Starting phenix.real_space_refine on Thu Aug 6 15:44:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9til_55960/08_2026/9til_55960.cif Found real_map, /net/cci-nas-00/data/ceres_data/9til_55960/08_2026/9til_55960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9til_55960/08_2026/9til_55960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9til_55960/08_2026/9til_55960.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9til_55960/08_2026/9til_55960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9til_55960/08_2026/9til_55960.map" } resolution = 4.1 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 39 5.16 5 C 9939 2.51 5 N 2574 2.21 5 O 3091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15643 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3957 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 469} Chain breaks: 5 Chain: "B" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 4075 Classifications: {'peptide': 508} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 486} Chain breaks: 2 Chain: "C" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2416 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain breaks: 2 Chain: "D" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1540 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "E" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1529 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "F" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1529 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "G" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 597 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Time building chain proxies: 2.61, per 1000 atoms: 0.17 Number of scatterers: 15643 At special positions: 0 Unit cell: (108.368, 140.045, 131.709, 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 39 16.00 O 3091 8.00 N 2574 7.00 C 9939 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: 0.87 Conformation dependent library (CDL) restraints added in 563.3 milliseconds 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 25 sheets defined 11.1% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.723A pdb=" N LEU A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 285' Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.723A pdb=" N GLY A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.870A pdb=" N ASN A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.941A pdb=" N ASN B 152 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.992A pdb=" N LYS B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.615A pdb=" N GLY B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.741A pdb=" N ASN B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 441 removed outlier: 3.813A pdb=" N THR B 441 " --> pdb=" O ASP B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 462 Processing helix chain 'B' and resid 537 through 541 Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 148 through 152 removed outlier: 4.041A pdb=" N ASN C 152 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 removed outlier: 4.244A pdb=" N GLY C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 442 removed outlier: 3.726A pdb=" N THR C 441 " --> pdb=" O ASP C 437 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 462 removed outlier: 3.629A pdb=" N GLY C 461 " --> pdb=" O THR C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 46 Processing helix chain 'D' and resid 81 through 88 Processing helix chain 'E' and resid 34 through 47 removed outlier: 3.941A pdb=" N LYS E 47 " --> pdb=" O TYR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 81 through 88 removed outlier: 3.713A pdb=" N THR E 87 " --> pdb=" O ARG E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.832A pdb=" N ILE E 126 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'F' and resid 34 through 48 removed outlier: 4.654A pdb=" N LEU F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL F 42 " --> pdb=" O THR F 38 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR F 43 " --> pdb=" O ASP F 39 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN F 46 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS F 47 " --> pdb=" O TYR F 43 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER F 48 " --> pdb=" O ASN F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 81 through 86 Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'G' and resid 43 through 45 No H-bonds generated for 'chain 'G' and resid 43 through 45' Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 128 removed outlier: 6.616A pdb=" N GLU A 124 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR A 140 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASN A 126 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 141 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY A 154 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 207 removed outlier: 6.473A pdb=" N THR A 206 " --> pdb=" O TYR A 224 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 252 through 255 current: chain 'A' and resid 346 through 354 Processing sheet with id=AA3, first strand: chain 'A' and resid 228 through 235 removed outlier: 3.772A pdb=" N GLY A 229 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR A 240 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 233 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU A 238 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 10.725A pdb=" N ASN A 239 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU A 369 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N TYR A 367 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LYS A 277 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU A 369 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR A 275 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 324 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 413 through 414 Processing sheet with id=AA5, first strand: chain 'A' and resid 423 through 425 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 483 through 485 current: chain 'A' and resid 495 through 497 removed outlier: 3.633A pdb=" N THR A 497 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 515 through 525 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 515 through 525 current: chain 'A' and resid 557 through 558 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 557 through 558 current: chain 'B' and resid 445 through 451 removed outlier: 3.737A pdb=" N VAL B 484 " --> pdb=" O TYR B 500 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 506 " --> pdb=" O GLY B 501 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 506 through 507 current: chain 'G' and resid 21 through 28 Processing