Starting phenix.real_space_refine on Fri Oct 11 10:32:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaw_36136/10_2024/8jaw_36136_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaw_36136/10_2024/8jaw_36136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaw_36136/10_2024/8jaw_36136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaw_36136/10_2024/8jaw_36136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaw_36136/10_2024/8jaw_36136_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaw_36136/10_2024/8jaw_36136_neut_trim.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.062 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: 4 Type Number sf(0) Gaussians S 312 5.16 5 C 34944 2.51 5 N 9714 2.21 5 O 10434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 267 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 55404 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5065 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 622} Chain breaks: 2 Chain: "B" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "C" Number of atoms: 5065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5065 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 622} Chain breaks: 2 Chain: "D" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "E" Number of atoms: 5065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5065 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 622} Chain breaks: 2 Chain: "F" Number of atoms: 5065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5065 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 622} Chain breaks: 2 Chain: "G" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "H" Number of atoms: 5065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5065 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 622} Chain breaks: 2 Chain: "I" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "J" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "K" Number of atoms: 5065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5065 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 622} Chain breaks: 2 Chain: "L" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.94, per 1000 atoms: 0.41 Number of scatterers: 55404 At special positions: 0 Unit cell: (161.391, 150.412, 227.265, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 312 16.00 O 10434 8.00 N 9714 7.00 C 34944 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 - 3.00 Amino acid : True - 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.06 Conformation dependent library (CDL) restraints added in 5.4 seconds 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13116 Finding SS restraints... Secondary structure from input PDB file: 288 helices and 78 sheets defined 43.7% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain 'A' and resid 57 through 72 removed outlier: 3.523A pdb=" N ALA A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 4.488A pdb=" N ASN A 85 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 109 through 120 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 223 through 233 Processing helix chain 'A' and resid 295 through 313 Processing helix chain 'A' and resid 343 through 352 removed outlier: 4.492A pdb=" N THR A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 504 through 530 removed outlier: 3.622A pdb=" N GLN A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 639 through 646 removed outlier: 3.890A pdb=" N GLN A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN A 646 " --> pdb=" O SER A 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 65 removed outlier: 3.638A pdb=" N LEU B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 114 through 117 Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 146 through 164 Processing helix chain 'B' and resid 177 through 184 removed outlier: 5.812A pdb=" N ALA B 182 " --> pdb=" O PRO B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 removed outlier: 4.291A pdb=" N PHE B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.581A pdb=" N ALA B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 252 Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 261 through 269 removed outlier: 4.146A pdb=" N LEU B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 316 through 322 Processing helix chain 'B' and resid 330 through 337 removed outlier: 3.926A pdb=" N VAL B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 6.672A pdb=" N GLY B 341 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 395 Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 417 through 432 removed outlier: 3.570A pdb=" N MET B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 452 removed outlier: 4.109A pdb=" N TYR B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'B' and resid 474 through 494 removed outlier: 3.622A pdb=" N LYS B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 517 Proline residue: B 508 - end of helix Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.657A pdb=" N ARG B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 536 through 549 Processing helix chain 'C' and resid 57 through 72 removed outlier: 3.523A pdb=" N ALA C 61 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 4.488A pdb=" N ASN C 85 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 109 through 120 Processing helix chain 'C' and resid 135 through 145 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 162 through 174 Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 223 through 233 Processing helix chain 'C' and resid 295 through 313 Processing helix chain 'C' and resid 343 through 352 removed outlier: 4.493A pdb=" N THR C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 365 Processing helix chain 'C' and resid 443 through 457 Processing helix chain 'C' and resid 466 through 476 Processing helix chain 'C' and resid 476 through 482 Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 492 through 497 Processing helix chain 'C' and resid 504 through 530 removed outlier: 3.622A pdb=" N GLN C 529 " --> pdb=" O THR C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 634 through 639 Processing helix chain 'C' and resid 639 through 646 removed outlier: 3.890A pdb=" N GLN C 643 " --> pdb=" O SER C 639 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN C 646 " --> pdb=" O SER C 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 65 removed outlier: 3.637A pdb=" N LEU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 114 through 117 Processing helix chain 'D' and resid 140 through 144 Processing helix chain 'D' and resid 146 through 164 Processing helix chain 'D' and resid 177 through 184 removed outlier: 5.812A pdb=" N ALA D 182 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 204 removed outlier: 4.290A pdb=" N PHE D 195 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 227 removed outlier: 3.579A pdb=" N ALA D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 252 Processing helix chain 'D' and resid 256 through 261 Processing helix chain 'D' and resid 261 through 269 removed outlier: 4.146A pdb=" N LEU D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 293 Processing helix chain 'D' and resid 316 through 322 Processing helix chain 'D' and resid 330 through 337 removed outlier: 3.925A pdb=" N VAL D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 337 " --> pdb=" O GLU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 removed outlier: 6.672A pdb=" N GLY D 341 " --> pdb=" O ILE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 395 Processing helix chain 'D' and resid 410 through 416 Processing helix chain 'D' and resid 417 through 432 removed outlier: 3.570A pdb=" N MET D 425 " --> pdb=" O ASP D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 452 removed outlier: 4.108A pdb=" N TYR D 450 " --> pdb=" O GLY D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 458 Processing helix chain 'D' and resid 474 through 494 removed outlier: 3.622A pdb=" N LYS D 487 " --> pdb=" O ALA D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 517 Proline residue: D 508 - end of helix Processing helix chain 'D' and resid 518 through 525 removed outlier: 3.657A pdb=" N ARG D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 536 through 549 Processing helix chain 'E' and resid 57 through 72 removed outlier: 3.523A pdb=" N ALA E 61 " --> pdb=" O ARG E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 85 removed outlier: 4.487A pdb=" N ASN E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 109 through 120 Processing helix chain 'E' and resid 135 through 145 Processing helix chain 'E' and resid 153 through 162 Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 187 through 199 Processing helix chain 'E' and resid 223 through 233 Processing helix chain 'E' and resid 295 through 313 Processing helix chain 'E' and resid 343 through 352 removed outlier: 4.493A pdb=" N THR E 347 " --> pdb=" O GLU E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 365 Processing helix chain 'E' and resid 443 through 456 Processing helix chain 'E' and resid 466 through 476 Processing helix chain 'E' and resid 476 through 482 Processing helix chain 'E' and resid 487 through 492 Processing helix chain 'E' and resid 492 through 497 Processing helix chain 'E' and resid 504 through 530 removed outlier: 3.622A pdb=" N GLN E 529 " --> pdb=" O THR E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 539 Processing helix chain 'E' and resid 634 through 639 Processing helix chain 'E' and resid 639 through 646 removed outlier: 3.889A pdb=" N GLN E 643 " --> pdb=" O SER E 639 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN E 646 " --> pdb=" O SER E 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 72 removed outlier: 3.523A pdb=" N ALA F 61 " --> pdb=" O ARG F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 removed outlier: 4.487A pdb=" N ASN F 85 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 92 Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 109 through 120 Processing helix chain 'F' and resid 135 through 145 Processing helix chain 'F' and resid 153 through 162 Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'F' and resid 187 through 199 Processing helix chain 'F' and resid 223 through 233 Processing helix chain 'F' and resid 295 through 313 Processing helix chain 'F' and resid 343 through 352 removed outlier: 4.493A pdb=" N THR F 347 " --> pdb=" O GLU F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 Processing helix chain 'F' and resid 443 through 456 Processing helix chain 'F' and resid 466 through 476 Processing helix chain 'F' and resid 476 through 482 Processing helix chain 'F' and resid 487 through 492 Processing helix chain 'F' and resid 492 through 497 Processing helix chain 'F' and resid 504 through 530 removed outlier: 3.623A pdb=" N GLN F 529 " --> pdb=" O THR F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 539 Processing helix chain 'F' and resid 634 through 639 Processing helix chain 'F' and resid 639 through 646 removed outlier: 3.889A pdb=" N GLN F 643 " --> pdb=" O SER F 639 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN F 646 " --> pdb=" O SER F 642 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 65 removed outlier: 3.638A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 78 Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 114 through 117 Processing helix chain 