Starting phenix.real_space_refine on Wed Dec 13 07:11:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/12_2023/3jd4_6633_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/12_2023/3jd4_6633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/12_2023/3jd4_6633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/12_2023/3jd4_6633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/12_2023/3jd4_6633_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/12_2023/3jd4_6633_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 114 5.16 5 C 15060 2.51 5 N 4194 2.21 5 O 4644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 24054 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "B" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "C" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "D" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "E" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "F" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 12.90, per 1000 atoms: 0.54 Number of scatterers: 24054 At special positions: 0 Unit cell: (114.12, 129.421, 165.123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 42 15.00 O 4644 8.00 N 4194 7.00 C 15060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.34 Conformation dependent library (CDL) restraints added in 4.8 seconds 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5412 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 22 sheets defined 49.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.49 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.615A pdb=" N ILE A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.998A pdb=" N SER A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 removed outlier: 4.091A pdb=" N ALA A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 155 removed outlier: 3.526A pdb=" N LYS A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.569A pdb=" N TRP A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 214 through 227 Processing helix chain 'A' and resid 230 through 236 removed outlier: 4.201A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 288 through 297 removed outlier: 3.558A pdb=" N PHE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 333 through 338 Proline residue: A 337 - end of helix No H-bonds generated for 'chain 'A' and resid 333 through 338' Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.859A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 387 removed outlier: 4.376A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLY A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 420 removed outlier: 3.648A pdb=" N PHE A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR A 401 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 402 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG A 403 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU A 410 " --> pdb=" O TYR A 407 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET A 411 " --> pdb=" O HIS A 408 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 413 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 418 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.752A pdb=" N ASP A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 439' Processing helix chain 'A' and resid 445 through 470 removed outlier: 3.645A pdb=" N VAL A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 461 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 495 removed outlier: 3.531A pdb=" N ARG A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.615A pdb=" N ILE B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 53 removed outlier: 3.998A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 117 removed outlier: 4.091A pdb=" N ALA B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 155 removed outlier: 3.525A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.570A pdb=" N TRP B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 230 through 236 removed outlier: 4.201A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 288 through 297 removed outlier: 3.558A pdb=" N PHE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 333 through 338 Proline residue: B 337 - end of helix No H-bonds generated for 'chain 'B' and resid 333 through 338' Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.858A pdb=" N LYS B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 387 removed outlier: 4.376A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 378 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 420 removed outlier: 3.648A pdb=" N PHE B 399 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS B 400 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR B 401 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 402 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG B 403 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU B 410 " --> pdb=" O TYR B 407 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET B 411 " --> pdb=" O HIS B 408 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 413 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 418 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.752A pdb=" N ASP B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 434 through 439' Processing helix chain 'B' and resid 445 through 470 removed outlier: 3.645A pdb=" N VAL B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 470 " --> pdb=" O ARG B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 removed outlier: 3.531A pdb=" N ARG