sheet with id=AA7, first strand: chain 'A' and resid 532 through 533 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 532 through 533 current: chain 'A' and resid 586 through 594 removed outlier: 3.686A pdb=" N LYS A 607 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A 592 " --> pdb=" O MET A 605 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET A 605 " --> pdb=" O TYR A 592 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR A 594 " --> pdb=" O PRO A 603 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 622 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR A 610 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL A 620 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ASP A 612 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR A 618 " --> pdb=" O ASP A 612 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 128 removed outlier: 6.883A pdb=" N GLU B 124 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR B 140 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN B 126 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 139 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY B 154 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 168 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 167 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER B 178 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 181 " --> pdb=" O GLN B 399 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 399 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 222 through 224 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 252 through 255 current: chain 'B' and resid 311 through 314 Processing sheet with id=AB1, first strand: chain 'B' and resid 228 through 235 removed outlier: 4.320A pdb=" N THR B 240 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 233 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU B 238 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N ASN B 239 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU B 369 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER B 273 " --> pdb=" O PRO B 370 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 372 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR B 271 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 330 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 272 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 328 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 276 " --> pdb=" O LYS B 324 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS B 324 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 515 through 525 removed outlier: 6.832A pdb=" N ILE B 634 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS B 521 " --> pdb=" O TYR B 632 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N TYR B 632 " --> pdb=" O LYS B 521 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR B 523 " --> pdb=" O LYS B 630 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N LYS B 630 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL B 631 " --> pdb=" O TRP B 549 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N TRP B 549 " --> pdb=" O VAL B 631 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN B 633 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE B 556 " --> pdb=" O ASP C 562 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG C 560 " --> pdb=" O THR B 558 " (cutoff:3.500A) removed outlier: 9.545A pdb=" N ARG B 560 " --> pdb=" O THR C 558 " (cutoff:3.500A) removed outlier: 12.571A pdb=" N THR C 558 " --> pdb=" O ARG B 560 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 557 " --> pdb=" O TYR C 548 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASN C 633 " --> pdb=" O THR C 547 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TRP C 549 " --> pdb=" O VAL C 631 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL C 631 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN C 633 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY C 522 " --> pdb=" O ASN C 633 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N MET C 635 " --> pdb=" O TRP C 520 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TRP C 520 " --> pdb=" O MET C 635 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N ILE C 637 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N LEU C 518 " --> pdb=" O ILE C 637 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 532 through 533 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 532 through 533 current: chain 'B' and resid 586 through 594 removed outlier: 3.575A pdb=" N THR B 594 " --> pdb=" O GLN B 602 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 600 through 603 current: chain 'B' and resid 617 through 622 Processing sheet with id=AB4, first strand: chain 'C' and resid 124 through 128 removed outlier: 6.777A pdb=" N GLU C 124 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR C 140 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN C 126 " --> pdb=" O TYR C 140 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA C 141 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLY C 154 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 423 through 425 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 495 through 496 current: chain 'C' and resid 506 through 507 Processing sheet with id=AB6, first strand: chain 'C' and resid 532 through 533 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 532 through 533 current: chain 'C' and resid 586 through 594 removed outlier: 5.586A pdb=" N THR C 594 " --> pdb=" O PRO C 603 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL C 606 " --> pdb=" O TRP C 623 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP C 623 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER C 608 " --> pdb=" O ALA C 621 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 621 " --> pdb=" O SER C 608 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 80 removed outlier: 3.838A pdb=" N GLY D 76 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 142 through 144 Processing sheet with id=AB9, first strand: chain 'D' and resid 147 through 148 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 147 through 148 current: chain 'F' and resid 98 through 105 removed outlier: 4.102A pdb=" N ASP F 98 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR F 117 " --> pdb=" O VAL F 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 154 through 157 removed outlier: 4.292A pdb=" N GLY D 157 " --> pdb=" O MET D 172 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N MET D 174 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG D 197 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 208 