'G' and resid 140 through 144 Processing helix chain 'G' and resid 146 through 164 Processing helix chain 'G' and resid 177 through 184 removed outlier: 5.811A pdb=" N ALA G 182 " --> pdb=" O PRO G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 204 removed outlier: 4.290A pdb=" N PHE G 195 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 227 removed outlier: 3.580A pdb=" N ALA G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 252 Processing helix chain 'G' and resid 256 through 261 Processing helix chain 'G' and resid 261 through 269 removed outlier: 4.146A pdb=" N LEU G 265 " --> pdb=" O GLY G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 293 Processing helix chain 'G' and resid 316 through 322 Processing helix chain 'G' and resid 330 through 337 removed outlier: 3.925A pdb=" N VAL G 334 " --> pdb=" O ASP G 330 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG G 337 " --> pdb=" O GLU G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 343 removed outlier: 6.672A pdb=" N GLY G 341 " --> pdb=" O ILE G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 395 Processing helix chain 'G' and resid 410 through 416 Processing helix chain 'G' and resid 417 through 432 removed outlier: 3.569A pdb=" N MET G 425 " --> pdb=" O ASP G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 452 removed outlier: 4.108A pdb=" N TYR G 450 " --> pdb=" O GLY G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 454 through 458 Processing helix chain 'G' and resid 474 through 494 removed outlier: 3.623A pdb=" N LYS G 487 " --> pdb=" O ALA G 483 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 517 Proline residue: G 508 - end of helix Processing helix chain 'G' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG G 525 " --> pdb=" O TYR G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 535 No H-bonds generated for 'chain 'G' and resid 533 through 535' Processing helix chain 'G' and resid 536 through 549 Processing helix chain 'H' and resid 57 through 72 removed outlier: 3.524A pdb=" N ALA H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 4.488A pdb=" N ASN H 85 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 92 Processing helix chain 'H' and resid 102 through 106 Processing helix chain 'H' and resid 109 through 120 Processing helix chain 'H' and resid 135 through 145 Processing helix chain 'H' and resid 153 through 162 Processing helix chain 'H' and resid 162 through 174 Processing helix chain 'H' and resid 187 through 199 Processing helix chain 'H' and resid 223 through 233 Processing helix chain 'H' and resid 295 through 313 Processing helix chain 'H' and resid 343 through 352 removed outlier: 4.491A pdb=" N THR H 347 " --> pdb=" O GLU H 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 365 Processing helix chain 'H' and resid 443 through 457 Processing helix chain 'H' and resid 466 through 476 Processing helix chain 'H' and resid 476 through 482 Processing helix chain 'H' and resid 487 through 492 Processing helix chain 'H' and resid 492 through 497 Processing helix chain 'H' and resid 504 through 530 removed outlier: 3.622A pdb=" N GLN H 529 " --> pdb=" O THR H 525 " (cutoff:3.500A) Processing helix chain 'H' and resid 535 through 539 Processing helix chain 'H' and resid 634 through 639 Processing helix chain 'H' and resid 639 through 646 removed outlier: 3.890A pdb=" N GLN H 643 " --> pdb=" O SER H 639 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN H 646 " --> pdb=" O SER H 642 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 65 removed outlier: 3.638A pdb=" N LEU I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 78 Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 114 through 117 Processing helix chain 'I' and resid 140 through 144 Processing helix chain 'I' and resid 146 through 164 Processing helix chain 'I' and resid 177 through 184 removed outlier: 5.811A pdb=" N ALA I 182 " --> pdb=" O PRO I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 204 removed outlier: 4.291A pdb=" N PHE I 195 " --> pdb=" O PHE I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 227 removed outlier: 3.580A pdb=" N ALA I 225 " --> pdb=" O ALA I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 243 through 252 Processing helix chain 'I' and resid 256 through 261 Processing helix chain 'I' and resid 261 through 269 removed outlier: 4.146A pdb=" N LEU I 265 " --> pdb=" O GLY I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 293 Processing helix chain 'I' and resid 316 through 322 Processing helix chain 'I' and resid 330 through 337 removed outlier: 3.925A pdb=" N VAL I 334 " --> pdb=" O ASP I 330 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG I 337 " --> pdb=" O GLU I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 343 removed outlier: 6.672A pdb=" N GLY I 341 " --> pdb=" O ILE I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 395 Processing helix chain 'I' and resid 410 through 416 Processing helix chain 'I' and resid 417 through 432 removed outlier: 3.569A pdb=" N MET I 425 " --> pdb=" O ASP I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 446 through 452 removed outlier: 4.108A pdb=" N TYR I 450 " --> pdb=" O GLY I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 454 through 458 Processing helix chain 'I' and resid 474 through 494 removed outlier: 3.623A pdb=" N LYS I 487 " --> pdb=" O ALA I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 498 through 517 Proline residue: I 508 - end of helix Processing helix chain 'I' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG I 525 " --> pdb=" O TYR I 521 " (cutoff:3.500A) Processing helix chain 'I' and resid 533 through 535 No H-bonds generated for 'chain 'I' and resid 533 through 535' Processing helix chain 'I' and resid 536 through 549 Processing helix chain 'J' and resid 39 through 65 removed outlier: 3.638A pdb=" N LEU J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 78 Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 114 through 117 Processing helix chain 'J' and resid 140 through 144 Processing helix chain 'J' and resid 146 through 164 Processing helix chain 'J' and resid 177 through 184 removed outlier: 5.812A pdb=" N ALA J 182 " --> pdb=" O PRO J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 204 removed outlier: 4.291A pdb=" N PHE J 195 " --> pdb=" O PHE J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 227 removed outlier: 3.581A pdb=" N ALA J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 252 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 261 through 269 removed outlier: 4.145A pdb=" N LEU J 265 " --> pdb=" O GLY J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 293 Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 330 through 337 removed outlier: 3.925A pdb=" N VAL J 334 " --> pdb=" O ASP J 330 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG J 337 " --> pdb=" O GLU J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 343 removed outlier: 6.672A pdb=" N GLY J 341 " --> pdb=" O ILE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 395 Processing helix chain 'J' and resid 410 through 416 Processing helix chain 'J' and resid 417 through 432 removed outlier: 3.569A pdb=" N MET J 425 " --> pdb=" O ASP J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 452 removed outlier: 4.108A pdb=" N TYR J 450 " --> pdb=" O GLY J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 458 Processing helix chain 'J' and resid 474 through 494 removed outlier: 3.623A pdb=" N LYS J 487 " --> pdb=" O ALA J 483 " (cutoff:3.500A) Processing helix chain 'J' and resid 498 through 517 Proline residue: J 508 - end of helix Processing helix chain 'J' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG J 525 " --> pdb=" O TYR J 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 535 No H-bonds generated for 'chain 'J' and resid 533 through 535' Processing helix chain 'J' and resid 536 through 549 Processing helix chain 'K' and resid 57 through 72 removed outlier: 3.523A pdb=" N ALA K 61 " --> pdb=" O ARG K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 removed outlier: 4.488A pdb=" N ASN K 85 " --> pdb=" O ALA K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 92 Processing helix chain 'K' and resid 102 through 106 Processing helix chain 'K' and resid 109 through 120 Processing helix chain 'K' and resid 135 through 145 Processing helix chain 'K' and resid 153 through 162 Processing helix chain 'K' and resid 162 through 174 Processing helix chain 'K' and resid 187 through 199 Processing helix chain 'K' and resid 223 through 233 Processing helix chain 'K' and resid 295 through 313 Processing helix chain 'K' and resid 343 through 352 removed outlier: 4.493A pdb=" N THR K 347 " --> pdb=" O GLU K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 365 Processing helix chain 'K' and resid 443 through 456 Processing helix chain 'K' and resid 466 through 476 Processing helix chain 'K' and resid 476 through 482 Processing helix chain 'K' and resid 487 through 492 Processing helix chain 'K' and resid 492 through 497 Processing helix chain 'K' and resid 504 through 530 removed outlier: 3.623A pdb=" N GLN K 529 " --> pdb=" O THR K 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 535 through 539 Processing helix chain 'K' and resid 634 through 639 Processing helix chain 'K' and resid 639 through 646 removed outlier: 3.890A pdb=" N GLN K 643 " --> pdb=" O SER K 639 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN K 646 " --> pdb=" O SER K 642 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 65 removed outlier: 3.638A pdb=" N LEU L 65 " --> pdb=" O GLU L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 78 Processing helix chain 'L' and resid 82 through 91 Processing helix chain 'L' and resid 114 through 117 Processing helix chain 'L' and resid 140 through 144 Processing helix chain 'L' and resid 146 through 164 Processing helix chain 'L' and resid 177 through 184 removed outlier: 5.811A pdb=" N ALA L 182 " --> pdb=" O PRO L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 204 removed outlier: 4.291A pdb=" N PHE L 195 " --> pdb=" O PHE L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 227 removed outlier: 3.580A pdb=" N ALA L 225 " --> pdb=" O ALA L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 252 Processing helix chain 'L' and resid 256 through 261 Processing helix chain 'L' and resid 261 through 269 removed outlier: 4.146A pdb=" N LEU L 265 " --> pdb=" O GLY L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 279 through 293 Processing helix chain 'L' and resid 316 through 322 Processing helix chain 'L' and resid 330 through 337 removed outlier: 3.924A pdb=" N VAL L 334 " --> pdb=" O ASP L 330 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG L 337 " --> pdb=" O GLU L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 343 removed outlier: 6.672A pdb=" N GLY L 341 " --> pdb=" O ILE L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 377 through 395 Processing helix chain 'L' and resid 410 through 416 Processing helix chain 'L' and resid 417 through 432 removed outlier: 3.569A pdb=" N MET L 425 " --> pdb=" O ASP L 421 " (cutoff:3.500A) Processing helix chain 'L' and resid 446 through 452 removed outlier: 4.108A pdb=" N TYR L 450 " --> pdb=" O GLY L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 458 Processing helix chain 'L' and