B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 492 " --> pdb=" O LYS B 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.615A pdb=" N ILE C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 53 removed outlier: 3.998A pdb=" N SER C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 117 removed outlier: 4.091A pdb=" N ALA C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 155 removed outlier: 3.526A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 186 removed outlier: 3.570A pdb=" N TRP C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'C' and resid 230 through 236 removed outlier: 4.201A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 288 through 297 removed outlier: 3.558A pdb=" N PHE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 333 through 338 Proline residue: C 337 - end of helix No H-bonds generated for 'chain 'C' and resid 333 through 338' Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.858A pdb=" N LYS C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 387 removed outlier: 4.377A pdb=" N ALA C 375 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY C 376 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL C 378 " --> pdb=" O ASN C 374 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 420 removed outlier: 3.649A pdb=" N PHE C 399 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS C 400 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR C 401 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 402 " --> pdb=" O PHE C 399 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG C 403 " --> pdb=" O LYS C 400 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU C 410 " --> pdb=" O TYR C 407 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET C 411 " --> pdb=" O HIS C 408 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 413 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 418 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'C' and resid 434 through 439 removed outlier: 3.752A pdb=" N ASP C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 434 through 439' Processing helix chain 'C' and resid 445 through 470 removed outlier: 3.645A pdb=" N VAL C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 454 " --> pdb=" O HIS C 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C 461 " --> pdb=" O MET C 457 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 470 " --> pdb=" O ARG C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 495 removed outlier: 3.532A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 492 " --> pdb=" O LYS C 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.614A pdb=" N ILE D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 53 removed outlier: 3.998A pdb=" N SER D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 117 removed outlier: 4.091A pdb=" N ALA D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 155 removed outlier: 3.526A pdb=" N LYS D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 186 removed outlier: 3.569A pdb=" N TRP D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 230 through 236 removed outlier: 4.201A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 288 through 297 removed outlier: 3.557A pdb=" N PHE D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.859A pdb=" N LYS D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 387 removed outlier: 4.376A pdb=" N ALA D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY D 376 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL D 378 " --> pdb=" O ASN D 374 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE D 383 " --> pdb=" O THR D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 420 removed outlier: 3.648A pdb=" N PHE D 399 " --> pdb=" O ARG D 396 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS D 400 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR D 401 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU D 402 " --> pdb=" O PHE D 399 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG D 403 " --> pdb=" O LYS D 400 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN D 406 " --> pdb=" O ARG D 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU D 410 " --> pdb=" O TYR D 407 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET D 411 " --> pdb=" O HIS D 408 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D 413 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU D 418 " --> pdb=" O GLU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 434 through 439 removed outlier: 3.752A pdb=" N ASP D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG D 439 " --> pdb=" O GLU D 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 434 through 439' Processing helix chain 'D' and resid 445 through 470 removed outlier: 3.645A pdb=" N VAL D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA D 461 " --> pdb=" O MET D 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D 470 " --> pdb=" O ARG D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 495 removed outlier: 3.530A pdb=" N ARG D 491 " --> pdb=" O GLU D 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 492 " --> pdb=" O LYS D 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 29 removed outlier: 3.614A pdb=" N ILE E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 53 removed outlier: 3.998A pdb=" N SER E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 117 removed outlier: 4.092A pdb=" N ALA E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 116 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 