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 80 removed outlier: 3.582A pdb=" N GLY E 76 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP E 98 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E 113 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E 129 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E 137 " --> pdb=" O SER E 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 142 through 144 Processing sheet with id=AC4, first strand: chain 'E' and resid 153 through 157 removed outlier: 7.175A pdb=" N ALA E 153 " --> pdb=" O PHE E 170 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N MET E 172 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE E 155 " --> pdb=" O MET E 172 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET E 174 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY E 157 " --> pdb=" O MET E 174 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 210 through 211 Processing sheet with id=AC6, first strand: chain 'F' and resid 154 through 155 removed outlier: 3.635A pdb=" N MET F 172 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY F 185 " --> pdb=" O VAL F 171 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 58 through 59 384 hydrogen bonds defined for protein. 966 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: 2.33 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4982 1.34 - 1.46: 3552 1.46 - 1.58: 7388 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 15992 Sorted by residual: bond pdb=" CA VAL B 233 " pdb=" CB VAL B 233 " ideal model delta sigma weight residual 1.527 1.540 -0.014 1.31e-02 5.83e+03 1.07e+00 bond pdb=" CA LEU A 369 " pdb=" CB LEU A 369 " ideal model delta sigma weight residual 1.522 1.529 -0.007 7.00e-03 2.04e+04 1.04e+00 bond pdb=" CA ILE B 211 " pdb=" CB ILE B 211 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.01e+00 bond pdb=" CA VAL A 344 " pdb=" CB VAL A 344 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 9.44e-01 bond pdb=" CA LEU B 369 " pdb=" C LEU B 369 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 7.48e-01 ... (remaining 15987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 21181 1.09 - 2.18: 410 2.18 - 3.26: 86 3.26 - 4.35: 19 4.35 - 5.44: 1 Bond angle restraints: 21697 Sorted by residual: angle pdb=" C ASP B 562 " pdb=" N ILE B 563 " pdb=" CA ILE B 563 " ideal model delta sigma weight residual 123.16 120.25 2.91 1.06e+00 8.90e-01 7.51e+00 angle pdb=" C SER C 581 " pdb=" CA SER C 581 " pdb=" CB SER C 581 " ideal model delta sigma weight residual 110.42 114.63 -4.21 1.99e+00 2.53e-01 4.47e+00 angle pdb=" N ILE B 563 " pdb=" CA ILE B 563 " pdb=" CB ILE B 563 " ideal model delta sigma weight residual 111.64 109.95 1.69 8.20e-01 1.49e+00 4.25e+00 angle pdb=" CA LEU A 570 " pdb=" C LEU A 570 " pdb=" N TYR A 571 " ideal model delta sigma weight residual 114.90 117.66 -2.76 1.37e+00 5.33e-01 4.07e+00 angle pdb=" CA ASN C 568 " pdb=" C ASN C 568 " pdb=" N LEU C 569 " ideal model delta sigma weight residual 114.76 117.02 -2.26 1.14e+00 7.69e-01 3.93e+00 ... (remaining 21692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 9332 17.23 - 34.46: 124 34.46 - 51.69: 19 51.69 - 68.92: 1 68.92 - 86.15: 1 Dihedral angle restraints: 9477 sinusoidal: 3776 harmonic: 5701 Sorted by residual: dihedral pdb=" CA ILE B 563 " pdb=" C ILE B 563 " pdb=" N LYS B 564 " pdb=" CA LYS B 564 " ideal model delta harmonic sigma weight residual 180.00 -163.78 -16.22 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" N LYS B 474 " pdb=" CA LYS B 474 " pdb=" CB LYS B 474 " pdb=" CG LYS B 474 " ideal model delta sinusoidal sigma weight residual 60.00 110.50 -50.50 3 1.50e+01 4.44e-03 8.91e+00 dihedral pdb=" N LYS D 52 " pdb=" CA LYS D 52 " pdb=" CB LYS D 52 " pdb=" CG LYS D 52 " ideal model delta sinusoidal sigma weight residual -60.00 -108.79 48.79 3 1.50e+01 4.44e-03 8.69e+00 ... (remaining 9474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1441 0.027 - 0.053: 664 0.053 - 0.080: 82 0.080 - 0.106: 98 0.106 - 0.133: 114 Chirality restraints: 2399 Sorted by residual: chirality pdb=" CA ILE C 572 " pdb=" N ILE C 572 " pdb=" C ILE C 572 " pdb=" CB ILE C 572 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE B 394 " pdb=" N ILE B 394 " pdb=" C ILE B 394 " pdb=" CB ILE B 394 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA VAL D 104 " pdb=" N VAL D 104 " pdb=" C VAL D 104 " pdb=" CB VAL D 104 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 2396 not shown) Planarity restraints: 2763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 442 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 443 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 443 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 443 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 165 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO D 166 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 166 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 166 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 165 " -0.019 5.00e-02 4.00e+02 2.81e-02 1.27e+00 pdb=" N PRO E 166 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO E 166 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 166 " -0.016 5.00e-02 4.00e+02 ... (remaining 2760 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 212 2.63 - 3.20: 14117 3.20 - 3.76: 22396 3.76 - 4.33: 33158 4.33 - 4.90: 55527 Nonbonded interactions: 125410 Sorted by model distance: nonbonded pdb=" OG SER B 516 " pdb=" OE2 GLU C 514 " model vdw 2.062 3.040 nonbonded pdb=" OG SER A 265 " pdb=" OD2 ASP A 268 " model vdw 2.141 3.040 nonbonded pdb=" OG SER E 48 " pdb=" O GLN F 49 " model vdw 2.171 3.040 nonbonded pdb=" NZ LYS D 52 " pdb=" O ASN F 46 " model vdw 2.184 3.120 nonbonded pdb=" OD2 ASP D 195 " pdb=" NZ LYS D 214 " model vdw 2.193 3.120 ... (remaining 125405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 122 through 337 or resid 344 through 640)) selection = (chain 'B' and (resid 122 through 300 or resid 305 through 337 or resid 344 thro \ ugh 472 or resid 481 through 501 or resid 507 through 578 or resid 585 through 6 \ 40)) } ncs_group { reference = (chain 'D' and resid 33 through 228) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.410 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: 0.140 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 11.730 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 : 0.002 0.014 15992 Z= 0.087 Angle : 0.407 5.438 21697 Z= 0.237 Chirality : 0.040 0.133 2399 Planarity : 0.003 0.033 2763 Dihedral : 6.387 86.153 5837 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.11 % Allowed : 1.14 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.68 (0.20), residues: 1927 