resid 474 through 494 removed outlier: 3.623A pdb=" N LYS L 487 " --> pdb=" O ALA L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 498 through 517 Proline residue: L 508 - end of helix Processing helix chain 'L' and resid 518 through 525 removed outlier: 3.655A pdb=" N ARG L 525 " --> pdb=" O TYR L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 533 through 535 No H-bonds generated for 'chain 'L' and resid 533 through 535' Processing helix chain 'L' and resid 536 through 549 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 97 removed outlier: 3.931A pdb=" N VAL A 78 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS A 51 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS A 126 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 53 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 275 removed outlier: 3.959A pdb=" N GLN A 259 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU A 273 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU A 257 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASP A 275 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS A 255 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 254 " --> pdb=" O MET A 325 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU A 335 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE A 324 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE A 333 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 279 through 280 Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 406 Processing sheet with id=AA6, first strand: chain 'A' and resid 543 through 544 removed outlier: 3.924A pdb=" N ARG A 544 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 547 " --> pdb=" O ARG A 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 550 through 557 removed outlier: 4.715A pdb=" N THR A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 683 through 687 removed outlier: 3.580A pdb=" N MET A 675 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU A 674 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL A 660 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 676 " --> pdb=" O GLU A 658 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 694 through 697 Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR B 121 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS B 167 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL B 211 " --> pdb=" O CYS B 167 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR B 169 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN B 230 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA B 277 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 232 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 215 through 217 Processing sheet with id=AB3, first strand: chain 'B' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU B 399 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY B 368 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU B 401 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 370 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 461 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 443 through 445 removed outlier: 6.112A pdb=" N SER B 444 " --> pdb=" O SER B 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 94 through 97 removed outlier: 3.930A pdb=" N VAL C 78 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS C 51 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N HIS C 126 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 53 " --> pdb=" O HIS C 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 268 through 275 removed outlier: 3.959A pdb=" N GLN C 259 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU C 273 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU C 257 " --> pdb=" O GLU C 273 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP C 275 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N HIS C 255 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG C 254 " --> pdb=" O MET C 325 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU C 335 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE C 324 " --> pdb=" O PHE C 333 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE C 333 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 279 through 280 Processing sheet with id=AB8, first strand: chain 'C' and resid 286 through 289 Processing sheet with id=AB9, first strand: chain 'C' and resid 404 through 406 Processing sheet with id=AC1, first strand: chain 'C' and resid 543 through 544 removed outlier: 3.924A pdb=" N ARG C 544 " --> pdb=" O ILE C 547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE C 547 " --> pdb=" O ARG C 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 550 through 557 removed outlier: 4.715A pdb=" N THR C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 683 through 687 removed outlier: 3.579A pdb=" N MET C 675 " --> pdb=" O ILE C 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU C 674 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL C 660 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL C 676 " --> pdb=" O GLU C 658 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 694 through 697 Processing sheet with id=AC5, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR D 121 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS D 167 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL D 211 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR D 169 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN D 230 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA D 277 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE D 232 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 215 through 217 removed outlier: 3.653A pdb=" N PHE D 240 " --> pdb=" O CYS D 216 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU D 399 " --> pdb=" O PRO D 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY D 368 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU D 401 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL D 370 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 461 " --> pdb=" O LYS D 436 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 443 through 445 removed outlier: 6.111A pdb=" N SER D 444 " --> pdb=" O SER D 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 94 through 97 removed outlier: 3.931A pdb=" N VAL E 78 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS E 51 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N HIS E 126 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU E 53 " --> pdb=" O HIS E 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 268 through 275 removed outlier: 3.959A pdb=" N GLN E 259 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU E 273 " --> pdb=" O GLU E 257 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU E 257 " --> pdb=" O GLU E 273 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASP E 275 " --> pdb=" O HIS E 255 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS E 255 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG E 254 " --> pdb=" O MET E 325 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU E 335 " --> pdb=" O GLU E 322 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE E 324 " --> pdb=" O PHE E 333 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE E 333 " --> pdb=" O ILE E 324 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 279 through 280 Processing sheet with id=AD3, first strand: chain 'E' and resid 286 through 289 Processing sheet with id=AD4, first strand: chain 'E' and resid 404 through 406 Processing sheet with id=AD5, first strand: chain 'E' and resid 543 through 544 removed outlier: 3.924A pdb=" N ARG E 544 " --> pdb=" O ILE E 547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE E 547 " --> pdb=" O ARG E 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 550 through 557 removed outlier: 4.715A pdb=" N THR E 596 " --> pdb=" O LEU E 611 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 683 through 687 removed outlier: 3.580A pdb=" N MET E 675 " --> pdb=" O ILE E 686 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU E 674 " --> pdb=" O VAL E 660 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL E 660 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL E 676 " --> pdb=" O GLU E 658 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 694 through 697 Processing sheet with id=AD9, first strand: chain 'F' and resid 94 through 97 removed outlier: 3.930A pdb=" N VAL F 78 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS F 51 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N HIS F 126 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU F 53 " --> pdb=" O HIS F 126 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 268 through 275 removed outlier: 3.959A pdb=" N GLN F 259 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU F 273 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU F 257 " --> pdb=" O GLU F 273 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASP F 275 " --> pdb=" O HIS F 255 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS F 255 " --> pdb=" O ASP F 275 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG F 254 " --> pdb=" O MET F 325 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU F 335 " --> pdb=" O GLU F 322 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE F 324 " --> pdb=" O PHE F 333 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE F 333 " --> pdb=" O ILE F 324 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 279 through 280 Processing sheet with id=AE3, first strand: chain 'F' and resid 286 through 289 Processing sheet with id=AE4, first strand: chain 'F' and resid 404 through 406 Processing sheet with id=AE5, first strand: chain 'F' and resid 543 through 544 removed outlier: 3.924A pdb=" N ARG F 544 " --> pdb=" O ILE F 547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE F 547 " --> pdb=" O ARG F 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'F' and resid 550 through 557 removed outlier: 4.715A pdb=" N THR F 596 " --> pdb=" O LEU F 611 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 683 through 687 removed outlier: 3.580A pdb=" N MET F 675 " --> pdb=" O ILE F 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU F 674 " --> pdb=" O VAL F 660 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL F 660 " --> pdb=" O LEU F 674 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL F 676 " --> pdb=" O GLU F 658 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 694 through 697 Processing sheet with id=AE9, first strand: chain 'G' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR G 121 " --> pdb=" O LEU G 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS G 167 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL G 211 " --> pdb=" O CYS G 167 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR G 169 " --> pdb=" O VAL G 211 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN G 230 " --> pdb=" O HIS G 275 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA G 277 " --> pdb=" O ASN G 230 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE G 232 " --> pdb=" O ALA G 277 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 215 through 217 removed outlier: 3.654A pdb=" N PHE G 240 " --> pdb=" O CYS G 216 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU G 399 " --> pdb=" O PRO G 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY G 368 " --> pdb=" O LEU G 399 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU G 401 " --> pdb=" O GLY G 368 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL G 370 " --> pdb=" O LEU G 401 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE G 461 " --> pdb=" O LYS G 436 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 443 through 445 removed outlier: 6.112A pdb=" N SER G 444 " --> pdb=" O SER G 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'H' and resid 94 through 97 removed outlier: 3.931A pdb=" N VAL H 78 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS H 51 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N HIS H 126 " --> pdb=" O LYS H 51 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU H 53 " --> pdb=" O HIS H 126 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 268 through 275 removed outlier: 3.960A pdb=" N GLN H 259 " --> pdb=" O LEU H 271 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU H 273 " --> pdb=" O GLU H 257 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU H 257 " --> pdb=" O GLU H 273 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASP H 275 " --> pdb=" O HIS H 255 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS H 255 " --> pdb=" O ASP H 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG H 254 " --> pdb=" O MET H 325 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU H 335 " --> pdb=" O GLU H 322 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE H 324 " --> pdb=" O PHE H 333 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE H 333 " --> pdb=" O ILE H 324 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 279 through 280 Processing sheet with id=AF7, first strand: chain 'H' and resid 286 through 289 Processing sheet with id=AF8, first strand: chain 'H' and resid 404 through 406 Processing sheet with id=AF9, first strand: chain 'H' and resid 543 through 544 removed outlier: 3.924A pdb=" N ARG H 544 " --> pdb=" O ILE H 547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE H 547 " --> pdb=" O ARG H 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'H' and resid 550 through 557 removed outlier: 4.715A pdb=" N THR H 596 " --> pdb=" O LEU H 611 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 683 through 687 removed outlier: 3.580A pdb=" N MET H 675 " --> pdb=" O ILE H 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU H 674 " --> pdb=" O VAL H 660 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL H 660 " --> pdb=" O LEU H 674 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL H 676 " --> pdb=" O GLU H 658 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 694 through 697 Processing sheet with id=AG4, first strand: chain 'I' and resid 98 through 100 removed outlier: 4.729A pdb=" N THR I 121 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS I 167 " --> pdb=" O ILE I 209 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL I 211 " --> pdb=" O CYS I 167 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR I 169 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN I 230 " --> pdb=" O HIS I 275 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA I 277 " --> pdb=" O ASN I 230 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE I 232 " --> pdb=" O ALA I 277 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 215 through 217 removed outlier: 3.653A pdb=" N PHE I 240 " --> pdb=" O CYS I 216 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU I 399 " --> pdb=" O PRO I 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY I 368 " --> pdb=" O LEU I 399 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU I 401 " --> pdb=" O GLY I 368 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL I 370 " --> pdb=" O LEU I 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE I 461 " --> pdb=" O LYS I 436 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 443 through 445 removed outlier: 6.112A pdb=" N SER I 444 " --> pdb=" O SER I 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'J' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR J 121 " --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS J 167 " --> pdb=" O ILE J 209 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL J 211 " --> pdb=" O CYS J 167 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR J 169 " --> pdb=" O VAL J 211 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN J 230 " --> pdb=" O HIS J 275 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA J 277 " --> pdb=" O ASN J 230 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE J 232 " --> pdb=" O ALA J 277 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 215 through 217 removed outlier: 3.653A pdb=" N PHE J 240 " --> pdb=" O CYS J 216 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU J 399 " --> pdb=" O PRO J 366 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY J 368 " --> pdb=" O LEU J 399 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU J 401 " --> pdb=" O GLY J 368 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL J 370 " --> pdb=" O LEU J 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE J 461 " --> pdb=" O LYS J 436 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 443 through 445 removed outlier: 6.112A pdb=" N SER J 444 " --> pdb=" O SER J 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'K' and resid 94 through 97 removed outlier: 3.930A pdb=" N VAL K 78 " --> pdb=" O ILE K 54 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS K 51 " --> pdb=" O ALA K 124 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS K 126 " --> pdb=" O LYS K 51 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU K 53 " --> pdb=" O HIS K 126 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 268 through 275 removed outlier: 3.959A pdb=" N GLN K 259 " --> pdb=" O LEU K 271 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU K 273 " --> pdb=" O GLU K 257 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU K 257 " --> pdb=" O GLU K 273 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASP K 275 " --> pdb=" O HIS K 255 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS K 255 " --> pdb=" O ASP K 275 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG K 254 " --> pdb=" O MET K 325 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU K 335 " --> pdb=" O GLU K 322 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE K 324 " --> pdb=" O PHE K 333 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE K 333 " --> pdb=" O ILE K 324 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 279 through 280 Processing sheet with id=AH6, first strand: chain 'K' and resid 286 through 289 Processing sheet with id=AH7, first strand: chain 'K' and resid 404 through 406 Processing sheet with id=AH8, first strand: chain 'K' and resid 543 through 544 removed outlier: 3.924A pdb=" N ARG K 544 " --> pdb=" O ILE K 547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE K 547 " --> pdb=" O ARG K 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'K' and resid 550 through 557 removed outlier: 4.715A pdb=" N THR K 596 " --> pdb=" O LEU K 611 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 683 through 687 removed outlier: 3.580A pdb=" N MET K 675 " --> pdb=" O ILE K 686 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU K 674 " --> pdb=" O VAL K 660 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL K 660 " --> pdb=" O LEU K 674 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL K 676 " --> pdb=" O GLU K 658 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 694 through 697 Processing sheet with id=AI3, first strand: chain 'L' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR L 121 " --> pdb=" O LEU L 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS L 167 " --> pdb=" O ILE L 209 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL L 211 " --> pdb=" O CYS L 167 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR L 169 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN L 230 " --> pdb=" O HIS L 275 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ALA L 277 " --> pdb=" O ASN L 230 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE L 232 " --> pdb=" O ALA L 277 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 215 through 217 removed outlier: 3.653A pdb=" N PHE L 240 " --> pdb=" O CYS L 216 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU L 399 " --> pdb=" O PRO L 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY L 368 " --> pdb=" O LEU L 399 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU L 401 " --> pdb=" O GLY L 368 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL L 370 " --> pdb=" O LEU L 401 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE L 461 " --> pdb=" O LYS L 436 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 443 through 445 removed outlier: 6.112A pdb=" N SER L 444 " --> pdb=" O SER L 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 2729 hydrogen bonds defined for protein. 7572 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: 24.97 Time building geometry restraints manager: 11.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 9456 1.31 - 1.44: 14235 1.44 - 1.56: 32265 1.56 - 1.69: 0 1.69 - 1.82: 522 Bond restraints: 56478 Sorted by residual: bond pdb=" C MET E 680 " pdb=" N LYS E 681 " ideal model delta sigma weight residual 1.330 1.484 -0.154 1.30e-02 5.92e+03 1.41e+02 bond pdb=" C MET F 680 " pdb=" N LYS F 681 " ideal model delta sigma weight residual 1.330 1.484 -0.154 1.30e-02 5.92e+03 1.40e+02 bond pdb=" C MET H 680 " pdb=" N LYS H 681 " ideal model delta sigma weight residual 1.330 1.484 -0.154 1.30e-02 5.92e+03 1.40e+02 bond pdb=" C MET A 680 " pdb=" N LYS A 681 " ideal model delta sigma weight residual 1.330 1.484 -0.153 1.30e-02 5.92e+03 1.39e+02 bond pdb=" C MET C 680 " pdb=" N LYS C 681 " ideal model delta sigma weight residual 1.330 1.483 -0.153 1.30e-02 5.92e+03 1.38e+02 ... (remaining 56473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 66975 2.09 - 4.18: 8687 4.18 - 6.27: 547 6.27 - 8.36: 54 8.36 - 10.45: 27 Bond angle restraints: 76290 Sorted by residual: angle pdb=" N LYS L 487 " pdb=" CA LYS L 487 " pdb=" C LYS L 487 " ideal model delta sigma weight residual 111.36 103.09 8.27 1.09e+00 8.42e-01 5.75e+01 angle pdb=" N LYS D 487 " pdb=" CA LYS D 487 " pdb=" C LYS D 487 " ideal model delta sigma weight residual 111.36 103.09 8.27 1.09e+00 8.42e-01 5.75e+01 angle pdb=" N LYS G 487 " pdb=" CA LYS G 487 " pdb=" C LYS G 487 " ideal model delta sigma weight residual 111.36 103.10 8.26 1.09e+00 8.42e-01 5.74e+01 angle pdb=" N LYS I 487 " pdb=" CA LYS I 487 " pdb=" C LYS I 487 " ideal model delta sigma weight residual 111.36 103.11 8.25 1.09e+00 8.42e-01 5.73e+01 angle pdb=" N LYS J 487 " pdb=" CA LYS J 487 " pdb=" C LYS J 487 " ideal model delta sigma weight residual 111.36 103.12 8.24 1.09e+00 8.42e-01 5.71e+01 ... (remaining 76285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 31725 17.88 - 35.77: 1949 35.77 - 53.65: 476 53.65 - 71.54: 97 71.54 - 89.42: 31 Dihedral angle restraints: 34278 sinusoidal: 13788 harmonic: 20490 Sorted by residual: dihedral pdb=" C THR K 486 " pdb=" N THR K 486 " pdb=" CA THR K 486 " pdb=" CB THR K 486 " ideal model delta harmonic sigma weight residual -122.00 -140.71 18.71 0 2.50e+00 1.60e-01 5.60e+01 dihedral pdb=" C THR C 486 " pdb=" N THR C 486 " pdb=" CA THR