155 removed outlier: 3.525A pdb=" N LYS E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 186 removed outlier: 3.569A pdb=" N TRP E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 214 through 227 Processing helix chain 'E' and resid 230 through 236 removed outlier: 4.200A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 288 through 297 removed outlier: 3.558A pdb=" N PHE E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 316 No H-bonds generated for 'chain 'E' and resid 314 through 316' Processing helix chain 'E' and resid 333 through 338 Proline residue: E 337 - end of helix No H-bonds generated for 'chain 'E' and resid 333 through 338' Processing helix chain 'E' and resid 354 through 362 removed outlier: 3.859A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 387 removed outlier: 4.375A pdb=" N ALA E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY E 377 " --> pdb=" O LEU E 373 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL E 378 " --> pdb=" O ASN E 374 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE E 383 " --> pdb=" O THR E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 420 removed outlier: 3.648A pdb=" N PHE E 399 " --> pdb=" O ARG E 396 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS E 400 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR E 401 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU E 402 " --> pdb=" O PHE E 399 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG E 403 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU E 410 " --> pdb=" O TYR E 407 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET E 411 " --> pdb=" O HIS E 408 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL E 413 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU E 418 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 424 No H-bonds generated for 'chain 'E' and resid 422 through 424' Processing helix chain 'E' and resid 434 through 439 removed outlier: 3.753A pdb=" N ASP E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 434 through 439' Processing helix chain 'E' and resid 445 through 470 removed outlier: 3.645A pdb=" N VAL E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA E 454 " --> pdb=" O HIS E 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA E 461 " --> pdb=" O MET E 457 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 470 " --> pdb=" O ARG E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 495 removed outlier: 3.530A pdb=" N ARG E 491 " --> pdb=" O GLU E 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 removed outlier: 3.615A pdb=" N ILE F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 53 removed outlier: 3.998A pdb=" N SER F 47 " --> pdb=" O ASN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 117 removed outlier: 4.092A pdb=" N ALA F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 155 removed outlier: 3.526A pdb=" N LYS F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.570A pdb=" N TRP F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 214 through 227 Processing helix chain 'F' and resid 230 through 236 removed outlier: 4.201A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 264 Processing helix chain 'F' and resid 288 through 297 removed outlier: 3.558A pdb=" N PHE F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 333 through 338 Proline residue: F 337 - end of helix No H-bonds generated for 'chain 'F' and resid 333 through 338' Processing helix chain 'F' and resid 354 through 362 removed outlier: 3.859A pdb=" N LYS F 358 " --> pdb=" O PRO F 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE F 359 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 387 removed outlier: 4.376A pdb=" N ALA F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY F 376 " --> pdb=" O TYR F 372 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY F 377 " --> pdb=" O LEU F 373 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL F 378 " --> pdb=" O ASN F 374 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE F 383 " --> pdb=" O THR F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 420 removed outlier: 3.649A pdb=" N PHE F 399 " --> pdb=" O ARG F 396 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS F 400 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR F 401 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 402 " --> pdb=" O PHE F 399 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG F 403 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU F 410 " --> pdb=" O TYR F 407 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET F 411 " --> pdb=" O HIS F 408 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL F 413 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 418 " --> pdb=" O GLU F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 424 No H-bonds generated for 'chain 'F' and resid 422 through 424' Processing helix chain 'F' and resid 434 through 439 removed outlier: 3.752A pdb=" N ASP F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG F 439 " --> pdb=" O GLU F 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 434 through 439' Processing helix chain 'F' and resid 445 through 470 removed outlier: 3.644A pdb=" N VAL F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA F 454 " --> pdb=" O HIS F 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA F 461 " --> pdb=" O MET F 457 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS F 470 " --> pdb=" O ARG F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 