helix: 0.82 (0.49), residues: 131 sheet: 0.92 (0.22), residues: 570 loop : 0.27 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 352 TYR 0.005 0.000 TYR E 117 PHE 0.004 0.000 PHE A 526 TRP 0.003 0.000 TRP B 549 HIS 0.002 0.000 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00153 / 0.09 (15992) covalent geometry : angle 0.40723 / 0.24 (21697) hydrogen bonds : bond 0.28219 / 18.14 ( 384) hydrogen bonds : angle 9.70287 / 6.65 ( 966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 535 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7398 (tp30) cc_final: 0.7000 (tp30) REVERT: A 199 SER cc_start: 0.9229 (m) cc_final: 0.8490 (t) REVERT: A 202 VAL cc_start: 0.8500 (m) cc_final: 0.8280 (t) REVERT: A 284 LEU cc_start: 0.7418 (tp) cc_final: 0.6854 (tp) REVERT: A 377 LYS cc_start: 0.7958 (tttt) cc_final: 0.7566 (pttm) REVERT: A 418 ASN cc_start: 0.7261 (t0) cc_final: 0.6954 (t0) REVERT: A 529 THR cc_start: 0.7984 (p) cc_final: 0.7774 (t) REVERT: A 585 SER cc_start: 0.7396 (m) cc_final: 0.7134 (p) REVERT: B 143 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.5994 (mp) REVERT: B 153 THR cc_start: 0.7793 (m) cc_final: 0.7277 (p) REVERT: B 247 SER cc_start: 0.6953 (p) cc_final: 0.6607 (t) REVERT: B 277 LYS cc_start: 0.7928 (pttt) cc_final: 0.7696 (ptmm) REVERT: B 402 ILE cc_start: 0.9001 (pt) cc_final: 0.8770 (mt) REVERT: B 558 THR cc_start: 0.8474 (m) cc_final: 0.8025 (p) REVERT: B 623 TRP cc_start: 0.6952 (t-100) cc_final: 0.6732 (t-100) REVERT: C 168 LEU cc_start: 0.8720 (tp) cc_final: 0.8501 (tp) REVERT: C 170 GLU cc_start: 0.7274 (tt0) cc_final: 0.7069 (tt0) REVERT: C 402 ILE cc_start: 0.8683 (tt) cc_final: 0.8455 (mt) REVERT: C 410 HIS cc_start: 0.7884 (m-70) cc_final: 0.7682 (m-70) REVERT: C 438 LEU cc_start: 0.8102 (mt) cc_final: 0.7688 (mt) REVERT: C 487 LEU cc_start: 0.8400 (tp) cc_final: 0.8188 (tp) REVERT: C 500 TYR cc_start: 0.7166 (t80) cc_final: 0.6912 (t80) REVERT: C 514 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6898 (pp20) REVERT: C 520 TRP cc_start: 0.7920 (t60) cc_final: 0.7474 (t60) REVERT: C 545 GLU cc_start: 0.7048 (tt0) cc_final: 0.6829 (tt0) REVERT: C 547 THR cc_start: 0.9041 (m) cc_final: 0.8798 (p) REVERT: C 573 ARG cc_start: 0.8005 (mtt180) cc_final: 0.7498 (mtp85) REVERT: D 39 ASP cc_start: 0.6843 (t70) cc_final: 0.6589 (t0) REVERT: D 88 LEU cc_start: 0.7325 (mt) cc_final: 0.7076 (mt) REVERT: D 119 LEU cc_start: 0.8870 (mt) cc_final: 0.8659 (mt) REVERT: D 149 SER cc_start: 0.8845 (m) cc_final: 0.7996 (t) REVERT: D 169 TYR cc_start: 0.7381 (m-80) cc_final: 0.7085 (m-80) REVERT: D 206 THR cc_start: 0.7077 (p) cc_final: 0.6639 (m) REVERT: D 210 TYR cc_start: 0.7246 (m-80) cc_final: 0.6713 (m-10) REVERT: E 47 LYS cc_start: 0.7936 (mttt) cc_final: 0.7607 (mtpt) REVERT: E 99 VAL cc_start: 0.9249 (t) cc_final: 0.9020 (p) REVERT: E 150 ASN cc_start: 0.8669 (t0) cc_final: 0.8318 (t0) REVERT: F 43 TYR cc_start: 0.6289 (t80) cc_final: 0.6067 (t80) REVERT: F 106 LEU cc_start: 0.8523 (mt) cc_final: 0.8261 (mm) REVERT: F 178 MET cc_start: 0.6268 (mmm) cc_final: 0.5889 (mmm) REVERT: F 224 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7427 (mttm) REVERT: G 11 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7430 (mt-10) REVERT: G 56 GLU cc_start: 0.7692 (mt-10) cc_final: 0.6834 (tt0) outliers start: 2 outliers final: 1 residues processed: 537 average time/residue: 0.1086 time to fit residues: 86.6334 Evaluate side-chains 294 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN A 305 ASN A 345 ASN A 410 HIS A 469 GLN A 576 ASN A 616 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN B 361 ASN B 452 GLN B 624 ASN C 447 HIS E 46 ASN E 136 ASN F 124 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133010 restraints weight = 23912.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.132865 restraints weight = 24767.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133192 restraints weight = 21731.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133401 restraints weight = 17936.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133565 restraints weight = 16129.580| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15992 Z= 0.193 Angle : 0.618 7.183 21697 Z= 0.332 Chirality : 0.046 0.181 2399 Planarity : 0.004 0.049 2763 Dihedral : 4.507 22.396 2129 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.11 % Allowed : 2.56 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.00 (0.19), residues: 1927 helix: -0.40 (0.44), residues: 139 sheet: 0.65 (0.21), residues: 625 loop : -0.26 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 639 TYR 0.026 0.002 TYR C 420 PHE 0.017 0.002 PHE B 589 TRP 0.013 0.002 TRP B 426 HIS 0.005 0.002 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (15992) covalent geometry : angle 0.61795 / 0.33 (21697) hydrogen bonds : bond 0.04415 / 2.82 ( 384) hydrogen bonds : angle 6.70790 / 4.60 ( 966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 379 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.7965 (tttt) cc_final: 0.7498 (pttm) REVERT: A 545 GLU cc_start: 0.7440 (tp30) cc_final: 0.7162 (tp30) REVERT: A 585 SER cc_start: 0.7303 (m) cc_final: 0.6812 (p) REVERT: A 635 MET cc_start: 0.8695 (ttm) cc_final: 0.8426 (ttp) REVERT: B 153 THR cc_start: 0.7666 (m) cc_final: 0.7307 (p) REVERT: B 224 TYR cc_start: 0.7318 (m-80) cc_final: 0.6863 (m-80) REVERT: B 247 SER cc_start: 0.7238 (p) cc_final: 0.6699 (t) REVERT: B 440 MET cc_start: 0.8645 (mmt) cc_final: 0.8285 (mmm) REVERT: C 129 ASN cc_start: 0.6989 (t0) cc_final: 0.6687 (t0) REVERT: C 133 LEU cc_start: 0.8569 (mp) cc_final: 0.8041 (tp) REVERT: C 158 TYR cc_start: 0.8448 (t80) cc_final: 0.8109 (t80) REVERT: C 438 LEU cc_start: 0.8017 (mt) cc_final: 0.7735 (mt) REVERT: C 500 TYR cc_start: 0.7669 (t80) cc_final: 0.7292 (t80) REVERT: C 541 TYR cc_start: 0.6601 (m-80) cc_final: 0.6095 (m-80) REVERT: C 545 GLU cc_start: 0.7087 (tt0) cc_final: 0.6868 (tt0) REVERT: C 547 THR cc_start: 0.9248 (m) cc_final: 0.8788 (p) REVERT: D 140 GLU cc_start: 0.8673 (mp0) cc_final: 0.8452 (mp0) REVERT: D 169 TYR cc_start: 0.7621 (m-80) cc_final: 0.7087 (m-80) REVERT: D 206 THR cc_start: 0.7593 (p) cc_final: 0.6691 (m) REVERT: D 210 TYR cc_start: 0.7614 (m-80) cc_final: 0.7109 (m-10) REVERT: E 99 VAL cc_start: 0.9428 (t) cc_final: 0.9169 (p) REVERT: E 139 SER cc_start: 0.9035 (t) cc_final: 0.8769 (p) REVERT: E 169 TYR cc_start: 0.8043 (m-80) cc_final: 0.7599 (m-80) REVERT: E 178 MET cc_start: 0.9094 (tpp) cc_final: 0.8827 (tpp) REVERT: F 50 LYS cc_start: 0.8334 (tptp) cc_final: 0.7827 (mtmt) REVERT: F 59 LEU cc_start: 0.8253 (mt) cc_final: 0.7993 (mp) REVERT: F 159 ASN cc_start: 0.8082 (t0) cc_final: 0.7755 (t0) REVERT: F 178 MET cc_start: 0.6545 (mmm) cc_final: 0.6071 (mmm) outliers start: 2 outliers final: 1 residues processed: 381 average time/residue: 0.0989 time to fit residues: 57.4049 Evaluate side-chains 253 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 144 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 103 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 109 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN A 444 GLN ** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN C 410 HIS E 124 ASN E 136 ASN E 152 ASN F 124 ASN F 145 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.140312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133893 restraints weight = 24031.