C 486 " pdb=" CB THR C 486 " ideal model delta harmonic sigma weight residual -122.00 -140.69 18.69 0 2.50e+00 1.60e-01 5.59e+01 dihedral pdb=" C THR H 486 " pdb=" N THR H 486 " pdb=" CA THR H 486 " pdb=" CB THR H 486 " ideal model delta harmonic sigma weight residual -122.00 -140.68 18.68 0 2.50e+00 1.60e-01 5.58e+01 ... (remaining 34275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 7051 0.128 - 0.256: 1312 0.256 - 0.384: 67 0.384 - 0.512: 0 0.512 - 0.639: 6 Chirality restraints: 8436 Sorted by residual: chirality pdb=" CA THR K 486 " pdb=" N THR K 486 " pdb=" C THR K 486 " pdb=" CB THR K 486 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA THR C 486 " pdb=" N THR C 486 " pdb=" C THR C 486 " pdb=" CB THR C 486 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA THR E 486 " pdb=" N THR E 486 " pdb=" C THR E 486 " pdb=" CB THR E 486 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 8433 not shown) Planarity restraints: 9996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU H 223 " 0.015 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" CD GLU H 223 " -0.055 2.00e-02 2.50e+03 pdb=" OE1 GLU H 223 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU H 223 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 223 " -0.015 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" CD GLU F 223 " 0.055 2.00e-02 2.50e+03 pdb=" OE1 GLU F 223 " -0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU F 223 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 223 " 0.015 2.00e-02 2.50e+03 3.15e-02 9.91e+00 pdb=" CD GLU A 223 " -0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU A 223 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU A 223 " 0.019 2.00e-02 2.50e+03 ... (remaining 9993 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 15282 2.82 - 3.34: 50708 3.34 - 3.86: 92051 3.86 - 4.38: 112200 4.38 - 4.90: 183771 Nonbonded interactions: 454012 Sorted by model distance: nonbonded pdb=" CD1 LEU F 340 " pdb=" OE1 GLN F 359 " model vdw 2.299 3.460 nonbonded pdb=" CD1 LEU K 340 " pdb=" OE1 GLN K 359 " model vdw 2.300 3.460 nonbonded pdb=" CD1 LEU A 340 " pdb=" OE1 GLN A 359 " model vdw 2.300 3.460 nonbonded pdb=" CD1 LEU E 340 " pdb=" OE1 GLN E 359 " model vdw 2.300 3.460 nonbonded pdb=" CD1 LEU C 340 " pdb=" OE1 GLN C 359 " model vdw 2.300 3.460 ... (remaining 454007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 1.540 Check model and map are aligned: 0.310 Set scattering table: 0.390 Process input model: 97.900 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.009 0.154 56478 Z= 0.625 Angle : 1.283 10.453 76290 Z= 0.947 Chirality : 0.093 0.639 8436 Planarity : 0.005 0.059 9996 Dihedral : 12.774 89.420 21162 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.83 % Favored : 98.07 % Rotamer: Outliers : 0.75 % Allowed : 8.32 % Favored : 90.94 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 3.85 % 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: 1.44 (0.10), residues: 7104 helix: 1.96 (0.10), residues: 2676 sheet: 1.32 (0.13), residues: 1320 loop : -0.07 (0.11), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 276 HIS 0.013 0.002 HIS A 380 PHE 0.038 0.003 PHE E 249 TYR 0.033 0.003 TYR F 200 ARG 0.006 0.001 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 668 time to evaluate : 4.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9042 (mtt) cc_final: 0.8671 (mtt) REVERT: A 653 MET cc_start: 0.8517 (mtp) cc_final: 0.8279 (mmm) REVERT: C 218 VAL cc_start: 0.5604 (OUTLIER) cc_final: 0.5396 (t) REVERT: C 261 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8570 (t80) REVERT: E 261 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: E 576 MET cc_start: 0.9178 (mtt) cc_final: 0.8846 (mtm) REVERT: E 653 MET cc_start: 0.8765 (mtp) cc_final: 0.8506 (mtm) REVERT: F 261 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: F 576 MET cc_start: 0.9186 (mtt) cc_final: 0.8844 (mtm) REVERT: F 653 MET cc_start: 0.8706 (mtp) cc_final: 0.8445 (mtm) REVERT: G 201 MET cc_start: 0.9327 (mtm) cc_final: 0.9125 (mtp) REVERT: G 425 MET cc_start: 0.8921 (ttp) cc_final: 0.8691 (ttp) REVERT: H 576 MET cc_start: 0.9150 (mtt) cc_final: 0.8719 (mtt) REVERT: K 261 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8558 (t80) outliers start: 44 outliers final: 6 residues processed: 705 average time/residue: 1.7109 time to fit residues: 1456.1856 Evaluate side-chains 366 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 355 time to evaluate : 4.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain H residue 261 PHE Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 678 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 602 optimal weight: 7.9990 chunk 541 optimal weight: 8.9990 chunk 300 optimal weight: 20.0000 chunk 184 optimal weight: 8.9990 chunk 365 optimal weight: 20.0000 chunk 289 optimal weight: 4.9990 chunk 559 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 340 optimal weight: 5.9990 chunk 416 optimal weight: 0.0070 chunk 648 optimal weight: 2.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 279 GLN A 283 GLN A 337 ASN A 341 GLN A 429 HIS A 491 GLN A 708 HIS B 477 GLN ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN C 283 GLN C 337 ASN C 429 HIS C 491 GLN C 708 HIS E 255 HIS E 279 GLN E 283 GLN E 337 ASN E 429 HIS E 491 GLN E 708 HIS ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 GLN F 283 GLN F 337 ASN F 429 HIS F 491 GLN F 708 HIS G 477 GLN ** H 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 GLN H 283 GLN H 337 ASN H 341 GLN H 429 HIS H 491 GLN H 708 HIS J 477 GLN ** K 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 279 GLN K 283 GLN K 337 ASN K 429 HIS K 491 GLN K 708 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 56478 Z= 0.396 Angle : 0.695 13.186 76290 Z= 0.373 Chirality : 0.049 0.354 8436 Planarity : 0.005 0.067 9996 Dihedral : 5.456 72.336 7901 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.53 % Allowed : 11.67 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.10), residues: 7104 helix: 1.83 (0.10), residues: 2754 sheet: 1.39 (0.13), residues: 1296 loop : -0.08 (0.11), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 276 HIS 0.008 0.001 HIS I 285 PHE 0.020 0.002 PHE D 497 TYR 0.026 0.002 TYR L 457 ARG 0.012 0.001 ARG I 490 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 401 time to evaluate : 4.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.5968 (mmp) cc_final: 0.5677 (mmt) REVERT: A 653 MET cc_start: 0.8747 (mtp) cc_final: 0.8026 (mmm) REVERT: B 269 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7549 (mptt) REVERT: B 416 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7663 (mp0) REVERT: B 425 MET cc_start: 0.9447 (ttm) cc_final: 0.9193 (ttt) REVERT: C 91 MET cc_start: 0.8903 (ttm) cc_final: 0.8671 (mtm) REVERT: C 261 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8665 (t80) REVERT: C 276 CYS cc_start: 0.7412 (m) cc_final: 0.4626 (t) REVERT: C 284 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8408 (pttt) REVERT: D 110 ASP cc_start: 0.7946 (p0) cc_final: 0.7723 (p0) REVERT: D 254 GLU cc_start: 0.7120 (mp0) cc_final: 0.6556 (mp0) REVERT: E 67 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8845 (m) REVERT: E 244 MET cc_start: 0.1283 (mmm) cc_final: 0.0935 (mpt) REVERT: E 261 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: E 576 MET cc_start: 0.9223 (mtt) cc_final: 0.9009 (mtt) REVERT: E 677 MET cc_start: 0.8647 (ttt) cc_final: 0.8386 (ttt) REVERT: F 67 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8804 (m) REVERT: F 261 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8653 (m-80) REVERT: F 576 MET cc_start: 0.9223 (mtt) cc_final: 0.9011 (mtt) REVERT: F 677 MET cc_start: 0.8634 (ttt) cc_final: 0.8376 (ttt) REVERT: G 254 GLU cc_start: 0.7616 (mp0) cc_final: 0.7346 (mp0) REVERT: G 416 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7566 (mp0) REVERT: G 505 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8887 (pp) REVERT: H 91 MET cc_start: 0.8678 (mtp) cc_final: 0.8323 (mtp) REVERT: J 269 LYS cc_start: 0.7946 (mtmt) cc_final: 0.7569 (mptt) REVERT: J 416 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7690 (mp0) REVERT: J 425 MET cc_start: 0.9435 (ttm) cc_final: 0.9198 (ttt) REVERT: J 505 LEU cc_start: 0.9042 (mt) cc_final: 0.8840 (mt) REVERT: K 91 MET cc_start: 0.8865 (ttm) cc_final: 0.8653 (mtm) REVERT: K 160 MET cc_start: 0.5690 (mmp) cc_final: 0.5489 (mmt) REVERT: K 261 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8712 (t80) REVERT: K 276 CYS cc_start: 0.7370 (m) cc_final: 0.4665 (t) REVERT: L 110 ASP cc_start: 0.7954 (p0) cc_final: 0.7713 (p0) REVERT: L 254 GLU cc_start: 0.7121 (mp0) cc_final: 0.6556 (mp0) REVERT: L 407 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7397 (t80) outliers start: 149 outliers final: 28 residues processed: 508 average time/residue: 1.5522 time to fit residues: 970.6376 Evaluate side-chains 373 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 336 time to evaluate : 4.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 464 HIS Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 623 LYS Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 261 PHE Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain I residue 404 ILE Chi-restraints excluded: chain I residue 484 THR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 464 HIS Chi-restraints excluded: chain K residue 658 GLU Chi-restraints excluded: chain L residue 407 PHE Chi-restraints excluded: chain L residue 481 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 360 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 539 optimal weight: 0.9990 chunk 441 optimal weight: 20.0000 chunk 178 optimal weight: 0.0030 chunk 649 optimal weight: 1.9990 chunk 701 optimal weight: 4.9990 chunk 578 optimal weight: 1.9990 chunk 644 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 521 optimal weight: 0.9980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 265 HIS A 344 HIS ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 HIS C 492 HIS C 646 GLN E 344 HIS E 646 GLN ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS F 646 GLN ** H 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 HIS H 492 HIS ** K 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 344 HIS K 457 GLN K 492 HIS K 646 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 56478 Z= 0.163 Angle : 0.543 10.044 76290 Z= 0.289 Chirality : 0.045 0.261 8436 Planarity : 0.004 0.056 9996 Dihedral : 4.804 58.645 7890 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.45 % Allowed : 13.96 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.52 (0.10), residues: 7104 helix: 2.10 (0.10), residues: 2760 sheet: 1.07 (0.13), residues: 1410 loop : -0.03 (0.11), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 276 HIS 0.005 0.001 HIS C 255 PHE 0.025 0.001 PHE G 497 TYR 0.011 0.001 TYR H 453 ARG 0.010 0.000 ARG L 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 365 time to evaluate : 5.