495 removed outlier: 3.531A pdb=" N ARG F 491 " --> pdb=" O GLU F 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL F 492 " --> pdb=" O LYS F 488 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 57 through 60 removed outlier: 4.407A pdb=" N GLY A 92 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 272 through 274 removed outlier: 4.494A pdb=" N SER A 279 " --> pdb=" O TYR A 310 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 308 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 321 through 324 removed outlier: 6.523A pdb=" N ILE A 343 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA A 345 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= E, first strand: chain 'B' and resid 89 through 92 Processing sheet with id= F, first strand: chain 'B' and resid 272 through 274 removed outlier: 4.494A pdb=" N SER B 279 " --> pdb=" O TYR B 310 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 308 " --> pdb=" O TRP B 281 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 321 through 324 removed outlier: 6.524A pdb=" N ILE B 343 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA B 345 " --> pdb=" O PRO B 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= I, first strand: chain 'C' and resid 89 through 92 Processing sheet with id= J, first strand: chain 'C' and resid 272 through 274 removed outlier: 4.495A pdb=" N SER C 279 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 308 " --> pdb=" O TRP C 281 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 321 through 324 removed outlier: 6.523A pdb=" N ILE C 343 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA C 345 " --> pdb=" O PRO C 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= M, first strand: chain 'D' and resid 89 through 92 Processing sheet with id= N, first strand: chain 'D' and resid 272 through 274 removed outlier: 4.494A pdb=" N SER D 279 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 308 " --> pdb=" O TRP D 281 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 321 through 324 removed outlier: 6.523A pdb=" N ILE D 343 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA D 345 " --> pdb=" O PRO D 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= Q, first strand: chain 'E' and resid 89 through 92 Processing sheet with id= R, first strand: chain 'E' and resid 272 through 274 removed outlier: 4.494A pdb=" N SER E 279 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS E 308 " --> pdb=" O TRP E 281 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 321 through 324 removed outlier: 6.523A pdb=" N ILE E 343 " --> pdb=" O LEU E 322 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA E 345 " --> pdb=" O PRO E 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'F' and resid 57 through 60 removed outlier: 4.408A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 272 through 274 removed outlier: 4.494A pdb=" N SER F 279 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F 308 " --> pdb=" O TRP F 281 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 321 through 324 removed outlier: 6.524A pdb=" N ILE F 343 " --> pdb=" O LEU F 322 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA F 345 " --> pdb=" O PRO F 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= V 912 hydrogen bonds defined for protein. 2478 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.40 Time building geometry restraints manager: 11.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7511 1.33 - 1.45: 3456 1.45 - 1.57: 13375 1.57 - 1.68: 78 1.68 - 1.80: 192 Bond restraints: 24612 Sorted by residual: bond pdb=" C4A NAI A 601 " pdb=" C5A NAI A 601 " ideal model delta sigma weight residual 1.386 1.466 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" N PRO F 429 " pdb=" CD PRO F 429 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.60e+01 bond pdb=" C4A NAI B 602 " pdb=" C5A NAI B 602 " ideal model delta sigma weight residual 1.386 1.466 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C4A NAI C 602 " pdb=" C5A NAI C 602 " ideal model delta sigma weight residual 1.386 1.466 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C4A NAI E 602 " pdb=" C5A NAI E 602 " ideal model delta sigma weight residual 1.386 1.466 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 24607 not shown) Histogram of bond angle deviations from ideal: 98.66 - 106.79: 849 106.79 - 114.93: 14871 114.93 - 123.06: 16450 123.06 - 131.19: 1096 131.19 - 139.32: 118 Bond angle restraints: 33384 Sorted by residual: angle pdb=" C ILE A 428 " pdb=" N PRO A 429 " pdb=" CA PRO A 429 " ideal model delta sigma weight residual 119.84 114.17 5.67 1.25e+00 6.40e-01 2.06e+01 angle pdb=" C ILE C 428 " pdb=" N PRO C 429 " pdb=" CA PRO C 429 " ideal model delta sigma weight residual 119.84 114.19 5.65 1.25e+00 6.40e-01 2.04e+01 angle pdb=" C ILE E 428 " pdb=" N PRO E 429 " pdb=" CA PRO E 429 " ideal model delta sigma weight residual 119.84 114.20 5.64 1.25e+00 6.40e-01 2.04e+01 angle pdb=" C ILE B 428 " pdb=" N PRO B 429 " pdb=" CA PRO B 429 " ideal model delta sigma weight residual 119.84 114.20 5.64 1.25e+00 6.40e-01 2.03e+01 angle pdb=" C ILE F 428 " pdb=" N PRO F 429 " pdb=" CA PRO F 429 " ideal model delta sigma weight residual 119.84 114.21 5.63 1.25e+00 6.40e-01 2.03e+01 ... (remaining 33379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.47: 14779 33.47 - 66.95: 293 66.95 - 100.42: 12 100.42 - 133.89: 6 133.89 - 167.37: 6 Dihedral angle restraints: 15096 sinusoidal: 6600 