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134513 restraints weight = 20070.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134645 restraints weight = 18199.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135770 restraints weight = 16145.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135886 restraints weight = 12940.072| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15992 Z= 0.116 Angle : 0.535 7.440 21697 Z= 0.283 Chirality : 0.043 0.163 2399 Planarity : 0.004 0.037 2763 Dihedral : 4.372 20.642 2129 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.06 % Allowed : 2.33 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.02 (0.19), residues: 1927 helix: -0.32 (0.44), residues: 140 sheet: 0.61 (0.21), residues: 618 loop : -0.27 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 628 TYR 0.014 0.001 TYR F 220 PHE 0.016 0.001 PHE B 221 TRP 0.009 0.001 TRP C 549 HIS 0.004 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (15992) covalent geometry : angle 0.53546 / 0.28 (21697) hydrogen bonds : bond 0.03697 / 2.38 ( 384) hydrogen bonds : angle 6.22774 / 4.27 ( 966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 338 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 THR cc_start: 0.8711 (t) cc_final: 0.8464 (t) REVERT: A 259 LYS cc_start: 0.7558 (tmtt) cc_final: 0.6899 (tmtt) REVERT: A 377 LYS cc_start: 0.7951 (tttt) cc_final: 0.7497 (pttm) REVERT: A 585 SER cc_start: 0.7307 (m) cc_final: 0.6823 (p) REVERT: A 605 MET cc_start: 0.7861 (tpp) cc_final: 0.7626 (mmt) REVERT: A 627 GLU cc_start: 0.6400 (tp30) cc_final: 0.5972 (tp30) REVERT: A 635 MET cc_start: 0.8746 (ttm) cc_final: 0.8408 (ttp) REVERT: B 221 PHE cc_start: 0.7802 (m-10) cc_final: 0.7575 (m-10) REVERT: B 224 TYR cc_start: 0.7441 (m-80) cc_final: 0.6907 (m-80) REVERT: B 247 SER cc_start: 0.7241 (p) cc_final: 0.6725 (t) REVERT: B 440 MET cc_start: 0.8588 (mmt) cc_final: 0.8252 (mmm) REVERT: C 158 TYR cc_start: 0.8545 (t80) cc_final: 0.8067 (t80) REVERT: C 438 LEU cc_start: 0.8157 (mt) cc_final: 0.7692 (mt) REVERT: C 440 MET cc_start: 0.6775 (mmp) cc_final: 0.6525 (mmm) REVERT: C 500 TYR cc_start: 0.7440 (t80) cc_final: 0.7210 (t80) REVERT: C 541 TYR cc_start: 0.6198 (m-80) cc_final: 0.5677 (m-80) REVERT: C 545 GLU cc_start: 0.7001 (tt0) cc_final: 0.6703 (tt0) REVERT: C 547 THR cc_start: 0.9203 (m) cc_final: 0.8720 (p) REVERT: C 558 THR cc_start: 0.9036 (p) cc_final: 0.8802 (p) REVERT: D 169 TYR cc_start: 0.7447 (m-80) cc_final: 0.7186 (m-80) REVERT: D 206 THR cc_start: 0.7494 (p) cc_final: 0.6886 (m) REVERT: D 210 TYR cc_start: 0.7401 (m-80) cc_final: 0.6903 (m-10) REVERT: E 124 ASN cc_start: 0.6817 (OUTLIER) cc_final: 0.6503 (p0) REVERT: E 139 SER cc_start: 0.9032 (t) cc_final: 0.8655 (p) REVERT: F 50 LYS cc_start: 0.8236 (tptp) cc_final: 0.7804 (mtmt) REVERT: F 139 SER cc_start: 0.8432 (t) cc_final: 0.8061 (m) REVERT: F 159 ASN cc_start: 0.8020 (t0) cc_final: 0.7686 (t0) REVERT: F 178 MET cc_start: 0.6323 (mmm) cc_final: 0.6087 (mmm) REVERT: F 215 LYS cc_start: 0.8165 (mttp) cc_final: 0.7955 (mttp) REVERT: F 220 TYR cc_start: 0.7021 (m-10) cc_final: 0.6764 (m-10) REVERT: F 224 LYS cc_start: 0.7526 (ttpt) cc_final: 0.7056 (mttm) outliers start: 1 outliers final: 0 residues processed: 339 average time/residue: 0.0946 time to fit residues: 49.6481 Evaluate side-chains 243 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 0.0970 chunk 15 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 ASN A 444 GLN ** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN F 124 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133190 restraints weight = 23869.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133204 restraints weight = 27492.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133291 restraints weight = 22487.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133236 restraints weight = 19365.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133362 restraints weight = 17551.485| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15992 Z= 0.149 Angle : 0.549 7.865 21697 Z= 0.293 Chirality : 0.044 0.166 2399 Planarity : 0.004 0.038 2763 Dihedral : 4.634 21.795 2129 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.30 (0.19), residues: 1927 helix: -0.40 (0.45), residues: 140 sheet: 0.31 (0.20), residues: 632 loop : -0.42 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 83 TYR 0.015 0.002 TYR F 117 PHE 0.018 0.002 PHE E 186 TRP 0.009 0.001 TRP A 425 HIS 0.004 0.001 HIS C 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (15992) covalent geometry : angle 0.54940 / 0.29 (21697) hydrogen bonds : bond 0.03630 / 2.34 ( 384) hydrogen bonds : angle 6.08804 / 4.16 ( 966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: 0.7657 (t80) cc_final: 0.7407 (t80) REVERT: A 199 SER cc_start: 0.9207 (m) cc_final: 0.8675 (t) REVERT: A 259 LYS cc_start: 0.7254 (tmtt) cc_final: 0.6797 (tmtt) REVERT: A 364 VAL cc_start: 0.8186 (m) cc_final: 0.7880 (p) REVERT: A 585 SER cc_start: 0.7321 (m) cc_final: 0.6794 (p) REVERT: A 635 MET cc_start: 0.8715 (ttm) cc_final: 0.8435 (ttp) REVERT: B 224 TYR cc_start: 0.7466 (m-80) cc_final: 0.6794 (m-80) REVERT: B 247 SER cc_start: 0.7036 (p) cc_final: 0.6558 (t) REVERT: B 440 MET cc_start: 0.8583 (mmt) cc_final: 0.8347 (mmm) REVERT: B 574 ASP cc_start: 0.7845 (t0) cc_final: 0.7304 (t0) REVERT: C 158 TYR cc_start: 0.8551 (t80) cc_final: 0.8120 (t80) REVERT: C 438 LEU cc_start: 0.8156 (mt) cc_final: 0.7917 (mt) REVERT: C 440 MET cc_start: 0.6708 (mmp) cc_final: 0.6478 (mmm) REVERT: C 500 TYR cc_start: 0.7746 (t80) cc_final: 0.7377 (t80) REVERT: C 510 LEU cc_start: 0.7918 (mm) cc_final: 0.7262 (mt) REVERT: C 541 TYR cc_start: 0.6226 (m-80) cc_final: 0.5605 (m-80) REVERT: C 545 GLU cc_start: 0.6924 (tt0) cc_final: 0.6632 (tt0) REVERT: C 547 THR cc_start: 0.9188 (m) cc_final: 0.8706 (p) REVERT: D 140 GLU cc_start: 0.8845 (mp0) cc_final: 0.8566 (mm-30) REVERT: D 206 THR cc_start: 0.7476 (p) cc_final: 0.6905 (m) REVERT: D 210 TYR cc_start: 0.7407 (m-80) cc_final: 