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8789 (mtp) cc_final: 0.8559 (mtp) REVERT: A 302 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8348 (mm) REVERT: A 653 MET cc_start: 0.8546 (mtp) cc_final: 0.8211 (mmm) REVERT: B 269 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7637 (mptt) REVERT: B 416 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7701 (mp0) REVERT: B 505 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8491 (pp) REVERT: C 261 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8746 (t80) REVERT: C 658 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8755 (mm-30) REVERT: D 254 GLU cc_start: 0.7323 (mp0) cc_final: 0.7024 (mp0) REVERT: D 407 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7627 (t80) REVERT: E 677 MET cc_start: 0.8684 (ttp) cc_final: 0.8423 (ttt) REVERT: F 677 MET cc_start: 0.8651 (ttp) cc_final: 0.8360 (ttt) REVERT: G 254 GLU cc_start: 0.7592 (mp0) cc_final: 0.7370 (mp0) REVERT: G 505 LEU cc_start: 0.9121 (mt) cc_final: 0.8801 (pp) REVERT: H 302 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8242 (mm) REVERT: I 130 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8930 (mp0) REVERT: I 407 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.7939 (t80) REVERT: I 505 LEU cc_start: 0.8969 (mt) cc_final: 0.8537 (pp) REVERT: J 269 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7647 (mptt) REVERT: J 416 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7702 (mp0) REVERT: K 91 MET cc_start: 0.8647 (ttm) cc_final: 0.8444 (mtm) REVERT: K 658 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8753 (mm-30) REVERT: L 254 GLU cc_start: 0.7327 (mp0) cc_final: 0.7028 (mp0) REVERT: L 407 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7386 (t80) outliers start: 85 outliers final: 13 residues processed: 424 average time/residue: 1.5582 time to fit residues: 827.4773 Evaluate side-chains 341 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 318 time to evaluate : 4.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 495 LYS Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 623 LYS Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 407 PHE Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 658 GLU Chi-restraints excluded: chain L residue 407 PHE Chi-restraints excluded: chain L residue 495 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 641 optimal weight: 0.1980 chunk 488 optimal weight: 7.9990 chunk 337 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 309 optimal weight: 9.9990 chunk 436 optimal weight: 30.0000 chunk 651 optimal weight: 7.9990 chunk 690 optimal weight: 10.0000 chunk 340 optimal weight: 20.0000 chunk 617 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 646 GLN B 230 ASN C 255 HIS E 194 HIS E 265 HIS F 255 HIS F 265 HIS H 255 HIS H 341 GLN H 646 GLN J 230 ASN J 477 GLN K 255 HIS K 464 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 56478 Z= 0.516 Angle : 0.657 7.523 76290 Z= 0.353 Chirality : 0.049 0.224 8436 Planarity : 0.005 0.054 9996 Dihedral : 4.968 59.279 7886 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.41 % Allowed : 13.20 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.19 (0.10), residues: 7104 helix: 1.86 (0.10), residues: 2718 sheet: 0.86 (0.13), residues: 1350 loop : -0.17 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 358 HIS 0.006 0.001 HIS E 88 PHE 0.034 0.002 PHE D 497 TYR 0.027 0.002 TYR D 457 ARG 0.019 0.001 ARG D 490 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 352 time to evaluate : 4.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.5405 (mmp) cc_final: 0.4784 (mmm) REVERT: A 302 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8433 (mm) REVERT: A 653 MET cc_start: 0.8572 (mtp) cc_final: 0.8302 (mmm) REVERT: B 416 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7822 (mp0) REVERT: B 505 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8687 (pp) REVERT: C 67 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8910 (m) REVERT: C 261 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8697 (t80) REVERT: C 284 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8443 (pttt) REVERT: C 302 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8576 (mm) REVERT: C 433 MET cc_start: 0.9100 (ttm) cc_final: 0.8812 (tpp) REVERT: D 254 GLU cc_start: 0.7529 (mp0) cc_final: 0.7192 (mp0) REVERT: D 416 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7876 (mm-30) REVERT: D 495 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8470 (mptt) REVERT: E 67 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8951 (m) REVERT: E 261 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8719 (m-80) REVERT: E 284 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8301 (pttt) REVERT: E 658 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: F 67 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8942 (m) REVERT: F 261 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8711 (m-80) REVERT: F 284 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8284 (pttt) REVERT: F 677 MET cc_start: 0.8676 (ttp) cc_final: 0.8444 (ttt) REVERT: G 130 GLU cc_start: 0.9344 (OUTLIER) cc_final: 0.9009 (mp0) REVERT: G 254 GLU cc_start: 0.7768 (mp0) cc_final: 0.7522 (mp0) REVERT: G 482 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8989 (tm) REVERT: H 302 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8235 (mm) REVERT: I 130 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.8996 (mp0) REVERT: I 269 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8205 (mppt) REVERT: I 416 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8052 (mp0) REVERT: I 505 LEU cc_start: 0.9197 (mt) cc_final: 0.8819 (pp) REVERT: J 416 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7822 (mp0) REVERT: K 67 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8900 (m) REVERT: K 261 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8693 (t80) REVERT: K 302 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8597 (mm) REVERT: K 433 MET cc_start: 0.9100 (ttm) cc_final: 0.8786 (tpp) REVERT: L 495 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8294 (mptt) outliers start: 142 outliers final: 34 residues processed: 452 average time/residue: 1.5341 time to fit residues: 859.3121 Evaluate side-chains 383 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 326 time to evaluate : 4.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 464 HIS Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 495 LYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain E residue 553 MET Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 553 MET Chi-restraints excluded: chain F residue 623 LYS Chi-restraints excluded: chain F residue 653 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 269 LYS Chi-restraints excluded: chain I residue 299 LYS Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain I residue 404 ILE Chi-restraints excluded: chain I residue 484 THR Chi-restraints excluded: chain I residue 555 LYS Chi-restraints excluded: chain J residue 217 THR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 658 GLU Chi-restraints excluded: chain L residue 481 VAL Chi-restraints excluded: chain L residue 495 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 574 optimal weight: 1.9990 chunk 391 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 513 optimal weight: 0.9980 chunk 284 optimal weight: 3.9990 chunk 588 optimal weight: 9.9990 chunk 477 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 352 optimal weight: 5.9990 chunk 619 optimal weight: 0.0980 chunk 174 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 GLN C 464 HIS ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 341 GLN L 496 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 56478 Z= 0.186 Angle : 0.532 9.245 76290 Z= 0.283 Chirality : 0.044 0.193 8436 Planarity : 0.004 0.065 9996 Dihedral : 4.680 59.260 7886 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.58 % Allowed : 14.00 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.43 (0.10), residues: 7104 helix: 2.20 (0.10), residues: 2724 sheet: 0.85 (0.13), residues: 1452 loop : -0.16 (0.11), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 276 HIS 0.004 0.001 HIS C 255 PHE 0.019 0.001 PHE B 497 TYR 0.012 0.001 TYR I 457 ARG 0.018 0.000 ARG L 490 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 352 time to evaluate : 4.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8404 (mm) REVERT: A 717 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6390 (tp30) REVERT: B 269 LYS cc_start: 0.8678 (mppt) cc_final: 0.7985 (mptt) REVERT: B 416 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7914 (mp0) REVERT: B 505 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8829 (pp) REVERT: C 261 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8673 (t80) REVERT: C 302 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8462 (mm) REVERT: C 658 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8814 (mm-30) REVERT: D 407 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7368 (t80) REVERT: E 261 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8695 (m-80) REVERT: E 658 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8447 (mp0) REVERT: F 170 MET cc_start: 0.6503 (mmm) cc_final: 0.6294 (mmt) REVERT: F 261 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8646 (m-80) REVERT: G 130 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.8917 (mp0) REVERT: G 416 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7837 (mp0) REVERT: G 489 GLN cc_start: 0.8803 (tp-100) cc_final: 0.8275 (tm-30) REVERT: G 505 LEU cc_start: 0.9285 (mt) cc_final: 0.8949 (pp) REVERT: H 302 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8287 (mm) REVERT: I 130 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.8924 (mp0) REVERT: I 505 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8974 (pp) REVERT: J 269 LYS cc_start: 0.8685 (mppt) cc_final: 0.7976 (mptt) REVERT: J 416 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7894 (mp0) REVERT: J 505 LEU cc_start: 0.9183 (mt) cc_final: 0.8912 (pp) REVERT: K 261 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8672 (t80) REVERT: K 302 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8450 (mm) REVERT: K 658 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8806 (mm-30) REVERT: L 407 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7353 (t80) outliers start: 93 outliers final: 29 residues processed: 415 average time/residue: 1.5095 time to fit residues: 782.9181 Evaluate side-chains 361 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 314 time to evaluate : 4.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 663 LYS Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 623 LYS Chi-restraints excluded: chain F residue 653 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 269 LYS Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain I residue 497 PHE Chi-restraints excluded: chain I residue 505 LEU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 464 HIS Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain K residue 658 GLU Chi-restraints excluded: chain K residue 663 LYS Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 407 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 232 optimal weight: 3.9990 chunk 621 optimal weight: 40.0000 chunk 136 optimal weight: 10.0000 chunk 405 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 690 optimal weight: 0.8980 chunk 573 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 362 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 HIS D 496 GLN F 341 GLN H 341 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 56478 Z= 0.286 Angle : 0.552 9.197 76290 Z= 0.293 Chirality : 0.045 0.203 8436 Planarity : 0.004 0.057 9996 Dihedral : 4.670 59.407 7886 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.65 % Allowed : 14.63 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.41 (0.10), residues: 7104 helix: 2.22 (0.10), residues: 2724 sheet: 0.84 (0.13), residues: 1392 loop : -0.19 (0.11), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 276 HIS 0.005 0.001 HIS C 255 PHE 0.025 0.001 PHE G 497 TYR 0.020 0.001 TYR D 457 ARG 0.013 0.000 ARG D 490 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 337 time to evaluate : 5.