Starting phenix.real_space_refine on Tue Aug 26 16:12:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k91_36971/08_2025/8k91_36971.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k91_36971/08_2025/8k91_36971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k91_36971/08_2025/8k91_36971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k91_36971/08_2025/8k91_36971.map" model { file = "/net/cci-nas-00/data/ceres_data/8k91_36971/08_2025/8k91_36971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k91_36971/08_2025/8k91_36971.cif" } resolution = 3.03 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= 0.006 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 56 5.16 5 C 24675 2.51 5 N 7000 2.21 5 O 7322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39060 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "D" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "F" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "G" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.72, per 1000 atoms: 0.22 Number of scatterers: 39060 At special positions: 0 Unit cell: (151.7, 150.06, 157.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 7 15.00 O 7322 8.00 N 7000 7.00 C 24675 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: 3.28 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9240 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 71 sheets defined 53.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.579A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 119 removed outlier: 4.440A pdb=" N HIS A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 154 Processing helix chain 'A' and resid 173 through 221 removed outlier: 4.069A pdb=" N ARG A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ALA A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 314 through 321 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.733A pdb=" N GLY A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.612A pdb=" N SER A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 407 Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 436 through 452 Processing helix chain 'A' and resid 456 through 471 removed outlier: 4.060A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.796A pdb=" N GLY A 538 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 539 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN A 540 " --> pdb=" O LEU A 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 535 through 540' Processing helix chain 'A' and resid 544 through 557 removed outlier: 3.716A pdb=" N THR A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 597 Processing helix chain 'A' and resid 621 through 637 Processing helix chain 'A' and resid 649 through 654 removed outlier: 3.818A pdb=" N ALA A 652 " --> pdb=" O ALA A 649 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 654 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 694 through 719 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.628A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 70 " --> pdb=" O TYR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 110 through 119 removed outlier: 3.992A pdb=" N ARG B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 153 Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.682A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.248A pdb=" N ARG B 251 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.946A pdb=" N GLY B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.739A pdb=" N SER B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 407 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 451 Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 544 through 557 Processing helix chain 'B' and resid 585 through 597 Processing helix chain 'B' and resid 621 through 637 Processing helix chain 'B' and resid 649 through 654 removed outlier: 3.921A pdb=" N ALA B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 694 through 719 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 58 through 69 removed outlier: 3.598A pdb=" N THR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 111 Processing helix chain 'C' and resid 111 through 118 Processing helix chain 'C' and resid 121 through 154 Processing helix chain 'C' and resid 173 through 221 removed outlier: 4.971A pdb=" N ALA C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 242 Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.815A pdb=" N GLY C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.786A pdb=" N SER C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 407 Processing helix chain 'C' and resid 412 through 428 Processing helix chain 'C' and resid 436 through 452 Processing helix chain 'C' and resid 456 through 470 Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 532 through 539 removed outlier: 4.003A pdb=" N ALA C 535 " --> pdb=" O ASP C 532 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY C 536 " --> pdb=" O ARG C 533 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU C 537 " --> pdb=" O GLU C 534 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 539 " --> pdb=" O GLY C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 557 removed outlier: 3.707A pdb=" N THR C 548 " --> pdb=" O LYS C 544 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 549 " --> pdb=" O ALA C 545 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 597 Processing helix chain 'C' and resid 621 through 637 Processing helix chain 'C' and resid 649 through 654 removed outlier: 4.114A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 654 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 686 Processing helix chain 'C' and resid 694 through 719 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 58 through 69 removed outlier: 3.712A pdb=" N THR D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 111 Processing helix chain 'D' and resid 111 through 118 Processing helix chain 'D' and resid 121 through 154 Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.457A pdb=" N ALA D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 