0.6945 (m-10) REVERT: E 139 SER cc_start: 0.8935 (t) cc_final: 0.8574 (p) REVERT: E 174 MET cc_start: 0.6301 (mmm) cc_final: 0.5801 (tpp) REVERT: F 50 LYS cc_start: 0.8185 (tptp) cc_final: 0.7828 (mtmt) REVERT: F 215 LYS cc_start: 0.8235 (mttp) cc_final: 0.7988 (mttp) REVERT: F 224 LYS cc_start: 0.7541 (ttpt) cc_final: 0.7105 (mttm) REVERT: G 56 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7136 (tt0) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.0881 time to fit residues: 44.0646 Evaluate side-chains 239 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 0.2980 chunk 70 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 147 optimal weight: 0.2980 chunk 179 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN ** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN ** B 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN C 447 HIS ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN F 124 ASN G 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130605 restraints weight = 24077.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130511 restraints weight = 30426.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130827 restraints weight = 25001.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130711 restraints weight = 20642.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130849 restraints weight = 18186.220| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15992 Z= 0.169 Angle : 0.576 9.524 21697 Z= 0.304 Chirality : 0.045 0.204 2399 Planarity : 0.004 0.039 2763 Dihedral : 4.887 23.190 2129 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.06 % Allowed : 1.87 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.59 (0.19), residues: 1927 helix: -0.47 (0.44), residues: 140 sheet: 0.08 (0.20), residues: 635 loop : -0.62 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 83 TYR 0.017 0.002 TYR F 117 PHE 0.017 0.002 PHE D 45 TRP 0.015 0.002 TRP C 507 HIS 0.004 0.001 HIS C 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (15992) covalent geometry : angle 0.57577 / 0.30 (21697) hydrogen bonds : bond 0.03642 / 2.36 ( 384) hydrogen bonds : angle 6.15649 / 4.19 ( 966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 THR cc_start: 0.7866 (p) cc_final: 0.7608 (t) REVERT: A 259 LYS cc_start: 0.7319 (tmtt) cc_final: 0.6855 (tmtt) REVERT: A 364 VAL cc_start: 0.8312 (m) cc_final: 0.7906 (p) REVERT: A 585 SER cc_start: 0.7365 (m) cc_final: 0.6856 (p) REVERT: B 224 TYR cc_start: 0.7504 (m-80) cc_final: 0.6760 (m-80) REVERT: B 247 SER cc_start: 0.6838 (p) cc_final: 0.6269 (t) REVERT: B 299 VAL cc_start: 0.7311 (p) cc_final: 0.7101 (p) REVERT: C 438 LEU cc_start: 0.8364 (mt) cc_final: 0.8125 (mt) REVERT: C 440 MET cc_start: 0.6330 (mmp) cc_final: 0.6124 (mmm) REVERT: C 541 TYR cc_start: 0.6200 (m-80) cc_final: 0.5630 (m-80) REVERT: C 545 GLU cc_start: 0.6900 (tt0) cc_final: 0.6663 (tt0) REVERT: C 547 THR cc_start: 0.9238 (m) cc_final: 0.8853 (p) REVERT: C 559 LYS cc_start: 0.7110 (tptt) cc_final: 0.6745 (tttp) REVERT: D 140 GLU cc_start: 0.8703 (mp0) cc_final: 0.8345 (mm-30) REVERT: D 206 THR cc_start: 0.7483 (p) cc_final: 0.6941 (m) REVERT: D 210 TYR cc_start: 0.7520 (m-80) cc_final: 0.7041 (m-10) REVERT: D 219 THR cc_start: 0.8347 (t) cc_final: 0.8074 (p) REVERT: E 139 SER cc_start: 0.9067 (t) cc_final: 0.8702 (p) REVERT: F 159 ASN cc_start: 0.7990 (t0) cc_final: 0.7534 (t0) REVERT: F 224 LYS cc_start: 0.7655 (ttpt) cc_final: 0.7105 (mttm) REVERT: G 56 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7228 (tt0) outliers start: 1 outliers final: 1 residues processed: 303 average time/residue: 0.0925 time to fit residues: 43.9241 Evaluate side-chains 227 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 21 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 135 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 143 optimal weight: 0.2980 chunk 119 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN ** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.133115 restraints weight = 23665.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131907 restraints weight = 31289.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131847 restraints weight = 21363.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132203 restraints weight = 18459.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132708 restraints weight = 16077.146| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15992 Z= 0.110 Angle : 0.531 9.048 21697 Z= 0.278 Chirality : 0.043 0.177 2399 Planarity : 0.004 0.039 2763 Dihedral : 4.605 20.362 2129 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.54 (0.19), residues: 1927 helix: -0.39 (0.44), residues: 140 sheet: 0.08 (0.21), residues: 634 loop : -0.56 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 83 TYR 0.027 0.001 TYR B 541 PHE 0.013 0.001 PHE F 170 TRP 0.029 0.001 TRP A 623 HIS 0.005 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (15992) covalent geometry : angle 0.53141 / 0.28 (21697) hydrogen bonds : bond 0.03164 / 2.03 ( 384) hydrogen bonds : angle 5.88186 / 4.01 ( 966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.7301 (tmtt) cc_final: 0.6823 (tmtt) REVERT: A 288 LEU cc_start: 0.8333 (mm) cc_final: 0.8117 (mm) REVERT: A 364 VAL cc_start: 0.8257 (m) cc_final: 0.7837 (p) REVERT: A 440 MET cc_start: 0.8182 (mmm) cc_final: 0.6745 (mmm) REVERT: A 467 THR cc_start: 0.8509 (m) cc_final: 0.7903 (p) REVERT: A 585 SER cc_start: 0.7322 (m) cc_final: 0.6832 (p) REVERT: B 224 TYR cc_start: 0.7557 (m-80) cc_final: 0.6786 (m-80) REVERT: B 247 SER cc_start: 0.6836 (p) cc_final: 0.6340 (t) REVERT: B 319 ILE cc_start: 0.8562 (tt) cc_final: 0.8238 (tt) REVERT: B 404 LYS cc_start: 0.8852 (tttt) cc_final: 0.8428 (tttt) REVERT: B 534 LEU cc_start: 0.6826 (tp) cc_final: 0.6243 (mm) REVERT: B 629 ILE cc_start: 0.8838 (mt) cc_final: 0.8590 (mp) REVERT: C 541 TYR cc_start: 0.6071 (m-80) cc_final: 0.5341 (m-80) REVERT: C 547 THR cc_start: 0.9251 (m) cc_final: 0.8842 (p) REVERT: C 569 LEU cc_start: 0.4422 (mt) cc_final: 0.4049 (mp) REVERT: D 33 ASN cc_start: 0.7078 (p0) cc_final: 0.6828 (p0) REVERT: D 140 GLU cc_start: 0.8792 (mp0) cc_final: 0.8493 (mm-30) REVERT: D 206 THR cc_start: 0.7482 (p) cc_final: 0.6966 (m) REVERT: D 210 TYR cc_start: 0.7415 (m-80) cc_final: 0.7173 (m-80) REVERT: D 219 THR cc_start: 0.8309 (t) cc_final: 0.8003 (p) REVERT: E 139 SER cc_start: 0.8960 (t) cc_final: 0.8544 (p) REVERT: F 159 ASN cc_start: 0.7849 (t0) cc_final: 0.7524 (t0) REVERT: F 211 THR cc_start: 0.8178 (m) cc_final: 0.7909 (m) REVERT: F 224 LYS cc_start: 0.7642 (ttpt) cc_final: 0.7023 (mttm) REVERT: G 56 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7056 (tt0) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.0955 time to fit residues: 45.4718 Evaluate side-chains 236 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 20 optimal weight: 0.0670 chunk 95 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 192 optimal weight: 0.0670 chunk 16 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN C 481 ASN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.134634 restraints weight = 23490.