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8419 (mm) REVERT: A 623 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8700 (mmtp) REVERT: A 717 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6410 (tp30) REVERT: B 213 MET cc_start: 0.9570 (mtp) cc_final: 0.9359 (mtp) REVERT: B 505 LEU cc_start: 0.9241 (mt) cc_final: 0.8916 (pp) REVERT: C 91 MET cc_start: 0.8459 (mtp) cc_final: 0.8168 (mtm) REVERT: C 261 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8687 (t80) REVERT: C 302 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8544 (mm) REVERT: C 658 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8756 (mm-30) REVERT: D 416 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7822 (mm-30) REVERT: E 244 MET cc_start: 0.0662 (mtm) cc_final: 0.0324 (mtt) REVERT: E 261 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8678 (m-80) REVERT: E 284 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8204 (pttt) REVERT: E 658 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8600 (mm-30) REVERT: F 261 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8667 (m-80) REVERT: G 130 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.8984 (mp0) REVERT: G 505 LEU cc_start: 0.9327 (mt) cc_final: 0.9021 (pp) REVERT: G 563 MET cc_start: 0.8789 (mmm) cc_final: 0.8541 (mmp) REVERT: H 302 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8287 (mm) REVERT: I 130 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8970 (mp0) REVERT: I 416 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8047 (mp0) REVERT: I 425 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9166 (ttp) REVERT: I 505 LEU cc_start: 0.9306 (mt) cc_final: 0.9011 (pp) REVERT: J 505 LEU cc_start: 0.9285 (mt) cc_final: 0.8959 (pp) REVERT: K 261 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8687 (t80) REVERT: K 302 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8533 (mm) REVERT: K 658 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8745 (mm-30) REVERT: L 253 GLU cc_start: 0.7401 (mp0) cc_final: 0.7103 (mp0) REVERT: L 407 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7322 (t80) outliers start: 97 outliers final: 36 residues processed: 410 average time/residue: 1.5044 time to fit residues: 770.6798 Evaluate side-chains 365 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 311 time to evaluate : 4.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 663 LYS Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain E residue 276 CYS Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 623 LYS Chi-restraints excluded: chain F residue 653 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 261 PHE Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 269 LYS Chi-restraints excluded: chain I residue 299 LYS Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain I residue 497 PHE Chi-restraints excluded: chain J residue 315 ASP Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 464 HIS Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain K residue 658 GLU Chi-restraints excluded: chain K residue 663 LYS Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 407 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 666 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 393 optimal weight: 0.8980 chunk 504 optimal weight: 0.9980 chunk 390 optimal weight: 0.9990 chunk 581 optimal weight: 2.9990 chunk 385 optimal weight: 0.8980 chunk 688 optimal weight: 4.9990 chunk 430 optimal weight: 8.9990 chunk 419 optimal weight: 0.0980 chunk 317 optimal weight: 40.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 HIS H 341 GLN K 464 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 56478 Z= 0.149 Angle : 0.513 10.527 76290 Z= 0.270 Chirality : 0.044 0.184 8436 Planarity : 0.004 0.050 9996 Dihedral : 4.489 59.538 7886 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.43 % Allowed : 15.14 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.57 (0.10), residues: 7104 helix: 2.39 (0.10), residues: 2724 sheet: 0.85 (0.13), residues: 1464 loop : -0.13 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 276 HIS 0.003 0.001 HIS L 285 PHE 0.024 0.001 PHE G 497 TYR 0.011 0.001 TYR C 270 ARG 0.014 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 343 time to evaluate : 4.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8573 (mtmt) REVERT: A 302 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8403 (mm) REVERT: A 623 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8727 (mmtp) REVERT: B 505 LEU cc_start: 0.9229 (mt) cc_final: 0.8881 (pp) REVERT: C 261 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8632 (t80) REVERT: C 302 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8538 (mm) REVERT: C 658 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8745 (mm-30) REVERT: D 253 GLU cc_start: 0.7381 (mp0) cc_final: 0.7129 (mp0) REVERT: D 407 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7430 (t80) REVERT: D 416 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7828 (mm-30) REVERT: D 490 ARG cc_start: 0.8155 (ptm-80) cc_final: 0.7727 (ptp-170) REVERT: E 170 MET cc_start: 0.6346 (mmm) cc_final: 0.6045 (mmt) REVERT: E 244 MET cc_start: 0.0533 (mtm) cc_final: 0.0283 (mtt) REVERT: E 261 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8672 (m-80) REVERT: E 658 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8602 (mm-30) REVERT: F 170 MET cc_start: 0.6408 (mmm) cc_final: 0.6025 (mmt) REVERT: F 261 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8650 (m-80) REVERT: G 130 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8935 (mp0) REVERT: G 416 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7841 (mp0) REVERT: G 505 LEU cc_start: 0.9351 (mt) cc_final: 0.9063 (pp) REVERT: H 160 MET cc_start: 0.7107 (mmt) cc_final: 0.6719 (mmm) REVERT: H 302 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8445 (mt) REVERT: I 130 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8926 (mp0) REVERT: I 407 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7379 (t80) REVERT: I 416 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8051 (mp0) REVERT: I 505 LEU cc_start: 0.9345 (mt) cc_final: 0.9077 (pp) REVERT: J 505 LEU cc_start: 0.9272 (mt) cc_final: 0.8973 (pp) REVERT: K 136 MET cc_start: 0.6896 (mmm) cc_final: 0.5865 (tpp) REVERT: K 261 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8635 (t80) REVERT: K 302 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8556 (mm) REVERT: K 658 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8743 (mm-30) REVERT: L 253 GLU cc_start: 0.7274 (mp0) cc_final: 0.7021 (mp0) REVERT: L 407 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7384 (t80) outliers start: 84 outliers final: 27 residues processed: 407 average time/residue: 1.5086 time to fit residues: 764.9866 Evaluate side-chains 369 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 324 time to evaluate : 4.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 653 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain H residue 261 PHE Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 269 LYS Chi-restraints excluded: chain I residue 407 PHE Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain K residue 658 GLU Chi-restraints excluded: chain L residue 407 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 425 optimal weight: 10.0000 chunk 274 optimal weight: 0.9990 chunk 411 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 135 optimal weight: 30.0000 chunk 133 optimal weight: 50.0000 chunk 437 optimal weight: 1.9990 chunk 468 optimal weight: 1.9990 chunk 340 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 540 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 341 GLN C 464 HIS F 194 HIS H 341 GLN K 464 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 56478 Z= 0.209 Angle : 0.529 9.607 76290 Z= 0.278 Chirality : 0.044 0.225 8436 Planarity : 0.004 0.052 9996 Dihedral : 4.470 59.760 7886 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.33 % Allowed : 15.27 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.53 (0.10), residues: 7104 helix: 2.38 (0.10), residues: 2724 sheet: 0.77 (0.13), residues: 1404 loop : -0.11 (0.11), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 276 HIS 0.004 0.001 HIS I 75 PHE 0.016 0.001 PHE I 497 TYR 0.016 0.001 TYR L 457 ARG 0.012 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 343 time to evaluate : 4.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8424 (mm) REVERT: A 334 MET cc_start: 0.6069 (ptm) cc_final: 0.5772 (ptt) REVERT: A 623 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8700 (mmtp) REVERT: B 416 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7573 (mp0) REVERT: B 505 LEU cc_start: 0.9234 (mt) cc_final: 0.8918 (pp) REVERT: C 261 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8618 (t80) REVERT: C 302 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8551 (mm) REVERT: C 658 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8758 (mm-30) REVERT: D 253 GLU cc_start: 0.7498 (mp0) cc_final: 0.7214 (mp0) REVERT: D 407 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7354 (t80) REVERT: D 416 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7868 (mm-30) REVERT: D 490 ARG cc_start: 0.8161 (ptm-80) cc_final: 0.7785 (ptp-170) REVERT: E 244 MET cc_start: 0.0352 (mtm) cc_final: 0.0118 (mtt) REVERT: E 261 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8697 (m-80) REVERT: E 658 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8587 (mm-30) REVERT: F 261 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8571 (m-80) REVERT: F 334 MET cc_start: 0.5953 (ptm) cc_final: 0.5493 (ptm) REVERT: F 658 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: G 130 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8962 (mp0) REVERT: G 416 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7828 (mp0) REVERT: G 505 LEU cc_start: 0.9395 (mt) cc_final: 0.9088 (pp) REVERT: H 302 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8499 (mt) REVERT: I 130 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8943 (mp0) REVERT: I 416 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8044 (mp0) REVERT: I 505 LEU cc_start: 0.9428 (mt) cc_final: 0.9116 (pp) REVERT: J 416 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7574 (mp0) REVERT: J 505 LEU cc_start: 0.9251 (mt) cc_final: 0.8960 (pp) REVERT: K 136 MET cc_start: 0.7533 (mmm) cc_final: 0.7052 (tpp) REVERT: K 244 MET cc_start: 0.0658 (mtt) cc_final: 0.0437 (mtt) REVERT: K 261 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8635 (t80) REVERT: K 302 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8541 (mm) REVERT: K 658 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8752 (mm-30) REVERT: L 407 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7377 (t80) outliers start: 78 outliers final: 36 residues processed: 400 average time/residue: 