Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 23:51:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/04_2023/3jd4_6633_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/04_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_6633/04_2023/3jd4_6633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/04_2023/3jd4_6633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/04_2023/3jd4_6633_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/04_2023/3jd4_6633_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 12.20, per 1000 atoms: 0.51 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: 11.58 Conformation dependent library (CDL) restraints added in 3.5 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: 2.42 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: 8.11 Time building geometry restraints manager: 12.27 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: 14382 33.47 - 66.95: 96 66.95 - 100.42: 6 100.42 - 133.89: 6 133.89 - 167.37: 6 Dihedral angle restraints: 14496 sinusoidal: 6000 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 14493 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: 0.730 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: 6.060 Check model and map are aligned: 0.360 Set scattering table: 0.190 Process input model: 63.290 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.190 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.970 ------------------------------------------------------------------------------- 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 : 10.215 167.367 9084 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 % 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 *********************** 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 : 3.218 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: 0.4306 time to fit residues: 342.0134 Evaluate side-chains 278 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 3.138 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6071 ------------------------------------------------------------------------------- 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 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** 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 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** 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 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** 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 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 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** 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 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** 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 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** 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: 0.8322 moved from start: 0.2305 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 : 0.666 10.681 33384 Z= 0.337 Chirality : 0.046 0.192 3618 Planarity : 0.005 0.042 4242 Dihedral : 11.867 163.568 3480 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 2.16 % 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: -2.52 (0.26), residues: 282 loop : -1.53 (0.17), residues: 1374 *********************** 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 402 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 348 time to evaluate : 3.042 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 37 residues processed: 392 average time/residue: 0.3749 time to fit residues: 232.6347 Evaluate side-chains 276 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 239 time to evaluate : 2.892 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2300 time to fit residues: 20.1063 ------------------------------------------------------------------------------- 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: 8.9990 chunk 222 optimal weight: 6.9990 chunk 181 optimal weight: 30.0000 chunk 73 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 238 optimal weight: 30.0000 chunk 265 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 228 ASN ** 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 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 193 ASN B 221 HIS ** 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 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 84 GLN ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 HIS ** C 225 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 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN ** 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 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN E 189 HIS E 193 ASN E 221 HIS ** 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 388 ASN ** 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 189 HIS F 221 HIS ** F 225 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 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.059 24612 Z= 0.474 Angle : 0.704 11.904 33384 Z= 0.354 Chirality : 0.048 0.162 3618 Planarity : 0.005 0.043 4242 Dihedral : 11.679 160.329 3480 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 2.72 % 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: -1.37 (0.15), residues: 2970 helix: -0.26 (0.14), residues: 1308 sheet: -2.43 (0.21), residues: 420 loop : -0.85 (0.19), residues: 1242 *********************** 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 360 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 292 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 41 residues processed: 336 average time/residue: 0.3623 time to fit residues: 192.7332 Evaluate side-chains 285 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 244 time to evaluate : 3.000 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.2199 time to fit residues: 21.0458 ------------------------------------------------------------------------------- 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: 6.9990 chunk 201 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 127 optimal weight: 0.0770 chunk 179 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 overall best weight: 2.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** 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 330 GLN ** 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 189 HIS ** 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS 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 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** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 24612 Z= 0.186 Angle : 0.558 9.414 33384 Z= 0.278 Chirality : 0.042 0.152 3618 Planarity : 0.004 0.047 4242 Dihedral : 10.882 158.773 3480 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 1.32 % 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: -0.45 (0.16), residues: 2970 helix: 0.56 (0.15), residues: 1302 sheet: -1.62 (0.25), residues: 312 loop : -0.72 (0.18), residues: 1356 *********************** 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 334 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 301 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 13 residues processed: 324 average time/residue: 0.3539 time to fit residues: 183.7369 Evaluate side-chains 266 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 253 time to evaluate : 2.923 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2254 time to fit residues: 9.4064 ------------------------------------------------------------------------------- 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: 4.9990 chunk 161 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 242 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 255 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 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 189 HIS C 297 GLN ** C 330 GLN ** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN ** 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: 0.8327 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 24612 Z= 0.306 Angle : 0.596 9.974 33384 Z= 0.297 Chirality : 0.045 0.165 3618 Planarity : 0.004 0.044 4242 Dihedral : 10.758 156.316 3480 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 1.08 % 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: -0.21 (0.16), residues: 2970 helix: 0.74 (0.14), residues: 1308 sheet: -1.33 (0.28), residues: 276 loop : -0.66 (0.18), residues: 1386 *********************** 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 302 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 275 time to evaluate : 3.030 Fit side-chains outliers start: 27 outliers final: 14 residues processed: 294 average time/residue: 0.3516 time to fit residues: 167.8610 Evaluate side-chains 262 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 248 time to evaluate : 3.010 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2340 time to fit residues: 10.0086 ------------------------------------------------------------------------------- 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: 9.9990 chunk 255 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 284 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 23 optimal weight: 0.0050 