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.133840 restraints weight = 30514.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134396 restraints weight = 27058.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134411 restraints weight = 20057.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134544 restraints weight = 17523.131| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15992 Z= 0.101 Angle : 0.517 8.510 21697 Z= 0.271 Chirality : 0.043 0.166 2399 Planarity : 0.003 0.038 2763 Dihedral : 4.498 19.651 2129 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.06 % Allowed : 0.91 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.49 (0.19), residues: 1927 helix: -0.32 (0.45), residues: 140 sheet: 0.18 (0.20), residues: 643 loop : -0.59 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 83 TYR 0.014 0.001 TYR B 541 PHE 0.017 0.001 PHE C 483 TRP 0.013 0.001 TRP A 623 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (15992) covalent geometry : angle 0.51722 / 0.27 (21697) hydrogen bonds : bond 0.03104 / 2.01 ( 384) hydrogen bonds : angle 5.76385 / 3.93 ( 966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.7195 (tttt) cc_final: 0.6855 (tmtt) REVERT: A 288 LEU cc_start: 0.8296 (mm) cc_final: 0.8066 (mm) REVERT: A 364 VAL cc_start: 0.8187 (m) cc_final: 0.7741 (p) REVERT: A 467 THR cc_start: 0.8509 (m) cc_final: 0.8231 (p) REVERT: A 585 SER cc_start: 0.7256 (m) cc_final: 0.6795 (p) REVERT: A 635 MET cc_start: 0.8117 (ttp) cc_final: 0.7596 (ttp) REVERT: B 247 SER cc_start: 0.6710 (p) cc_final: 0.6225 (t) REVERT: B 629 ILE cc_start: 0.8892 (mt) cc_final: 0.8623 (mp) REVERT: C 129 ASN cc_start: 0.7168 (t0) cc_final: 0.6690 (t0) REVERT: C 438 LEU cc_start: 0.8046 (mt) cc_final: 0.7780 (mt) REVERT: C 541 TYR cc_start: 0.5731 (m-80) cc_final: 0.5177 (m-80) REVERT: C 545 GLU cc_start: 0.6803 (tt0) cc_final: 0.6592 (tt0) REVERT: C 547 THR cc_start: 0.9214 (m) cc_final: 0.8769 (p) REVERT: D 140 GLU cc_start: 0.8857 (mp0) cc_final: 0.8552 (mm-30) REVERT: D 206 THR cc_start: 0.7208 (p) cc_final: 0.6878 (m) REVERT: D 210 TYR cc_start: 0.7408 (m-80) cc_final: 0.7117 (m-80) REVERT: D 219 THR cc_start: 0.8363 (t) cc_final: 0.8091 (p) REVERT: E 139 SER cc_start: 0.8973 (t) cc_final: 0.8511 (p) REVERT: F 159 ASN cc_start: 0.7716 (t0) cc_final: 0.7458 (t0) REVERT: F 178 MET cc_start: 0.6603 (mmm) cc_final: 0.6379 (mmm) REVERT: F 211 THR cc_start: 0.8178 (m) cc_final: 0.7864 (m) REVERT: F 224 LYS cc_start: 0.7658 (ttpt) cc_final: 0.7042 (mttm) REVERT: G 56 GLU cc_start: 0.7935 (mt-10) cc_final: 0.6979 (tt0) outliers start: 1 outliers final: 1 residues processed: 310 average time/residue: 0.0991 time to fit residues: 47.9509 Evaluate side-chains 236 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 0.0000 chunk 169 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 128 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 602 GLN D 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.136982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132903 restraints weight = 23771.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132333 restraints weight = 25218.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132858 restraints weight = 23104.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132977 restraints weight = 16819.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132985 restraints weight = 15149.211| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15992 Z= 0.134 Angle : 0.563 8.900 21697 Z= 0.293 Chirality : 0.044 0.184 2399 Planarity : 0.004 0.039 2763 Dihedral : 4.663 20.817 2129 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.59 (0.19), residues: 1927 helix: -0.37 (0.44), residues: 140 sheet: 0.07 (0.20), residues: 637 loop : -0.62 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 639 TYR 0.024 0.001 TYR A 499 PHE 0.022 0.002 PHE A 526 TRP 0.042 0.001 TRP A 623 HIS 0.003 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (15992) covalent geometry : angle 0.56290 / 0.29 (21697) hydrogen bonds : bond 0.03262 / 2.10 ( 384) hydrogen bonds : angle 5.82327 / 3.97 ( 966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ASP cc_start: 0.7184 (m-30) cc_final: 0.6058 (m-30) REVERT: A 260 MET cc_start: 0.7735 (mmp) cc_final: 0.7447 (mmp) REVERT: A 264 LEU cc_start: 0.7122 (mt) cc_final: 0.6618 (mp) REVERT: A 364 VAL cc_start: 0.8232 (m) cc_final: 0.7845 (p) REVERT: A 440 MET cc_start: 0.8132 (mmm) cc_final: 0.6563 (mmm) REVERT: A 585 SER cc_start: 0.7287 (m) cc_final: 0.6775 (p) REVERT: A 635 MET cc_start: 0.8113 (ttp) cc_final: 0.7731 (ttp) REVERT: B 137 THR cc_start: 0.8893 (m) cc_final: 0.7964 (p) REVERT: B 247 SER cc_start: 0.6704 (p) cc_final: 0.6214 (t) REVERT: B 534 LEU cc_start: 0.6681 (tp) cc_final: 0.6127 (mm) REVERT: B 629 ILE cc_start: 0.8836 (mt) cc_final: 0.8596 (mp) REVERT: C 541 TYR cc_start: 0.5968 (m-80) cc_final: 0.5206 (m-80) REVERT: C 547 THR cc_start: 0.9183 (m) cc_final: 0.8714 (p) REVERT: D 140 GLU cc_start: 0.8674 (mp0) cc_final: 0.8304 (mm-30) REVERT: D 206 THR cc_start: 0.7182 (p) cc_final: 0.6901 (m) REVERT: D 210 TYR cc_start: 0.7433 (m-80) cc_final: 0.7206 (m-80) REVERT: D 219 THR cc_start: 0.8373 (t) cc_final: 0.8048 (p) REVERT: E 139 SER cc_start: 0.8910 (t) cc_final: 0.8472 (p) REVERT: F 159 ASN cc_start: 0.7676 (t0) cc_final: 0.7418 (t0) REVERT: F 211 THR cc_start: 0.8170 (m) cc_final: 0.7886 (m) REVERT: F 224 LYS cc_start: 0.7646 (ttpt) cc_final: 0.7084 (mttm) REVERT: G 56 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7018 (tt0) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.0981 time to fit residues: 46.2576 Evaluate side-chains 224 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 135 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 165 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 GLN ** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN C 481 ASN E 65 ASN F 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133336 restraints weight = 23738.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132742 restraints weight = 28779.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133335 restraints weight = 25185.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133423 restraints weight = 18014.