Starting phenix.real_space_refine on Thu Feb 5 00:18:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m7n_63689/02_2026/9m7n_63689.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m7n_63689/02_2026/9m7n_63689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m7n_63689/02_2026/9m7n_63689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m7n_63689/02_2026/9m7n_63689.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m7n_63689/02_2026/9m7n_63689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m7n_63689/02_2026/9m7n_63689.map" } resolution = 3.46 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 8805 2.51 5 N 2310 2.21 5 O 2766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13944 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4648 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 12, 'TRANS': 575} Chain: "B" Number of atoms: 4648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4648 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 12, 'TRANS': 575} Chain: "C" Number of atoms: 4648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4648 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 12, 'TRANS': 575} Time building chain proxies: 2.84, per 1000 atoms: 0.20 Number of scatterers: 13944 At special positions: 0 Unit cell: (100.8, 105.6, 190.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2766 8.00 N 2310 7.00 C 8805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 620.0 milliseconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3246 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 33 sheets defined 18.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 109 through 117 Processing helix chain 'A' and resid 143 through 152 removed outlier: 3.646A pdb=" N GLN A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 349 through 352 removed outlier: 4.232A pdb=" N SER A 352 " --> pdb=" O LEU A 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 352' Processing helix chain 'A' and resid 353 through 372 removed outlier: 3.689A pdb=" N SER A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 removed outlier: 3.648A pdb=" N ILE A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 423 through 427 removed outlier: 4.109A pdb=" N SER A 427 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 removed outlier: 3.732A pdb=" N GLN A 511 " --> pdb=" O ILE A 508 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS A 512 " --> pdb=" O ASN A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 508 through 512' Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.653A pdb=" N LEU B 52 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 53 " --> pdb=" O VAL B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 53' Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 143 through 152 removed outlier: 3.548A pdb=" N GLN B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.525A pdb=" N THR B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 293 removed outlier: 3.615A pdb=" N LEU B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 352 removed outlier: 4.213A pdb=" N SER B 352 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 352' Processing helix chain 'B' and resid 353 through 372 removed outlier: 3.590A pdb=" N SER B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.595A pdb=" N ILE B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.847A pdb=" N SER B 427 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.651A pdb=" N GLN B 511 " --> pdb=" O ILE B 508 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS B 512 " --> pdb=" O ASN B 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 508 through 512' Processing helix chain 'C' and resid 49 through 53 removed outlier: 3.728A pdb=" N LEU C 52 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU C 53 " --> pdb=" O VAL C 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 49 through 53' Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 143 through 152 removed outlier: 3.599A pdb=" N GLN C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 279 through 293 Processing helix chain 'C' and resid 349 through 352 removed outlier: 4.207A pdb=" N SER C 352 " --> pdb=" O LEU C 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 352' Processing helix chain 'C' and resid 353 through 372 removed outlier: 3.642A pdb=" N SER C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 391 removed outlier: 3.553A pdb=" N ILE C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 508 through 512 removed outlier: 3.672A pdb=" N GLN C 511 " --> pdb=" O ILE C 508 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS C 512 " --> pdb=" O ASN C 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 508 through 512' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 6.989A pdb=" N PHE A 5 " --> pdb=" O ILE A 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 12 through 15 current: chain 'A' and resid 38 through 47 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 47 current: chain 'A' and resid 67 through 78 removed outlier: 5.829A pdb=" N ILE A 72 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 87 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 74 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 76 " --> pdb=" O ASN A 83 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 81 through 88 current: chain 'A' and resid 297 through 304 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 297 through 304 current: chain 'A' and resid 323 through 335 removed outlier: 6.310A pdb=" N VAL A 329 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY A 346 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 331 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 340 " --> pdb=" O ASP A 335 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 340 through 346 current: chain 'B' and resid 12 through 15 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 12 through 15 current: chain 'B' and resid 39 through 47 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 39 through 47 current: chain 'B' and resid 67 through 78 removed outlier: 7.015A pdb=" N LYS B 85 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLU B 75 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN B 83 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE B 77 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 81 through 88 current: chain 'B' and resid 297 through 304 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 297 through 304 current: chain 'B' and resid 323 through 335 removed outlier: 6.282A pdb=" N VAL B 329 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY B 346 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 331 " --> pdb=" O SER B 344 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 341 through 346 current: chain 'C' and resid 12 through 15 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 12 through 15 current: chain 'C' and resid 39 through 47 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 39 through 47 current: chain 'C' and resid 67 through 77 removed outlier: 6.913A pdb=" N LYS C 85 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU C 75 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN C 83 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE C 77 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 81 through 88 current: chain 'C' and resid 297 through 304 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 297 through 304 current: chain 'C' and resid 323 through 335 removed outlier: 6.327A pdb=" N VAL C 329 " --> pdb=" O GLY C 346 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY C 346 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA C 331 " --> pdb=" O SER C 344 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 340 " --> pdb=" O ASP C 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 127 removed outlier: 6.545A pdb=" N LEU A 125 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL A 175 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR A 127 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP A 164 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER A 170 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP A 172 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 247 removed outlier: 6.683A pdb=" N SER A 208 " --> pdb=" O GLN A 269 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL A 271 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL A 210 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 257 through 258 Processing sheet with id=AA7, first strand: chain 'A' and resid 397 through 400 removed outlier: 3.990A pdb=" N GLN A 415 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 430 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN A 434 " --> pdb=" O GLY A 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 460 through 461 removed outlier: 5.819A pdb=" N PHE A 460 " --> pdb=" O ALA B 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 465 through 467 removed outlier: 6.501A pdb=" N PHE C 460 " --> pdb=" O ILE A 465 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 467 " --> pdb=" O PHE C 460 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.910A pdb=" N ILE C 480 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN C 489 " --> pdb=" O GLU C 500 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 500 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS C 501 " --> pdb=" O