chunk 94 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- 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 391 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 297 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** 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 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 ASN F 297 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 24612 Z= 0.149 Angle : 0.528 8.014 33384 Z= 0.263 Chirality : 0.042 0.152 3618 Planarity : 0.004 0.046 4242 Dihedral : 10.202 154.251 3480 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.56 % 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: 0.97 (0.14), residues: 1344 sheet: -1.33 (0.25), residues: 372 loop : -0.39 (0.19), residues: 1254 *********************** 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 301 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 287 time to evaluate : 3.106 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 301 average time/residue: 0.3623 time to fit residues: 174.5113 Evaluate side-chains 254 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 247 time to evaluate : 2.837 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2214 time to fit residues: 6.9173 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 158 optimal weight: 0.0970 chunk 283 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- 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 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** 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 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 414 GLN E 81 GLN ** 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 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 24612 Z= 0.202 Angle : 0.545 8.926 33384 Z= 0.269 Chirality : 0.042 0.146 3618 Planarity : 0.004 0.044 4242 Dihedral : 10.032 152.029 3480 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.68 % 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: 0.23 (0.16), residues: 2970 helix: 0.98 (0.14), residues: 1356 sheet: -0.93 (0.25), residues: 408 loop : -0.26 (0.20), residues: 1206 *********************** 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 281 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 264 time to evaluate : 3.044 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 277 average time/residue: 0.3570 time to fit residues: 159.6988 Evaluate side-chains 253 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 245 time to evaluate : 3.160 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2257 time to fit residues: 7.5454 ------------------------------------------------------------------------------- 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: 4.9990 chunk 113 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 193 optimal weight: 0.0670 chunk 140 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 overall best weight: 4.8126 ------------------------------------------------------------------------------- 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** B 81 GLN ** B 297 GLN ** 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 ** 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 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 414 GLN ** E 81 GLN ** 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 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 24612 Z= 0.276 Angle : 0.582 9.604 33384 Z= 0.288 Chirality : 0.044 0.148 3618 Planarity : 0.004 0.043 4242 Dihedral : 10.006 150.558 3480 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.92 % 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: 0.21 (0.16), residues: 2970 helix: 0.98 (0.14), residues: 1374 sheet: -0.97 (0.25), residues: 408 loop : -0.30 (0.20), residues: 1188 *********************** 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 276 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 3.058 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 272 average time/residue: 0.3449 time to fit residues: 153.0317 Evaluate side-chains 260 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 246 time to evaluate : 2.923 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2193 time to fit residues: 9.7293 ------------------------------------------------------------------------------- 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: 7.9990 chunk 271 optimal weight: 20.0000 chunk 247 optimal weight: 5.9990 chunk 264 optimal weight: 0.8980 chunk 158 optimal weight: 0.2980 chunk 115 optimal weight: 7.9990 chunk 207 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 238 optimal weight: 20.0000 chunk 249 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- 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 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** 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 ** 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 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 81 GLN ** 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 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 24612 Z= 0.202 Angle : 0.553 9.080 33384 Z= 0.273 Chirality : 0.043 0.163 3618 Planarity : 0.004 0.045 4242 Dihedral : 9.781 148.827 3480 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 0.32 % 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: 0.28 (0.16), residues: 2970 helix: 1.01 (0.14), residues: 1422 sheet: -0.95 (0.25), residues: 414 loop : -0.26 (0.21), residues: 1134 *********************** 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 274 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 266 time to evaluate : 3.267 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 271 average time/residue: 0.3634 time to fit residues: 157.5496 Evaluate side-chains 249 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 245 time to evaluate : 2.869 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2351 time to fit residues: 5.5495 ------------------------------------------------------------------------------- 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: 20.0000 chunk 279 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 132 optimal weight: 50.0000 chunk 194 optimal weight: 8.9990 chunk 292 optimal weight: 0.9990 chunk 269 optimal weight: 6.9990 chunk 233 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 ** A 330 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 40 GLN C 297 GLN ** 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 ** 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 414 GLN ** E 81 GLN ** 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 297 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: 0.8301 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 24612 Z= 0.260 Angle : 0.582 10.650 33384 Z= 0.287 Chirality : 0.044 0.146 3618 Planarity : 0.004 0.043 4242 Dihedral : 9.738 147.187 3480 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.48 % 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: 0.33 (0.16), residues: 2970 helix: 1.05 (0.14), residues: 1410 sheet: -0.83 (0.25), residues: 414 loop : -0.27 (0.20), residues: 1146 ********************** 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 265 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 253 time to evaluate : 2.889 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 262 average time/residue: 0.3848 time to fit residues: 164.8044 Evaluate side-chains 253 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 242 time to evaluate : 2.897 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2305 time to fit residues: 8.6438 ------------------------------------------------------------------------------- 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: 8.9990 chunk 248 optimal weight: 0.0870 chunk 71 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 233 optimal weight: 0.0470 chunk 97 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 overall best weight: 3.4262 ------------------------------------------------------------------------------- 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 391 HIS ** 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 ** 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 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 81 GLN ** 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 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.111358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085848 restraints weight = 44919.311| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.32 r_work: 0.3017 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 24612 Z= 0.220 Angle : 0.565 10.513 33384 Z= 0.279 Chirality : 0.043 0.146 3618 Planarity : 0.004 0.045 4242 Dihedral : 9.581 145.563 3480 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.32 % 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: 0.50 (0.16), residues: 2970 helix: 1.25 (0.14), residues: 1374 sheet: -0.74 (0.26), residues: 414 loop : -0.23 (0.20), residues: 1182 =============================================================================== Job complete usr+sys time: 4852.39 seconds wall clock time: 93 minutes 29.48 seconds (5609.48 seconds total)