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133570 restraints weight = 16256.135| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15992 Z= 0.117 Angle : 0.556 13.902 21697 Z= 0.287 Chirality : 0.044 0.229 2399 Planarity : 0.004 0.039 2763 Dihedral : 4.598 19.928 2129 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.06 % Allowed : 0.34 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.64 (0.19), residues: 1927 helix: -0.39 (0.44), residues: 141 sheet: -0.01 (0.20), residues: 650 loop : -0.64 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 83 TYR 0.017 0.001 TYR C 158 PHE 0.017 0.001 PHE A 449 TRP 0.014 0.001 TRP A 623 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (15992) covalent geometry : angle 0.55574 / 0.29 (21697) hydrogen bonds : bond 0.03170 / 2.03 ( 384) hydrogen bonds : angle 5.78276 / 3.93 ( 966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.6906 (mt) cc_final: 0.6546 (mp) REVERT: A 364 VAL cc_start: 0.8224 (m) cc_final: 0.7848 (p) REVERT: A 418 ASN cc_start: 0.7851 (t0) cc_final: 0.7346 (t0) REVERT: A 440 MET cc_start: 0.8134 (mmm) cc_final: 0.6627 (mmm) REVERT: A 585 SER cc_start: 0.7292 (m) cc_final: 0.6806 (p) REVERT: B 137 THR cc_start: 0.8785 (m) cc_final: 0.8011 (p) REVERT: B 139 GLN cc_start: 0.7340 (mp-120) cc_final: 0.7019 (mp10) REVERT: B 247 SER cc_start: 0.6691 (p) cc_final: 0.6204 (t) REVERT: B 534 LEU cc_start: 0.6536 (tp) cc_final: 0.6021 (mm) REVERT: B 629 ILE cc_start: 0.8870 (mt) cc_final: 0.8611 (mp) REVERT: C 510 LEU cc_start: 0.7648 (mm) cc_final: 0.7259 (mt) REVERT: C 541 TYR cc_start: 0.5963 (m-80) cc_final: 0.5207 (m-80) REVERT: C 547 THR cc_start: 0.9123 (m) cc_final: 0.8740 (p) REVERT: C 605 MET cc_start: 0.7448 (ppp) cc_final: 0.6393 (ppp) REVERT: D 140 GLU cc_start: 0.8626 (mp0) cc_final: 0.8297 (mm-30) REVERT: D 206 THR cc_start: 0.7124 (p) cc_final: 0.6867 (m) REVERT: D 210 TYR cc_start: 0.7381 (m-80) cc_final: 0.7173 (m-80) REVERT: D 219 THR cc_start: 0.8360 (t) cc_final: 0.8135 (p) REVERT: E 139 SER cc_start: 0.8987 (t) cc_final: 0.8557 (p) REVERT: F 211 THR cc_start: 0.8153 (m) cc_final: 0.7874 (m) REVERT: F 224 LYS cc_start: 0.7645 (ttpt) cc_final: 0.7072 (mttm) REVERT: G 56 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7038 (tt0) outliers start: 1 outliers final: 1 residues processed: 302 average time/residue: 0.0960 time to fit residues: 45.1754 Evaluate side-chains 233 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 75 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131041 restraints weight = 23930.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131376 restraints weight = 21834.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131536 restraints weight = 19724.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131949 restraints weight = 18597.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132076 restraints weight = 17246.743| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15992 Z= 0.119 Angle : 0.561 9.076 21697 Z= 0.290 Chirality : 0.044 0.169 2399 Planarity : 0.004 0.043 2763 Dihedral : 4.610 19.988 2129 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.67 (0.19), residues: 1927 helix: -0.37 (0.44), residues: 141 sheet: -0.02 (0.20), residues: 647 loop : -0.67 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 639 TYR 0.024 0.001 TYR A 499 PHE 0.016 0.001 PHE A 449 TRP 0.033 0.001 TRP A 623 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (15992) covalent geometry : angle 0.56066 / 0.29 (21697) hydrogen bonds : bond 0.03184 / 2.04 ( 384) hydrogen bonds : angle 5.74126 / 3.92 ( 966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.6788 (mt) cc_final: 0.6424 (mp) REVERT: A 364 VAL cc_start: 0.8265 (m) cc_final: 0.7867 (p) REVERT: A 418 ASN cc_start: 0.7864 (t0) cc_final: 0.7348 (t0) REVERT: A 440 MET cc_start: 0.8179 (mmm) cc_final: 0.6702 (mmm) REVERT: A 585 SER cc_start: 0.7383 (m) cc_final: 0.6877 (p) REVERT: A 635 MET cc_start: 0.7779 (ttm) cc_final: 0.7551 (ttm) REVERT: B 247 SER cc_start: 0.6980 (p) cc_final: 0.6443 (t) REVERT: B 534 LEU cc_start: 0.6797 (tp) cc_final: 0.6157 (mm) REVERT: B 629 ILE cc_start: 0.8889 (mt) cc_final: 0.8512 (mp) REVERT: C 510 LEU cc_start: 0.7630 (mm) cc_final: 0.7239 (mt) REVERT: C 541 TYR cc_start: 0.6043 (m-80) cc_final: 0.5235 (m-80) REVERT: C 545 GLU cc_start: 0.7271 (tt0) cc_final: 0.6879 (tt0) REVERT: C 605 MET cc_start: 0.7513 (ppp) cc_final: 0.6387 (ppp) REVERT: D 140 GLU cc_start: 0.8624 (mp0) cc_final: 0.8310 (mm-30) REVERT: D 171 VAL cc_start: 0.7805 (t) cc_final: 0.7502 (t) REVERT: D 206 THR cc_start: 0.7153 (p) cc_final: 0.6918 (m) REVERT: D 219 THR cc_start: 0.8420 (t) cc_final: 0.8158 (p) REVERT: E 139 SER cc_start: 0.9074 (t) cc_final: 0.8719 (p) REVERT: F 211 THR cc_start: 0.8126 (m) cc_final: 0.7841 (m) REVERT: F 224 LYS cc_start: 0.7619 (ttpt) cc_final: 0.6991 (mttm) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.0942 time to fit residues: 43.1612 Evaluate side-chains 228 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 39 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 145 optimal weight: 0.0770 chunk 41 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 chunk 48 optimal weight: 0.0020 chunk 174 optimal weight: 2.9990 chunk 129 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 overall best weight: 0.3146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 GLN E 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.136861 restraints weight = 23331.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.136193 restraints weight = 27662.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136614 restraints weight = 25655.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136633 restraints weight = 20276.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136786 restraints weight = 17658.100| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15992 Z= 0.095 Angle : 0.539 9.194 21697 Z= 0.277 Chirality : 0.043 0.161 2399 Planarity : 0.004 0.120 2763 Dihedral : 4.452 20.550 2129 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.06 % Allowed : 0.11 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.63 (0.19), residues: 1927 helix: -0.36 (0.43), residues: 141 sheet: 0.08 (0.20), residues: 633 loop : -0.68 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 560 TYR 0.016 0.001 TYR B 417 PHE 0.013 0.001 PHE A 449 TRP 0.015 0.001 TRP B 398 HIS 0.005 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (15992) covalent geometry : angle 0.53946 / 0.28 (21697) hydrogen bonds : bond 0.02914 / 1.84 ( 384) hydrogen bonds : angle 5.52656 / 3.76 ( 966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1968.70 seconds wall clock time: 35 minutes 12.45 seconds (2112.45 seconds total)