PRO C 515 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 530 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 524 " --> pdb=" O LEU C 528 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 531 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 541 " --> pdb=" O ILE A 557 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.572A pdb=" N LEU A 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 515 through 517 removed outlier: 6.156A pdb=" N LYS A 501 " --> pdb=" O PRO A 515 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 500 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 489 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 480 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 479 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.578A pdb=" N GLY A 530 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE A 531 " --> pdb=" O GLY B 542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 545 through 546 Processing sheet with id=AB6, first strand: chain 'A' and resid 574 through 576 removed outlier: 5.992A pdb=" N ARG A 575 " --> pdb=" O LEU C 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AB8, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AB9, first strand: chain 'B' and resid 124 through 128 removed outlier: 6.525A pdb=" N LEU B 125 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL B 175 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR B 127 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP B 164 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER B 170 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP B 172 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 246 through 247 removed outlier: 6.804A pdb=" N SER B 208 " --> pdb=" O GLN B 269 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL B 271 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL B 210 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 257 through 258 Processing sheet with id=AC3, first strand: chain 'B' and resid 397 through 400 removed outlier: 3.861A pdb=" N GLN B 415 " --> pdb=" O MET B 400 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 430 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN B 434 " --> pdb=" O GLY B 437 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 460 through 461 removed outlier: 5.758A pdb=" N PHE B 460 " --> pdb=" O ALA C 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 488 through 492 removed outlier: 3.887A pdb=" N GLN B 489 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 500 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE B 499 " --> pdb=" O MET B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 520 through 522 removed outlier: 3.795A pdb=" N GLY B 530 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 531 " --> pdb=" O SER C 540 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 545 through 546 Processing sheet with id=AC8, first strand: chain 'B' and resid 568 through 570 Processing sheet with id=AC9, first strand: chain 'C' and resid 98 through 99 Processing sheet with id=AD1, first strand: chain 'C' and resid 107 through 108 Processing sheet with id=AD2, first strand: chain 'C' and resid 124 through 128 removed outlier: 6.476A pdb=" N LEU C 125 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL C 175 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR C 127 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP C 164 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER C 170 " --> pdb=" O ASP C 162 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP C 172 " --> pdb=" O PHE C 160 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 246 through 247 removed outlier: 3.563A pdb=" N LEU C 209 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER C 208 " --> pdb=" O GLN C 269 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL C 271 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL C 210 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AD5, first strand: chain 'C' and resid 397 through 400 removed outlier: 4.174A pdb=" N GLN C 415 " --> pdb=" O MET C 400 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 430 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN C 434 " --> pdb=" O GLY C 437 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE C 438 " --> pdb=" O ALA C 453 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 545 through 546 321 hydrogen bonds defined for protein. 