242 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 273 through 279 Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 363 through 369 removed outlier: 3.975A pdb=" N GLY D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 379 removed outlier: 3.775A pdb=" N SER D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 407 Processing helix chain 'D' and resid 412 through 428 Processing helix chain 'D' and resid 436 through 452 Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.983A pdb=" N SER D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 543 through 557 Processing helix chain 'D' and resid 585 through 597 Processing helix chain 'D' and resid 621 through 637 Processing helix chain 'D' and resid 649 through 654 removed outlier: 4.166A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 Processing helix chain 'D' and resid 694 through 719 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.659A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 111 removed outlier: 4.566A pdb=" N HIS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 119 removed outlier: 3.563A pdb=" N PHE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 154 Processing helix chain 'E' and resid 173 through 221 removed outlier: 4.196A pdb=" N ALA E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) Proline residue: E 216 - end of helix Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 246 through 250 Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 322 through 332 Processing helix chain 'E' and resid 363 through 369 removed outlier: 4.214A pdb=" N GLY E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 379 removed outlier: 3.881A pdb=" N SER E 377 " --> pdb=" O ASP E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 407 Processing helix chain 'E' and resid 412 through 428 Processing helix chain 'E' and resid 436 through 451 Processing helix chain 'E' and resid 456 through 471 removed outlier: 3.978A pdb=" N SER E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 545 through 557 Processing helix chain 'E' and resid 584 through 597 Processing helix chain 'E' and resid 621 through 637 Processing helix chain 'E' and resid 649 through 651 No H-bonds generated for 'chain 'E' and resid 649 through 651' Processing helix chain 'E' and resid 657 through 666 Processing helix chain 'E' and resid 676 through 686 Processing helix chain 'E' and resid 694 through 719 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.766A pdb=" N THR F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 119 removed outlier: 4.417A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASN F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 153 Processing helix chain 'F' and resid 173 through 221 removed outlier: 4.412A pdb=" N ALA F 206 " --> pdb=" O ARG F 202 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 213 " --> pdb=" O TYR F 209 " (cutoff:3.500A) Proline residue: F 216 - end of helix Processing helix chain 'F' and resid 224 through 242 Processing helix chain 'F' and resid 246 through 250 Processing helix chain 'F' and resid 273 through 279 Processing helix chain 'F' and resid 293 through 295 No H-bonds generated for 'chain 'F' and resid 293 through 295' Processing helix chain 'F' and resid 300 through 305 Processing helix chain 'F' and resid 314 through 320 Processing helix chain 'F' and resid 322 through 333 Processing helix chain 'F' and resid 363 through 369 removed outlier: 4.058A pdb=" N GLY F 369 " --> pdb=" O GLU F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 379 removed outlier: 3.863A pdb=" N SER F 377 " --> pdb=" O ASP F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 407 Processing helix chain 'F' and resid 412 through 428 Processing helix chain 'F' and resid 436 through 452 Processing helix chain 'F' and resid 456 through 471 removed outlier: 4.000A pdb=" N SER F 471 " --> pdb=" O ARG F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 545 through 557 Processing helix chain 'F' and resid 584 through 597 Processing helix chain 'F' and resid 621 through 637 Processing helix chain 'F' and resid 649 through 654 removed outlier: 4.398A pdb=" N ALA F 652 " --> pdb=" O ALA F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 666 Processing helix chain 'F' and resid 676 through 686 Processing helix chain 'F' and resid 694 through 719 Processing helix chain 'G' and resid 4 through 9 Processing helix chain 'G' and resid 32 through 46 Processing helix chain 'G' and resid 58 through 69 removed outlier: 3.595A pdb=" N THR G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 111 removed outlier: 4.561A pdb=" N HIS G 100 " --> pdb=" O GLY G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 118 Processing helix chain 'G' and resid 121 through 153 Processing helix chain 'G' and resid 173 through 221 removed outlier: 4.435A pdb=" N ALA G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN G 212 " --> pdb=" O HIS G 208 " (cutoff:3.500A) Proline residue: G 216 - end of helix Processing helix chain 'G' and resid 224 through 241 Processing helix chain 'G' and resid 246 through 250 Processing helix chain 'G' and resid 273 through 279 Processing helix chain 'G' and resid 293 through 295 No H-bonds generated for 'chain 'G' and resid 293 through 295' Processing helix chain 'G' and resid 300 through 305 Processing helix chain 'G' and resid 314 through 320 Processing helix chain 'G' and resid 322 through 333 Processing helix chain 'G' and resid 363 through 369 removed outlier: 3.846A pdb=" N GLY G 369 " --> pdb=" O GLU G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 380 removed outlier: 3.713A pdb=" N SER G 377 " --> pdb=" O ASP G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 407 Processing helix chain 'G' and resid 412 through 428 Processing helix chain 'G' and resid 436 through 452 Processing helix chain 'G' and resid 456 through 471 removed outlier: 3.993A pdb=" N SER G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 484 Processing helix chain 'G' and resid 544 through 