harmonic: 8496 Sorted by residual: dihedral pdb=" C8 GTP D 602 " pdb=" C1' GTP D 602 " pdb=" N9 GTP D 602 " pdb=" O4' GTP D 602 " ideal model delta sinusoidal sigma weight residual 104.59 -62.77 167.37 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP F 603 " pdb=" C1' GTP F 603 " pdb=" N9 GTP F 603 " pdb=" O4' GTP F 603 " ideal model delta sinusoidal sigma weight residual 104.59 -62.72 167.32 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP C 603 " pdb=" C1' GTP C 603 " pdb=" N9 GTP C 603 " pdb=" O4' GTP C 603 " ideal model delta sinusoidal sigma weight residual 104.59 -62.72 167.31 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 15093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2508 0.049 - 0.097: 930 0.097 - 0.146: 135 0.146 - 0.195: 31 0.195 - 0.244: 14 Chirality restraints: 3618 Sorted by residual: chirality pdb=" C1B NAI E 602 " pdb=" C2B NAI E 602 " pdb=" N9A NAI E 602 " pdb=" O4B NAI E 602 " both_signs ideal model delta sigma weight residual False 2.31 2.55 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1B NAI D 601 " pdb=" C2B NAI D 601 " pdb=" N9A NAI D 601 " pdb=" O4B NAI D 601 " both_signs ideal model delta sigma weight residual False 2.31 2.55 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1B NAI B 602 " pdb=" C2B NAI B 602 " pdb=" N9A NAI B 602 " pdb=" O4B NAI B 602 " both_signs ideal model delta sigma weight residual False 2.31 2.55 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 3615 not shown) Planarity restraints: 4242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 282 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO D 283 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 283 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 283 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 282 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO F 283 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 283 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 283 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 282 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 283 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.028 5.00e-02 4.00e+02 ... (remaining 4239 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1174 2.71 - 3.25: 26475 3.25 - 3.80: 39019 3.80 - 4.35: 53457 4.35 - 4.90: 86124 Nonbonded interactions: 206249 Sorted by model distance: nonbonded pdb=" O HIS D 195 " pdb=" NZ LYS D 201 " model vdw 2.157 2.520 nonbonded pdb=" O HIS C 195 " pdb=" NZ LYS C 201 " model vdw 2.157 2.520 nonbonded pdb=" O HIS A 195 " pdb=" NZ LYS A 201 " model vdw 2.157 2.520 nonbonded pdb=" O HIS B 195 " pdb=" NZ LYS B 201 " model vdw 2.157 2.520 nonbonded pdb=" O HIS E 195 " pdb=" NZ LYS E 201 " model vdw 2.158 2.520 ... (remaining 206244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 501 or resid 601)) selection = (chain 'B' and (resid 5 through 501 or resid 602)) selection = (chain 'C' and (resid 5 through 501 or resid 601)) selection = (chain 'D' and (resid 5 through 501 or resid 601)) selection = (chain 'E' and (resid 5 through 501 or resid 602)) selection = (chain 'F' and (resid 5 through 501 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.160 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 66.390 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 0.080 24612 Z= 0.587 Angle : 0.963 14.319 33384 Z= 0.498 Chirality : 0.052 0.244 3618 Planarity : 0.004 0.051 4242 Dihedral : 12.302 167.367 9684 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.84 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.82 (0.12), residues: 2970 helix: -3.67 (0.08), residues: 1320 sheet: -3.54 (0.22), residues: 312 loop : -2.42 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 178 HIS 0.010 0.002 HIS E 450 PHE 0.034 0.003 PHE C 122 TYR 0.033 0.003 TYR A 78 ARG 0.005 0.001 ARG F 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 542 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 0.4365 time to fit residues: 347.7222 Evaluate side-chains 278 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 3.125 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 7.9990 chunk 222 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 140 optimal weight: 50.0000 chunk 171 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 HIS ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 HIS ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 ASN ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 24612 Z= 0.334 Angle : 0.665 10.730 33384 Z= 0.337 Chirality : 0.046 0.194 3618 Planarity : 0.005 0.043 4242 Dihedral : 13.611 163.601 4080 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.20 % Allowed : 7.99 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.14), residues: 2970 helix: -1.23 (0.12), residues: 1314 sheet: -2.51 (0.26), residues: 282 loop : -1.54 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 72 HIS 0.007 0.002 HIS E 450 PHE 0.022 0.002 PHE A 16 TYR 0.021 0.002 TYR C 78 ARG 0.005 0.001 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 350 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 38 residues processed: 394 average time/residue: 0.3534 time to fit residues: 219.7532 Evaluate side-chains 279 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 241 time to evaluate : 2.647 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2094 time to fit residues: 18.5686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 222 optimal weight: 0.8980 chunk 181 