876 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: 1.59 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2475 1.29 - 1.42: 3354 1.42 - 1.55: 8226 1.55 - 1.68: 0 1.68 - 1.81: 111 Bond restraints: 14166 Sorted by residual: bond pdb=" CA ASP C 185 " pdb=" C ASP C 185 " ideal model delta sigma weight residual 1.522 1.436 0.087 1.20e-02 6.94e+03 5.21e+01 bond pdb=" CA ASP B 185 " pdb=" CB ASP B 185 " ideal model delta sigma weight residual 1.533 1.426 0.107 1.60e-02 3.91e+03 4.46e+01 bond pdb=" CA ASP A 185 " pdb=" C ASP A 185 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.21e-02 6.83e+03 4.15e+01 bond pdb=" CA ASP B 185 " pdb=" C ASP B 185 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.19e-02 7.06e+03 3.37e+01 bond pdb=" CA ASP A 185 " pdb=" CB ASP A 185 " ideal model delta sigma weight residual 1.535 1.427 0.108 1.93e-02 2.68e+03 3.15e+01 ... (remaining 14161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 18590 1.73 - 3.46: 400 3.46 - 5.20: 48 5.20 - 6.93: 13 6.93 - 8.66: 2 Bond angle restraints: 19053 Sorted by residual: angle pdb=" C ASP A 584 " pdb=" N VAL A 585 " pdb=" CA VAL A 585 " ideal model delta sigma weight residual 121.97 130.63 -8.66 1.80e+00 3.09e-01 2.32e+01 angle pdb=" C VAL A 582 " pdb=" N ASN A 583 " pdb=" CA ASN A 583 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C ALA A 102 " pdb=" N ARG A 103 " pdb=" CA ARG A 103 " ideal model delta sigma weight residual 122.37 118.81 3.56 9.30e-01 1.16e+00 1.46e+01 angle pdb=" N GLU C 76 " pdb=" CA GLU C 76 " pdb=" C GLU C 76 " ideal model delta sigma weight residual 107.23 113.57 -6.34 1.67e+00 3.59e-01 1.44e+01 angle pdb=" N VAL A 576 " pdb=" CA VAL A 576 " pdb=" C VAL A 576 " ideal model delta sigma weight residual 106.32 112.21 -5.89 1.61e+00 3.86e-01 1.34e+01 ... (remaining 19048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 7775 17.49 - 34.98: 713 34.98 - 52.47: 82 52.47 - 69.95: 31 69.95 - 87.44: 9 Dihedral angle restraints: 8610 sinusoidal: 3543 harmonic: 5067 Sorted by residual: dihedral pdb=" CA ASP C 588 " pdb=" C ASP C 588 " pdb=" N SER C 589 " pdb=" CA SER C 589 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA TYR A 581 " pdb=" C TYR A 581 " pdb=" N VAL A 582 " pdb=" CA VAL A 582 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA GLY A 394 " pdb=" C GLY A 394 " pdb=" N GLY A 395 " pdb=" CA GLY A 395 " ideal model delta harmonic sigma weight residual -180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 8607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1400 0.040 - 0.079: 477 0.079 - 0.119: 207 0.119 - 0.158: 24 0.158 - 0.198: 4 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CB VAL B 585 " pdb=" CA VAL B 585 " pdb=" CG1 VAL B 585 " pdb=" CG2 VAL B 585 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA ASP B 185 " pdb=" N ASP B 185 " pdb=" C ASP B 185 " pdb=" CB ASP B 185 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA ASP A 185 " pdb=" N ASP A 185 " pdb=" C ASP A 185 " pdb=" CB ASP A 185 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 2109 not shown) Planarity restraints: 2457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 581 " 0.026 2.00e-02 2.50e+03 1.61e-02 5.16e+00 pdb=" CG TYR A 581 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 581 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 581 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 581 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 581 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 581 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 581 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 571 " -0.008 2.00e-02 2.50e+03 1.11e-02 2.17e+00 pdb=" CG PHE A 571 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 571 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 571 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 571 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 571 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 571 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 581 " -0.005 2.00e-02 2.50e+03 9.69e-03 1.88e+00 pdb=" CG TYR C 581 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR C 581 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR C 581 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR C 581 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 581 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 581 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 581 " 0.000 2.00e-02 2.50e+03 ... (remaining 2454 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1477 2.75 - 3.29: 12444 3.29 - 3.82: 21024 3.82 - 4.36: 23782 4.36 - 4.90: 43434 Nonbonded interactions: 102161 Sorted by model distance: nonbonded pdb=" OG SER A 540 " pdb=" O ASN C 529 " model vdw 2.210 3.040 nonbonded pdb=" O ASN A 529 " pdb=" OG SER B 540 " model vdw 2.249 3.040 nonbonded pdb=" O ASN B 529 " pdb=" OG SER C 540 " model vdw 2.256 3.040 nonbonded pdb=" O ASN A 583 " pdb=" N SER C 589 " model