVERT: B 158 MET cc_start: 0.5808 (OUTLIER) cc_final: 0.5381 (pmm) REVERT: C 550 MET cc_start: 0.7405 (ptp) cc_final: 0.7171 (ptm) REVERT: D 59 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8074 (tm) REVERT: D 163 PHE cc_start: 0.7274 (t80) cc_final: 0.6812 (t80) REVERT: D 173 TYR cc_start: 0.4518 (OUTLIER) cc_final: 0.2918 (p90) REVERT: D 508 MET cc_start: 0.7940 (mmt) cc_final: 0.7679 (mmt) REVERT: D 758 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.7877 (t80) REVERT: E 158 MET cc_start: 0.5527 (OUTLIER) cc_final: 0.5155 (ppp) REVERT: E 281 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7525 (tp30) REVERT: F 46 MET cc_start: 0.6212 (tpt) cc_final: 0.5945 (tpt) REVERT: F 158 MET cc_start: 0.4881 (pmm) cc_final: 0.4595 (pmm) REVERT: F 163 PHE cc_start: 0.7236 (t80) cc_final: 0.7021 (t80) REVERT: F 219 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8582 (ptp) REVERT: F 550 MET cc_start: 0.7425 (ptp) cc_final: 0.7180 (ptm) outliers start: 125 outliers final: 41 residues processed: 272 average time/residue: 1.1917 time to fit residues: 404.3806 Evaluate side-chains 225 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 173 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 758 PHE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 562 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 chunk 6 optimal weight: 50.0000 chunk 315 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 361 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 380 optimal weight: 30.0000 chunk 106 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 327 GLN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 35526 Z= 0.382 Angle : 0.614 9.075 48060 Z= 0.295 Chirality : 0.046 0.149 5436 Planarity : 0.003 0.034 6288 Dihedral : 7.086 59.095 5022 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.96 % Allowed : 20.23 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.13), residues: 4398 helix: 0.82 (0.13), residues: 1782 sheet: 0.75 (0.30), residues: 318 loop : -1.47 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP E 551 HIS 0.006 0.001 HIS E 406 PHE 0.020 0.002 PHE D 742 TYR 0.008 0.001 TYR F 173 ARG 0.005 0.001 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 178 time to evaluate : 4.195 Fit side-chains REVERT: A 59 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7990 (tm) REVERT: A 158 MET cc_start: 0.4901 (pmm) cc_final: 0.4464 (pmm) REVERT: A 281 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7487 (tp30) REVERT: A 508 MET cc_start: 0.8410 (mmt) cc_final: 0.8052 (mmt) REVERT: B 158 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.4955 (pmm) REVERT: C 550 MET cc_start: 0.7557 (ptp) cc_final: 0.7323 (ptm) REVERT: D 59 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8084 (tm) REVERT: D 163 PHE cc_start: 0.6890 (t80) cc_final: 0.6684 (t80) REVERT: D 508 MET cc_start: 0.8202 (mmt) cc_final: 0.7967 (mmt) REVERT: E 158 MET cc_start: 0.5614 (OUTLIER) cc_final: 0.5346 (ppp) REVERT: E 281 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7533 (tp30) REVERT: F 46 MET cc_start: 0.6141 (tpt) cc_final: 0.5873 (tpt) REVERT: F 158 MET cc_start: 0.5030 (pmm) cc_final: 0.4699 (pmm) REVERT: F 550 MET cc_start: 0.7622 (ptp) cc_final: 0.7407 (ptm) outliers start: 111 outliers final: 55 residues processed: 261 average time/residue: 1.2967 time to fit residues: 415.9390 Evaluate side-chains 236 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 175 time to evaluate : 3.