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 238 optimal weight: 20.0000 chunk 265 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN F 84 GLN F 189 HIS ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24612 Z= 0.210 Angle : 0.567 9.446 33384 Z= 0.287 Chirality : 0.043 0.152 3618 Planarity : 0.004 0.043 4242 Dihedral : 12.702 161.499 4080 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.56 % Allowed : 10.31 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2970 helix: 0.18 (0.14), residues: 1296 sheet: -2.30 (0.24), residues: 342 loop : -0.71 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 72 HIS 0.006 0.001 HIS F 258 PHE 0.017 0.002 PHE E 9 TYR 0.013 0.001 TYR F 78 ARG 0.004 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 338 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 19 residues processed: 360 average time/residue: 0.3626 time to fit residues: 209.3828 Evaluate side-chains 287 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 268 time to evaluate : 2.821 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2142 time to fit residues: 11.5997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 29 optimal weight: 0.0770 chunk 127 optimal weight: 0.0870 chunk 179 optimal weight: 7.9990 chunk 268 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 overall best weight: 2.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 84 GLN C 189 HIS ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN F 84 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24612 Z= 0.193 Angle : 0.542 9.562 33384 Z= 0.271 Chirality : 0.042 0.156 3618 Planarity : 0.004 0.046 4242 Dihedral : 12.162 159.066 4080 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.08 % Allowed : 10.71 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2970 helix: 0.68 (0.14), residues: 1296 sheet: -1.88 (0.24), residues: 378 loop : -0.46 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 72 HIS 0.005 0.001 HIS E 450 PHE 0.015 0.002 PHE F 9 TYR 0.009 0.001 TYR F 78 ARG 0.004 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 300 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 28 residues processed: 338 average time/residue: 0.3546 time to fit residues: 190.9597 Evaluate side-chains 284 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 256 time to evaluate : 2.585 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3019 time to fit residues: 17.4599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 HIS B 228 ASN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN C 221 HIS ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 HIS ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 ASN F 221 HIS ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24612 Z= 0.281 Angle : 0.580 9.940 33384 Z= 0.290 Chirality : 0.044 0.156 3618 Planarity : 0.004 0.048 4242 Dihedral : 11.895 156.248 4080 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.16 % Allowed : 12.67 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 2970 helix: 0.84 (0.14), residues: 1302 sheet: -1.27 (0.24), residues: 408 loop : -0.41 (0.19), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 72 HIS 0.006 0.001 HIS B 450 PHE 0.020 0.002 PHE B 122 TYR 0.013 0.002 TYR C 78 ARG 0.003 0.000 ARG F 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 270 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 291 average time/residue: 0.3458 time to fit residues: 163.8725 Evaluate side-chains 265 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 245 time to evaluate : 2.876 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2234 time to fit residues: 12.0362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 284 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 23 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 HIS ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 24612 Z= 0.295 Angle : 0.580 10.005 33384 Z= 0.289 Chirality : 0.044 0.152 3618 Planarity : 0.004 0.046 4242 Dihedral : 11.535 154.509 4080 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.32 % Allowed : 13.27 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2970 helix: 0.72 (0.14), residues: 1374 sheet: -1.07 (0.24), residues: 402 loop : -0.44 (0.20), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 72 HIS 0.006 0.001 HIS B 450 PHE 0.016 0.002 PHE E 122 TYR 0.013 0.002 TYR B 78 ARG 0.003 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 260 time to evaluate : 2.568 Fit side-chains outliers start: 33 outliers final: 16 residues processed: 286 average time/residue: 0.3521 time to fit residues: 161.7900 Evaluate side-chains 258 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 242 time to evaluate : 2.906 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2248 time to fit residues: 10.9042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 239 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 283 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24612 Z= 0.163 Angle : 0.525 8.051 33384 Z= 0.261 Chirality : 0.042 0.149 3618 Planarity : 0.004 0.046 4242 Dihedral : 11.008 152.376 4080 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.60 % Allowed : 14.03 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2970 helix: 1.08 (0.14), residues: 1350 sheet: -1.19 (0.25), residues: 378 loop : -0.30 (0.20), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 72 HIS 0.005 0.001 HIS D 450 PHE 0.013 0.001 PHE D 148 TYR 0.008 0.001 TYR C 183 ARG 0.003 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 303 