vdw 2.261 3.120 nonbonded pdb=" OE2 GLU C 500 " pdb=" NE2 HIS C 512 " model vdw 2.261 3.120 ... (remaining 102156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.010 Normalize map: mean=0, sd=1: 1.050 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.150 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.004 0.108 14166 Z= 0.233 Angle : 0.617 8.661 19053 Z= 0.350 Chirality : 0.047 0.198 2112 Planarity : 0.003 0.030 2457 Dihedral : 13.655 87.443 5364 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.39 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.20), residues: 1758 helix: 1.13 (0.34), residues: 285 sheet: -0.37 (0.23), residues: 555 loop : -2.09 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 411 TYR 0.036 0.001 TYR A 581 PHE 0.025 0.002 PHE A 571 TRP 0.019 0.002 TRP C 233 HIS 0.006 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00447 (14166) covalent geometry : angle 0.61740 (19053) hydrogen bonds : bond 0.23274 ( 321) hydrogen bonds : angle 8.89999 ( 876) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8086 (tpp) cc_final: 0.7614 (mtp) REVERT: A 409 GLN cc_start: 0.8211 (mp10) cc_final: 0.7976 (mp10) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1056 time to fit residues: 22.6342 Evaluate side-chains 108 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.087840 restraints weight = 23833.426| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.72 r_work: 0.3008 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14166 Z= 0.110 Angle : 0.540 8.808 19053 Z= 0.291 Chirality : 0.046 0.174 2112 Planarity : 0.003 0.030 2457 Dihedral : 5.040 22.632 1875 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.03 % Favored : 93.74 % Rotamer: Outliers : 0.77 % Allowed : 5.81 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.20), residues: 1758 helix: 1.51 (0.34), residues: 282 sheet: -0.15 (0.24), residues: 540 loop : -2.00 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 295 TYR 0.015 0.001 TYR C 581 PHE 0.025 0.001 PHE B 580 TRP 0.015 0.002 TRP B 233 HIS 0.005 0.001 HIS A 512 Details of bonding type rmsd covalent geometry : bond 0.00244 (14166) covalent geometry : angle 0.54040 (19053) hydrogen bonds : bond 0.03926 ( 321) hydrogen bonds : angle 6.10584 ( 876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 400 MET cc_start: 0.8777 (tpp) cc_final: 0.8320 (tpp) REVERT: C 114 LYS cc_start: 0.8866 (mmtp) cc_final: 0.8577 (mmmm) REVERT: C 406 ASN cc_start: 0.8626 (t0) cc_final: 0.8309 (t0) REVERT: C 516 MET cc_start: 0.6239 (mtp) cc_final: 0.5043 (ttt) outliers start: 12 outliers final: 11 residues processed: 140 average time/residue: 0.1043 time to fit residues: 22.4826 Evaluate side-chains 127 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 514 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.0050 chunk 27 optimal weight: 7.9990 chunk 76 optimal weight: 0.0770 overall best weight: 0.5754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.121602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.089854 restraints weight = 24265.662| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.76 r_work: 0.3043 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14166 Z= 0.087 Angle : 0.491 8.510 19053 Z= 0.265 Chirality : 0.045 0.164 2112 Planarity : 0.002 0.030 2457 Dihedral : 4.631 22.018 1875 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.95 % Favored : 94.82 % Rotamer: Outliers : 1.15 % Allowed : 7.54 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.20), residues: 1758 helix: 1.55 (0.34), residues: 285 sheet: 0.03 (0.24), residues: 552 loop : -1.98 (0.17), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 295 TYR 0.009 0.001 TYR C 581 PHE 0.011 0.001 PHE C 89 TRP 0.014 0.001 TRP B 233 HIS 0.004 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00185 (14166) covalent geometry : angle 0.49080 (19053) hydrogen bonds : bond 0.03165 ( 321) hydrogen bonds : angle 5.32804 ( 876) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7736 (mp0) cc_final: 0.7535 (mt-10) REVERT: B 80 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8169 (mm-30) REVERT: C 114 LYS cc_start: 0.8884 (mmtp) cc_final: 0.8613 (mmmm) REVERT: C 406 ASN cc_start: 0.8684 (t0) cc_final: 0.8430 (t0) REVERT: C 498 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.7274 (m) REVERT: C 516 MET cc_start: 0.6233 (mtp) cc_final: 0.5585 (ttt) REVERT: C 580 PHE cc_start: 0.5709 (m-80) cc_final: 0.5402 (m-80) outliers start: 18 outliers final: 13 residues processed: 150 average time/residue: 0.1035 time to fit residues: 24.0127 Evaluate side-chains 138 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 514 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 4 