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 1.9990 chunk 381 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 423 optimal weight: 20.0000 chunk 351 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 222 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35526 Z= 0.185 Angle : 0.518 10.123 48060 Z= 0.245 Chirality : 0.043 0.168 5436 Planarity : 0.003 0.042 6288 Dihedral : 6.761 58.296 5022 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.58 % Allowed : 20.95 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 4398 helix: 0.96 (0.13), residues: 1782 sheet: 0.74 (0.30), residues: 318 loop : -1.41 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 551 HIS 0.003 0.000 HIS B 226 PHE 0.013 0.001 PHE A 302 TYR 0.005 0.001 TYR A 517 ARG 0.003 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 174 time to evaluate : 4.319 Fit side-chains REVERT: A 59 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8006 (tm) REVERT: A 158 MET cc_start: 0.4971 (pmm) cc_final: 0.4497 (pmm) REVERT: A 508 MET cc_start: 0.8314 (mmt) cc_final: 0.8052 (mmt) REVERT: B 158 MET cc_start: 0.5470 (OUTLIER) cc_final: 0.5055 (ppp) REVERT: C 550 MET cc_start: 0.7623 (ptp) cc_final: 0.7412 (ptm) REVERT: D 59 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8075 (tm) REVERT: E 158 MET cc_start: 0.5664 (OUTLIER) cc_final: 0.5270 (ppp) REVERT: E 163 PHE cc_start: 0.6485 (t80) cc_final: 0.6252 (t80) REVERT: E 281 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: F 46 MET cc_start: 0.6187 (tpt) cc_final: 0.5914 (tpt) REVERT: F 158 MET cc_start: 0.5122 (pmm) cc_final: 0.4907 (pmm) REVERT: F 219 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8664 (ptp) REVERT: F 550 MET cc_start: 0.7626 (ptp) cc_final: 0.7416 (ptm) outliers start: 97 outliers final: 50 residues processed: 249 average time/residue: 1.2682 time to fit residues: 393.2934 Evaluate side-chains 230 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 174 time to evaluate : 3.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 241 optimal weight: 0.0570 chunk 309 optimal weight: 0.0470 chunk 239 optimal weight: 1.9990 chunk 356 optimal weight: 8.9990 chunk 236 optimal weight: 0.0010 chunk 422 optimal weight: 8.9990 chunk 264 optimal weight: 8.9990 chunk 257 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 overall best weight: 0.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35526 Z= 0.140 Angle : 0.512 11.195 48060 Z= 0.239 Chirality : 0.042 0.159 5436 Planarity : 0.003 0.036 6288 Dihedral : 6.371 58.461 5022 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.29 % Allowed : 21.57 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.13), residues: 4398 helix: 1.08 (0.13), residues: 1788 sheet: 0.45 (0.27), residues: 390 loop : -1.40 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP F 551 HIS 0.002 0.000 HIS F 317 PHE 0.023 0.001 PHE A 742 TYR 0.006 0.001 TYR D 517 ARG 0.004 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 180 time to evaluate : 4.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8163 (tm) REVERT: A 158 MET cc_start: 0.5184 (pmm) cc_final: 0.4694 (pmm) REVERT: A 508 MET cc_start: 0.8215 (mmt) cc_final: 0.7897 (mmt) REVERT: A 550 MET cc_start: 0.7475 (ptp) cc_final: 0.7248 (ptm) REVERT: B 158 MET cc_start: 0.5571 (OUTLIER) cc_final: 0.5047 (pmm) REVERT: C 158 MET cc_start: 0.5013 (pmm) cc_final: 0.4663 (pmm) REVERT: C 550 MET cc_start: 0.7574 (ptp) cc_final: 0.7320 (ptm) REVERT: D 59 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8062 (tm) REVERT: D 163 PHE cc_start: 0.7357 (t80) cc_final: 0.6959 (t80) REVERT: D 550 MET cc_start: 0.7447 (ptp) cc_final: 0.7189 (ptm) REVERT: E 158 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.5181 (pmm) REVERT: F 46 MET cc_start: 0.6315 (tpt) cc_final: 0.6045 (tpt) REVERT: F 158 MET cc_start: 0.5094 (pmm) cc_final: 0.4716 (pmm) REVERT: F 402 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8655 (mm-30) REVERT: F 454 TRP cc_start: 0.8846 (t-100) cc_final: 0.8477 (t-100) REVERT: F 458 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: F 550 MET cc_start: 0.7552 (ptp) cc_final: 0.7325 (ptm) outliers start: 86 outliers final: 50 residues processed: 240 average time/residue: 1.2791 time to fit residues: 379.3672 Evaluate side-chains 230 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 175 time to evaluate : 4.