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 312 average time/residue: 0.3656 time to fit residues: 181.4314 Evaluate side-chains 253 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 249 time to evaluate : 2.967 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2371 time to fit residues: 5.8537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 180 optimal weight: 20.0000 chunk 193 optimal weight: 0.3980 chunk 140 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 222 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN B 81 GLN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24612 Z= 0.180 Angle : 0.533 10.379 33384 Z= 0.263 Chirality : 0.042 0.146 3618 Planarity : 0.004 0.045 4242 Dihedral : 10.717 149.999 4080 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.56 % Allowed : 14.87 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 2970 helix: 1.00 (0.14), residues: 1410 sheet: -0.87 (0.25), residues: 414 loop : -0.24 (0.21), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 72 HIS 0.005 0.001 HIS D 450 PHE 0.014 0.001 PHE F 9 TYR 0.012 0.001 TYR D 372 ARG 0.003 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 265 time to evaluate : 2.558 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 274 average time/residue: 0.3480 time to fit residues: 153.9285 Evaluate side-chains 256 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 250 time to evaluate : 2.585 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2339 time to fit residues: 6.3677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 8.9990 chunk 271 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 249 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 ASN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24612 Z= 0.218 Angle : 0.547 10.612 33384 Z= 0.269 Chirality : 0.042 0.148 3618 Planarity : 0.004 0.046 4242 Dihedral : 10.569 148.087 4080 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.72 % Allowed : 14.87 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2970 helix: 1.03 (0.14), residues: 1392 sheet: -0.71 (0.25), residues: 402 loop : -0.24 (0.20), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 72 HIS 0.005 0.001 HIS D 450 PHE 0.015 0.002 PHE B 122 TYR 0.021 0.001 TYR D 372 ARG 0.004 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 270 time to evaluate : 2.980 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 283 average time/residue: 0.3588 time to fit residues: 162.2937 Evaluate side-chains 260 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 250 time to evaluate : 3.015 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2330 time to fit residues: 8.1736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 10.0000 chunk 279 optimal weight: 2.9990 chunk 170 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 194 optimal weight: 4.9990 chunk 292 optimal weight: 8.9990 chunk 269 optimal weight: 30.0000 chunk 233 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 180 optimal weight: 0.0010 chunk 143 optimal weight: 4.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 ASN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24612 Z= 0.219 Angle : 0.550 10.083 33384 Z= 0.271 Chirality : 0.043 0.147 3618 Planarity : 0.004 0.046 4242 Dihedral : 10.447 146.280 4080 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.36 % Allowed : 15.39 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2970 helix: 1.12 (0.14), residues: 1386 sheet: -0.67 (0.25), residues: 402 loop : -0.21 (0.20), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 72 HIS 0.005 0.001 HIS D 450 PHE 0.015 0.001 PHE B 122 TYR 0.029 0.001 TYR D 372 ARG 0.003 0.000 ARG C 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 266 time to evaluate : 2.972 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 274 average time/residue: 0.3534 time to fit residues: 156.7963 Evaluate side-chains 254 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 245 time to evaluate : 2.716 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2182 time to fit residues: 7.4589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.4980 chunk 248 optimal weight: 0.0030 chunk 71 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 29 optimal weight: 0.0270 chunk 43 optimal weight: 9.9990 overall best weight: 1.1052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 HIS ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 84 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN D 189 HIS ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN F 84 GLN F 135 ASN ** F 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.114801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089446 restraints weight = 45053.961| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.33 r_work: 0.3089 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24612 Z= 0.143 Angle : 0.519 9.763 33384 Z= 0.256 Chirality : 0.041 0.146 3618 Planarity : 0.004 0.046 4242 Dihedral : 10.200 143.146 4080 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.20 % Allowed : 15.35 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.16), residues: 2970 helix: 1.40 (0.15), residues: 1356 sheet: -0.66 (0.27), residues: 378 loop : -0.19 (0.20), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 72 HIS 0.004 0.001 HIS D 450 PHE 0.013 0.001 PHE C 122 TYR 0.028 0.001 TYR D 372 ARG 0.003 0.000 ARG C 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5072.01 seconds wall clock time: 94 minutes 22.11 seconds (5662.11 seconds total)