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 17 ASN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.116899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085017 restraints weight = 24526.219| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.77 r_work: 0.2962 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14166 Z= 0.169 Angle : 0.560 8.327 19053 Z= 0.301 Chirality : 0.047 0.154 2112 Planarity : 0.003 0.031 2457 Dihedral : 5.020 23.518 1875 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.71 % Favored : 93.06 % Rotamer: Outliers : 1.60 % Allowed : 9.26 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.20), residues: 1758 helix: 1.50 (0.34), residues: 279 sheet: 0.15 (0.24), residues: 510 loop : -2.07 (0.17), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 411 TYR 0.014 0.001 TYR B 323 PHE 0.012 0.002 PHE B 6 TRP 0.022 0.002 TRP C 454 HIS 0.004 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00404 (14166) covalent geometry : angle 0.56048 (19053) hydrogen bonds : bond 0.04709 ( 321) hydrogen bonds : angle 5.36680 ( 876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.514 Fit side-chains REVERT: A 51 GLU cc_start: 0.8607 (pt0) cc_final: 0.7917 (pm20) REVERT: A 66 VAL cc_start: 0.8613 (t) cc_final: 0.8360 (p) REVERT: A 371 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7855 (mpp) REVERT: C 51 GLU cc_start: 0.8043 (pm20) cc_final: 0.7682 (pm20) REVERT: C 406 ASN cc_start: 0.8789 (t0) cc_final: 0.8467 (t0) REVERT: C 516 MET cc_start: 0.6313 (mtp) cc_final: 0.5653 (ttt) outliers start: 25 outliers final: 20 residues processed: 138 average time/residue: 0.0885 time to fit residues: 19.1571 Evaluate side-chains 135 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 514 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.085667 restraints weight = 24545.170| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.78 r_work: 0.2974 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14166 Z= 0.140 Angle : 0.537 8.192 19053 Z= 0.288 Chirality : 0.046 0.168 2112 Planarity : 0.003 0.031 2457 Dihedral : 4.946 22.827 1875 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.03 % Favored : 93.74 % Rotamer: Outliers : 1.66 % Allowed : 10.54 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.20), residues: 1758 helix: 1.40 (0.34), residues: 285 sheet: 0.09 (0.24), residues: 510 loop : -2.08 (0.17), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 295 TYR 0.013 0.001 TYR A 323 PHE 0.016 0.001 PHE C 89 TRP 0.015 0.002 TRP C 454 HIS 0.003 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00330 (14166) covalent geometry : angle 0.53657 (19053) hydrogen bonds : bond 0.03934 ( 321) hydrogen bonds : angle 5.19142 ( 876) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.519 Fit side-chains REVERT: A 66 VAL cc_start: 0.8567 (t) cc_final: 0.8317 (p) REVERT: B 571 PHE cc_start: 0.7930 (t80) cc_final: 0.7355 (t80) REVERT: C 51 GLU cc_start: 0.8085 (pm20) cc_final: 0.7825 (pm20) REVERT: C 406 ASN cc_start: 0.8772 (t0) cc_final: 0.8411 (t0) REVERT: C 516 MET cc_start: 0.6305 (mtp) cc_final: 0.5743 (ttt) outliers start: 26 outliers final: 19 residues processed: 139 average time/residue: 0.0965 time to fit residues: 20.7158 Evaluate side-chains 136 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 514 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 158 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.085804 restraints weight = 24422.034| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.78 r_work: 0.2976 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14166 Z= 0.130 Angle : 0.529 8.149 19053 Z= 0.285 Chirality : 0.046 0.146 2112 Planarity : 0.003 0.030 2457 Dihedral : 4.857 22.568 1875 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.09 % Favored : 93.69 % Rotamer: Outliers : 1.92 % Allowed : 11.30 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.20), residues: 1758 helix: 1.71 (0.35), residues: 267 sheet: 0.10 (0.25), residues: 495 loop : -2.00 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 295 TYR 0.011 0.001 TYR B 323 PHE 0.012 0.001 PHE C 89 TRP 0.014 0.002 TRP C 454 HIS 0.003 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00309 (14166) covalent geometry : angle 0.52930 (19053) hydrogen bonds : bond 0.03761 ( 321) hydrogen bonds : angle 5.09644 ( 876) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.653 Fit side-chains REVERT: A 66 VAL cc_start: 0.8570 (t) cc_final: 0.8320 (p) REVERT: B 182 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: B 571 PHE cc_start: 0.8054 (t80) cc_final: 0.7453 (t80) REVERT: C 406 ASN cc_start: 0.8763 (t0) cc_final: 0.8452 (t0) REVERT: C 516 MET cc_start: 0.6332 (mtp) cc_final: 0.6056 (ttm) REVERT: C 556 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6632 (tm-30) outliers start: 30 outliers final: 24 residues processed: 140 average time/residue: 0.1100 time to fit residues: 23.9753 Evaluate side-chains 141 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 512 HIS Chi-restraints excluded: chain C residue 514 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN B 235 GLN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.118116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.086236 restraints weight = 24361.812| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.77 r_work: 0.2982 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14166 Z= 0.120 Angle : 0.522 8.037 19053 Z= 0.281 Chirality : 0.046 0.136 2112 Planarity : 0.003 0.031 2457 Dihedral : 4.768 22.137 1875 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.92 % Favored : 93.86 % Rotamer: Outliers : 1.79 % Allowed : 12.20 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.20), residues: 1758 helix: 1.75 (0.35), residues: 267 sheet: 0.15 (0.25), residues: 495 loop : -1.97 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 295 TYR 0.011 0.001 TYR A 323 PHE 0.010 0.001 PHE C 89 TRP 0.013 0.001 TRP C 454 HIS 0.003 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00280 (14166) covalent geometry : angle 0.52240 (19053) hydrogen bonds : bond 0.03547 ( 321) hydrogen bonds : angle 4.99288 ( 876) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.511 Fit side-chains REVERT: B 51 GLU cc_start: 0.8062 (pm20) cc_final: 0.7839 (pm20) REVERT: B 571 PHE cc_start: 0.8107 (t80) cc_final: 0.7490 (t80) REVERT: C 406 ASN cc_start: 0.8739 (t0) cc_final: 0.8429 (t0) REVERT: C 516 MET cc_start: 0.6331 (mtp) cc_final: 0.5856 (ttt) REVERT: C 556 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6674 (tm-30) outliers start: 28 outliers final: 21 residues processed: 137 average time/residue: 0.1090 time to fit residues: 23.0910 Evaluate side-chains 139 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 512 HIS Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 518 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 144 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 172 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 512 HIS ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 HIS C 415 GLN C 544 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.082685 restraints weight = 24451.397| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.76 r_work: 0.2925 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 14166 Z= 0.233 Angle : 0.619 7.987 19053 Z= 0.333 Chirality : 0.048 0.140 2112 Planarity : 0.003 0.033 2457 Dihedral : 5.319 23.826 1875 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.74 % Favored : 92.04 % Rotamer: Outliers : 2.04 % Allowed : 12.77 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.19), residues: 1758 helix: 1.00 (0.34), residues: 282 sheet: -0.16 (0.24), residues: 495 loop : -2.06 (0.17), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 411 TYR 0.018 0.001 TYR A 323 PHE 0.014 0.002 PHE C 375 TRP 0.029 0.002 TRP C 454 HIS 0.004 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00565 (14166) covalent geometry : angle 0.61931 (19053) hydrogen bonds : bond 0.05191 ( 321) hydrogen bonds : angle 5.34157 ( 876) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.567 Fit side-chains REVERT: A 66 VAL cc_start: 0.8647 (t) cc_final: 0.8366 (p) REVERT: B 182 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8324 (mp0) REVERT: B 571 PHE cc_start: 0.8281 (t80) cc_final: 0.7748 (t80) REVERT: C 406 ASN cc_start: 0.8890 (t0) cc_final: 0.8440 (t0) REVERT: C 516 MET cc_start: 0.6527 (mtp) cc_final: 0.6287 (ttm) REVERT: C 556 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6625 (tm-30) outliers start: 32 outliers final: 21 residues processed: 137 average time/residue: 0.0981 time to fit residues: 21.6131 Evaluate side-chains 130 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 512 HIS Chi-restraints excluded: chain C residue 514 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 102 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN ** B 406 ASN ** 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 = 0.3517 r_free = 0.3517 target = 0.113871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.082390 restraints weight = 24668.768| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.76 r_work: 0.2918 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14166 Z= 0.245 Angle : 0.639 8.064 19053 Z= 0.343 Chirality : 0.049 0.147 2112 Planarity : 0.003 0.032 2457 Dihedral : 5.447 23.520 1875 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.85 % Favored : 91.92 % Rotamer: Outliers : 1.72 % Allowed : 13.41 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.19), residues: 1758 helix: 0.78 (0.33), residues: 285 sheet: -0.46 (0.23), residues: 528 loop : -2.16 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 295 TYR 0.018 0.001 TYR A 323 PHE 0.029 0.002 PHE C 571 TRP 0.028 0.002 TRP C 454 HIS 0.004 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00592 (14166) covalent geometry : angle 0.63945 (19053) hydrogen bonds : bond 0.05191 ( 321) hydrogen bonds : angle 5.39956 ( 876) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.696 Fit side-chains REVERT: A 66 VAL cc_start: 0.8626 (t) cc_final: 0.8336 (p) REVERT: A 145 GLU cc_start: 0.7831 (mp0) cc_final: 0.7598 (mt-10) REVERT: A 498 THR cc_start: 0.7560 (m) cc_final: 0.7202 (p) REVERT: B 182 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: B 571 PHE cc_start: 0.8235 (t80) cc_final: 0.7754 (t80) REVERT: C 406 ASN cc_start: 0.8775 (t0) cc_final: 0.8348 (t0) REVERT: C 516 MET cc_start: 0.6592 (mtp) cc_final: 0.6334 (ttm) REVERT: C 556 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6575 (tm-30) outliers start: 27 outliers final: 22 residues processed: 130 average time/residue: 0.0985 time to fit residues: 20.3932 Evaluate side-chains 132 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 233 TRP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 512 HIS Chi-restraints excluded: chain C residue 514 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 168 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 173 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 0.0020 chunk 124 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.087676 restraints weight = 24165.976| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.76 r_work: 0.3007 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14166 Z= 0.093 Angle : 0.539 8.263 19053 Z= 0.287 Chirality : 0.045 0.141 2112 Planarity : 0.002 0.029 2457 Dihedral : 4.685 21.343 1875 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.35 % Favored : 94.43 % Rotamer: Outliers : 1.34 % Allowed : 13.86 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.20), residues: 1758 helix: 1.33 (0.35), residues: 285 sheet: -0.10 (0.24), residues: 525 loop : -2.04 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 295 TYR 0.007 0.001 TYR A 581 PHE 0.008 0.001 PHE C 89 TRP 0.009 0.001 TRP C 172 HIS 0.003 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00202 (14166) covalent geometry : angle 0.53879 (19053) hydrogen bonds : bond 0.02822 ( 321) hydrogen bonds : angle 4.92329 ( 876) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.578 Fit side-chains REVERT: A 145 GLU cc_start: 0.7656 (mp0) cc_final: 0.7427 (mt-10) REVERT: A 498 THR cc_start: 0.7485 (m) cc_final: 0.7144 (p) REVERT: A 516 MET cc_start: 0.6093 (ttm) cc_final: 0.5661 (ttt) REVERT: B 51 GLU cc_start: 0.8061 (pm20) cc_final: 0.7801 (pm20) REVERT: B 571 PHE cc_start: 0.8267 (t80) cc_final: 0.7668 (t80) REVERT: C 406 ASN cc_start: 0.8802 (t0) cc_final: 0.8457 (t0) REVERT: C 516 MET cc_start: 0.6473 (mtp) cc_final: 0.6243 (ttm) outliers start: 21 outliers final: 15 residues processed: 130 average time/residue: 0.1090 time to fit residues: 22.0620 Evaluate side-chains 127 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 TRP Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 512 HIS Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 512 HIS Chi-restraints excluded: chain C residue 514 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 130 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086405 restraints weight = 24381.645| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.76 r_work: 0.2987 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14166 Z= 0.117 Angle : 0.561 8.276 19053 Z= 0.296 Chirality : 0.046 0.176 2112 Planarity : 0.003 0.030 2457 Dihedral : 4.720 21.379 1875 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.92 % Favored : 93.86 % Rotamer: Outliers : 1.28 % Allowed : 13.60 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.20), residues: 1758 helix: 1.34 (0.35), residues: 285 sheet: 0.14 (0.24), residues: 507 loop : -2.06 (0.17), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 295 TYR 0.010 0.001 TYR A 323 PHE 0.027 0.001 PHE C 571 TRP 0.009 0.001 TRP B 172 HIS 0.002 0.000 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00271 (14166) covalent geometry : angle 0.56067 (19053) hydrogen bonds : bond 0.03460 ( 321) hydrogen bonds : angle 4.97994 ( 876) =============================================================================== Job complete usr+sys time: 2621.84 seconds wall clock time: 45 minutes 54.22 seconds (2754.22 seconds total)