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 551 TRP Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 458 GLN Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 252 optimal weight: 0.0970 chunk 127 optimal weight: 0.0030 chunk 82 optimal weight: 40.0000 chunk 81 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 287 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 331 optimal weight: 9.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35526 Z= 0.137 Angle : 0.507 12.240 48060 Z= 0.236 Chirality : 0.042 0.149 5436 Planarity : 0.003 0.037 6288 Dihedral : 6.227 58.013 5022 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.00 % Allowed : 21.73 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 4398 helix: 1.20 (0.13), residues: 1752 sheet: 0.53 (0.27), residues: 390 loop : -1.42 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 454 HIS 0.001 0.000 HIS B 317 PHE 0.010 0.001 PHE C 302 TYR 0.005 0.001 TYR E 517 ARG 0.006 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 179 time to evaluate : 3.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8172 (tm) REVERT: A 158 MET cc_start: 0.5136 (pmm) cc_final: 0.4623 (pmm) REVERT: A 508 MET cc_start: 0.8181 (mmt) cc_final: 0.7882 (mmt) REVERT: A 550 MET cc_start: 0.7405 (ptp) cc_final: 0.7173 (ptm) REVERT: B 158 MET cc_start: 0.5456 (OUTLIER) cc_final: 0.4781 (pmm) REVERT: C 158 MET cc_start: 0.5047 (pmm) cc_final: 0.4648 (pmm) REVERT: C 550 MET cc_start: 0.7483 (ptp) cc_final: 0.7228 (ptm) REVERT: D 59 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8076 (tm) REVERT: D 163 PHE cc_start: 0.7198 (t80) cc_final: 0.6798 (t80) REVERT: D 550 MET cc_start: 0.7390 (ptp) cc_final: 0.7123 (ptm) REVERT: E 158 MET cc_start: 0.5720 (OUTLIER) cc_final: 0.5337 (ppp) REVERT: F 46 MET cc_start: 0.6316 (tpt) cc_final: 0.6043 (tpt) REVERT: F 158 MET cc_start: 0.5158 (pmm) cc_final: 0.4763 (pmm) REVERT: F 550 MET cc_start: 0.7487 (ptp) cc_final: 0.7229 (ptm) outliers start: 75 outliers final: 51 residues processed: 235 average time/residue: 1.2833 time to fit residues: 373.4301 Evaluate side-chains 231 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 176 time to evaluate : 4.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 551 TRP Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 551 TRP Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 1.9990 chunk 404 optimal weight: 9.9990 chunk 368 optimal weight: 20.0000 chunk 393 optimal weight: 0.2980 chunk 236 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 308 optimal weight: 40.0000 chunk 120 optimal weight: 0.7980 chunk 355 optimal weight: 0.0670 chunk 372 optimal weight: 9.9990 chunk 392 optimal weight: 0.9980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35526 Z= 0.147 Angle : 0.520 12.907 48060 Z= 0.240 Chirality : 0.042 0.147 5436 Planarity : 0.003 0.038 6288 Dihedral : 6.177 57.399 5022 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.65 % Allowed : 22.07 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.13), residues: 4398 helix: 1.17 (0.13), residues: 1788 sheet: 0.56 (0.27), residues: 390 loop : -1.35 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP F 454 HIS 0.001 0.000 HIS F 317 PHE 0.017 0.001 PHE A 742 TYR 0.004 0.001 TYR A 517 ARG 0.006 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 175 time to evaluate : 3.732 Fit side-chains REVERT: A 59 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8070 (tm) REVERT: A 158 MET cc_start: 0.5277 (pmm) cc_final: 0.4769 (pmm) REVERT: A 550 MET cc_start: 0.7422 (ptp) cc_final: 0.7177 (ptm) REVERT: B 158 MET cc_start: 0.5543 (OUTLIER) cc_final: 0.4952 (pmm) REVERT: C 158 MET cc_start: 0.5159 (pmm) cc_final: 0.4725 (pmm) REVERT: C 550 MET cc_start: 0.7480 (ptp) cc_final: 0.7143 (ptm) REVERT: D 59 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8097 (tm) REVERT: D 163 PHE cc_start: 0.7155 (t80) cc_final: 0.6815 (t80) REVERT: D 550 MET cc_start: 0.7355 (ptp) cc_final: 0.7036 (ptm) REVERT: E 158 MET cc_start: 0.5808 (OUTLIER) cc_final: 0.5467 (ppp) REVERT: E 442 MET cc_start: 0.8854 (mmt) cc_final: 0.8623 (mmm) REVERT: F 46 MET cc_start: 0.6418 (tpt) cc_final: 0.6051 (tpt) REVERT: F 158 MET cc_start: 0.5233 (pmm) cc_final: 0.4830 (pmm) REVERT: F 550 MET cc_start: 0.7503 (ptp) cc_final: 0.7192 (ptm) outliers start: 62 outliers final: 48 residues processed: 223 average time/residue: 1.3097 time to fit residues: 361.8636 Evaluate side-chains 228 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 176 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 9.9990 chunk 415 optimal weight: 0.9990 chunk 253 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 chunk 436 optimal weight: 9.9990 chunk 401 optimal weight: 0.7980 chunk 347 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 268 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35526 Z= 0.211 Angle : 0.545 13.098 48060 Z= 0.253 Chirality : 0.043 0.181 5436 Planarity : 0.003 0.037 6288 Dihedral : 6.396 57.050 5022 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.68 % Allowed : 22.04 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.13), residues: 4398 helix: 1.12 (0.13), residues: 1806 sheet: 0.55 (0.27), residues: 390 loop : -1.24 (0.14), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP A 551 HIS 0.002 0.000 HIS A 384 PHE 0.011 0.001 PHE E 302 TYR 0.004 0.001 TYR A 173 ARG 0.006 0.000 ARG B 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 180 time to evaluate : 4.209 Fit side-chains REVERT: A 59 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8127 (tm) REVERT: A 158 MET cc_start: 0.5338 (pmm) cc_final: 0.5002 (pmm) REVERT: A 550 MET cc_start: 0.7374 (ptp) cc_final: 0.7118 (ptm) REVERT: B 158 MET cc_start: 0.5622 (OUTLIER) cc_final: 0.4991 (pmm) REVERT: C 158 MET cc_start: 0.4992 (pmm) cc_final: 0.4538 (pmm) REVERT: C 550 MET cc_start: 0.7445 (ptp) cc_final: 0.7079 (ptm) REVERT: D 59 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8139 (tm) REVERT: D 163 PHE cc_start: 0.7134 (t80) cc_final: 0.6784 (t80) REVERT: D 550 MET cc_start: 0.7335 (ptp) cc_final: 0.7027 (ptm) REVERT: E 158 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.5339 (ppp) REVERT: E 442 MET cc_start: 0.8890 (mmt) cc_final: 0.8632 (mmm) REVERT: F 46 MET cc_start: 0.6804 (tpt) cc_final: 0.6572 (tpt) REVERT: F 158 MET cc_start: 0.5150 (pmm) cc_final: 0.4897 (pmm) REVERT: F 550 MET cc_start: 0.7479 (ptp) cc_final: 0.7142 (ptm) outliers start: 63 outliers final: 52 residues processed: 225 average time/residue: 1.2942 time to fit residues: 358.0025 Evaluate side-chains 233 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 177 time to evaluate : 4.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 10.0000 chunk 370 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 320 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 348 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 357 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.123586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.074303 restraints weight = 69733.527| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.88 r_work: 0.2728 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35526 Z= 0.179 Angle : 0.550 13.120 48060 Z= 0.253 Chirality : 0.043 0.154 5436 Planarity : 0.003 0.037 6288 Dihedral : 6.402 57.615 5022 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.65 % Allowed : 22.18 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 4398 helix: 1.01 (0.13), residues: 1848 sheet: 0.54 (0.27), residues: 390 loop : -1.29 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP B 551 HIS 0.002 0.000 HIS D 384 PHE 0.018 0.001 PHE D 742 TYR 0.005 0.001 TYR A 517 ARG 0.005 0.000 ARG B 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8116.67 seconds wall clock time: 146 minutes 35.25 seconds (8795.25 seconds total)