1.5241 time to fit residues: 759.2774 Evaluate side-chains 378 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 325 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain E residue 276 CYS Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 653 MET Chi-restraints excluded: chain F residue 658 GLU Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 261 PHE Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 340 LEU Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 522 MET Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain J residue 315 ASP Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 302 LEU Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 330 ASN Chi-restraints excluded: chain K residue 338 THR Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 653 MET Chi-restraints excluded: chain K residue 658 GLU Chi-restraints excluded: chain L residue 407 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 626 optimal weight: 20.0000 chunk 659 optimal weight: 0.8980 chunk 601 optimal weight: 9.9990 chunk 641 optimal weight: 8.9990 chunk 385 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 503 optimal weight: 0.6980 chunk 196 optimal weight: 0.6980 chunk 579 optimal weight: 4.9990 chunk 606 optimal weight: 4.9990 chunk 639 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 HIS H 341 GLN I 496 GLN K 464 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 56478 Z= 0.192 Angle : 0.533 11.890 76290 Z= 0.279 Chirality : 0.044 0.230 8436 Planarity : 0.004 0.050 9996 Dihedral : 4.432 59.977 7886 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.16 % Allowed : 15.75 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.57 (0.10), residues: 7104 helix: 2.40 (0.10), residues: 2724 sheet: 0.77 (0.13), residues: 1380 loop : -0.05 (0.11), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 276 HIS 0.004 0.001 HIS L 285 PHE 0.018 0.001 PHE J 497 TYR 0.014 0.001 TYR L 457 ARG 0.015 0.000 ARG G 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 336 time to evaluate : 4.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6654 (mpp) REVERT: A 302 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8425 (mm) REVERT: A 334 MET cc_start: 0.6025 (ptm) cc_final: 0.5782 (ptt) REVERT: A 623 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8703 (mmtp) REVERT: B 416 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7621 (mp0) REVERT: B 505 LEU cc_start: 0.9270 (mt) cc_final: 0.8942 (pp) REVERT: C 261 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8598 (t80) REVERT: C 658 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8714 (mm-30) REVERT: D 253 GLU cc_start: 0.7556 (mp0) cc_final: 0.7286 (mp0) REVERT: D 407 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7346 (t80) REVERT: D 416 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7856 (mm-30) REVERT: D 490 ARG cc_start: 0.8199 (ptm-80) cc_final: 0.7891 (ptp-170) REVERT: E 160 MET cc_start: 0.6864 (mmt) cc_final: 0.6554 (mmm) REVERT: E 170 MET cc_start: 0.6393 (mmm) cc_final: 0.5964 (mmt) REVERT: E 244 MET cc_start: 0.0339 (mtm) cc_final: 0.0112 (mtt) REVERT: E 261 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: E 658 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8599 (mm-30) REVERT: F 160 MET cc_start: 0.6821 (mmt) cc_final: 0.6555 (mmm) REVERT: F 170 MET cc_start: 0.6267 (mmm) cc_final: 0.5856 (mmt) REVERT: F 261 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8593 (m-80) REVERT: F 334 MET cc_start: 0.6143 (ptm) cc_final: 0.5616 (ptm) REVERT: G 130 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8951 (mp0) REVERT: G 416 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7923 (mp0) REVERT: G 505 LEU cc_start: 0.9405 (mt) cc_final: 0.9025 (pp) REVERT: H 160 MET cc_start: 0.7233 (mmt) cc_final: 0.6795 (mmm) REVERT: H 302 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8505 (mt) REVERT: I 130 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8938 (mp0) REVERT: I 416 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8016 (mp0) REVERT: I 505 LEU cc_start: 0.9426 (mt) cc_final: 0.9089 (pp) REVERT: J 416 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7621 (mp0) REVERT: J 505 LEU cc_start: 0.9272 (mt) cc_final: 0.8981 (pp) REVERT: K 261 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8614 (t80) REVERT: K 658 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8771 (mm-30) REVERT: L 253 GLU cc_start: 0.7541 (mp0) cc_final: 0.7316 (mp0) REVERT: L 407 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7305 (t80) REVERT: L 490 ARG cc_start: 0.8125 (ptm-80) cc_final: 0.7897 (ptm-80) outliers start: 68 outliers final: 28 residues processed: 389 average time/residue: 1.5206 time to fit residues: 738.1318 Evaluate side-chains 367 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 324 time to evaluate : 4.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 653 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 261 PHE Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 340 LEU Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 338 THR Chi-restraints excluded: chain K residue 658 GLU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 407 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 421 optimal weight: 0.4980 chunk 678 optimal weight: 7.9990 chunk 413 optimal weight: 9.9990 chunk 321 optimal weight: 10.0000 chunk 471 optimal weight: 3.9990 chunk 711 optimal weight: 2.9990 chunk 654 optimal weight: 5.9990 chunk 566 optimal weight: 0.7980 chunk 58 optimal weight: 40.0000 chunk 437 optimal weight: 20.0000 chunk 347 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 HIS H 341 GLN K 341 GLN K 464 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 56478 Z= 0.218 Angle : 0.545 11.638 76290 Z= 0.284 Chirality : 0.044 0.236 8436 Planarity : 0.004 0.064 9996 Dihedral : 4.440 59.712 7886 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.97 % Allowed : 16.02 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.56 (0.10), residues: 7104 helix: 2.39 (0.10), residues: 2724 sheet: 0.76 (0.13), residues: 1380 loop : -0.06 (0.11), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 276 HIS 0.004 0.001 HIS I 75 PHE 0.016 0.001 PHE I 497 TYR 0.016 0.001 TYR L 457 ARG 0.015 0.000 ARG H 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14208 Ramachandran restraints generated. 7104 Oldfield, 0 Emsley, 7104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 330 time to evaluate : 5.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.7552 (mmm) cc_final: 0.6822 (tpp) REVERT: A 302 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8429 (mm) REVERT: A 409 ARG cc_start: 0.7227 (ttp80) cc_final: 0.7008 (tmm-80) REVERT: A 623 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8691 (mmtp) REVERT: B 416 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7628 (mp0) REVERT: B 505 LEU cc_start: 0.9262 (mt) cc_final: 0.8956 (pp) REVERT: C 261 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8606 (t80) REVERT: C 658 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8725 (mm-30) REVERT: D 253 GLU cc_start: 0.7599 (mp0) cc_final: 0.7326 (mp0) REVERT: D 407 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7302 (t80) REVERT: D 416 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7901 (mm-30) REVERT: D 490 ARG cc_start: 0.8194 (ptm-80) cc_final: 0.7894 (ptp-170) REVERT: E 160 MET cc_start: 0.6790 (mmt) cc_final: 0.6567 (mmm) REVERT: E 244 MET cc_start: 0.0323 (mtm) cc_final: 0.0104 (mtt) REVERT: E 261 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8733 (m-80) REVERT: E 325 MET cc_start: 0.7338 (tpt) cc_final: 0.7095 (tpt) REVERT: F 160 MET cc_start: 0.6739 (mmt) cc_final: 0.6527 (mmm) REVERT: F 170 MET cc_start: 0.6352 (mmm) cc_final: 0.5964 (mmt) REVERT: F 261 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8745 (m-80) REVERT: F 325 MET cc_start: 0.7244 (tpt) cc_final: 0.7022 (tpt) REVERT: F 334 MET cc_start: 0.6142 (ptm) cc_final: 0.5552 (ptm) REVERT: G 130 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.8968 (mp0) REVERT: G 254 GLU cc_start: 0.9038 (tt0) cc_final: 0.8551 (tp30) REVERT: G 416 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7936 (mp0) REVERT: G 489 GLN cc_start: 0.8585 (tp-100) cc_final: 0.8145 (tm-30) REVERT: G 505 LEU cc_start: 0.9414 (mt) cc_final: 0.9012 (pp) REVERT: H 160 MET cc_start: 0.7182 (mmt) cc_final: 0.6793 (mmm) REVERT: H 302 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8512 (mt) REVERT: I 130 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8950 (mp0) REVERT: I 416 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8028 (mp0) REVERT: I 505 LEU cc_start: 0.9437 (mt) cc_final: 0.9083 (pp) REVERT: J 416 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7628 (mp0) REVERT: J 505 LEU cc_start: 0.9275 (mt) cc_final: 0.8988 (pp) REVERT: K 160 MET cc_start: 0.6633 (mmt) cc_final: 0.6421 (mmm) REVERT: K 261 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8623 (t80) REVERT: K 658 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8785 (mm-30) REVERT: L 253 GLU cc_start: 0.7625 (mp0) cc_final: 0.7397 (mp0) REVERT: L 254 GLU cc_start: 0.9100 (tt0) cc_final: 0.8256 (tm-30) REVERT: L 407 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7299 (t80) REVERT: L 490 ARG cc_start: 0.8082 (ptm-80) cc_final: 0.7843 (ptm-80) outliers start: 57 outliers final: 32 residues processed: 379 average time/residue: 1.5237 time to fit residues: 722.2232 Evaluate side-chains 368 residues out of total 5880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 323 time to evaluate : 4.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain E residue 261 PHE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 261 PHE Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 340 LEU Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 269 LYS Chi-restraints excluded: chain J residue 301 ASP Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 338 THR Chi-restraints excluded: chain K residue 340 LEU Chi-restraints excluded: chain K residue 658 GLU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 407 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 449 optimal weight: 0.8980 chunk 603 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 522 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 567 optimal weight: 0.2980 chunk 237 optimal weight: 4.9990 chunk 582 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 HIS K 464 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.116368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.066634 restraints weight = 121776.148| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.67 r_work: 0.2671 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 56478 Z= 0.190 Angle : 0.539 12.687 76290 Z= 0.281 Chirality : 0.044 0.232 8436 Planarity : 0.004 0.051 9996 Dihedral : 4.405 59.437 7886 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.85 % Allowed : 16.19 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.60 (0.10), residues: 7104 helix: 2.43 (0.10), residues: 2724 sheet: 0.88 (0.13), residues: 1350 loop : -0.09 (0.11), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 276 HIS 0.003 0.001 HIS I 75 PHE 0.019 0.001 PHE J 497 TYR 0.014 0.001 TYR L 457 ARG 0.013 0.000 ARG G 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16539.08 seconds wall clock time: 287 minutes 38.40 seconds (17258.40 seconds total)