557 Processing helix chain 'G' and resid 584 through 597 Processing helix chain 'G' and resid 621 through 637 Processing helix chain 'G' and resid 649 through 654 removed outlier: 4.315A pdb=" N ALA G 652 " --> pdb=" O ALA G 649 " (cutoff:3.500A) Processing helix chain 'G' and resid 657 through 666 Processing helix chain 'G' and resid 676 through 686 Processing helix chain 'G' and resid 694 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 269 removed outlier: 4.244A pdb=" N ASP A 313 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU A 310 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL A 361 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 312 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N HIS A 48 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 382 " --> pdb=" O HIS A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 254 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 159 Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 411 removed outlier: 7.101A pdb=" N GLN A 410 " --> pdb=" O LEU A 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AA9, first strand: chain 'A' and resid 529 through 530 removed outlier: 4.032A pdb=" N TRP A 511 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N GLU A 498 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N VAL A 606 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASN A 500 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA A 605 " --> pdb=" O ILE A 645 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 609 through 610 Processing sheet with id=AB2, first strand: chain 'B' and resid 266 through 269 removed outlier: 4.376A pdb=" N ASP B 313 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N HIS B 48 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 253 through 254 removed outlier: 7.329A pdb=" N VAL B 88 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 159 Processing sheet with id=AB5, first strand: chain 'B' and resid 280 through 281 Processing sheet with id=AB6, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AB7, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AB8, first strand: chain 'B' and resid 410 through 411 removed outlier: 7.074A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AC1, first strand: chain 'B' and resid 527 through 530 removed outlier: 4.290A pdb=" N HIS B 527 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 567 " --> pdb=" O HIS B 527 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TRP B 511 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N GLU B 498 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N VAL B 606 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASN B 500 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA B 605 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL B 644 " --> pdb=" O TYR B 672 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL B 674 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 583 through 584 removed outlier: 4.407A pdb=" N ALA B 583 " --> pdb=" O VAL B 610 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 266 through 269 removed outlier: 4.475A pdb=" N ASP C 313 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N HIS C 48 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARG C 383 " --> pdb=" O HIS C 48 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR C 50 " --> pdb=" O ARG C 383 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU C 385 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL C 52 " --> pdb=" O GLU C 385 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 253 through 254 Processing sheet with id=AC5, first strand: chain 'C' and resid 156 through 157 Processing sheet with id=AC6, first strand: chain 'C' and resid 280 through 281 removed outlier: 3.606A pdb=" N ARG C 280 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AC8, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AC9, first strand: chain 'C' and resid 410 through 411 removed outlier: 7.162A pdb=" N GLN C 410 " --> pdb=" O LEU C 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AD2, first strand: chain 'C' and resid 528 through 530 removed outlier: 9.762A pdb=" N GLU C 498 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N VAL C 606 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASN C 500 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL C 644 " --> pdb=" O TYR C 672 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL C 674 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 583 through 584 removed outlier: 4.266A pdb=" N ALA C 583 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 266 through 269 removed outlier: 4.466A pdb=" N ASP D 313 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU D 310 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL D 361 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU D 312 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N HIS D 48 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 382 " --> pdb=" O HIS D 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.676A pdb=" N VAL D 88 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 156 through 160 removed outlier: 3.754A pdb=" N GLU D 165 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AD8, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AD9, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AE1, first strand: chain 'D' and resid 410 through 411 removed outlier: 7.379A pdb=" N GLN D 410 " --> pdb=" O LEU D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AE3, first strand: chain 'D' and resid 528 through 530 removed outlier: 3.685A pdb=" N TRP D 511 " --> pdb=" O VAL D 505 " (cutoff:3.500A) removed outlier: 9.828A pdb=" N GLU D 498 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N VAL D 606 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASN D 500 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL D 644 " --> pdb=" O TYR D 672 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL D 674 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU D 646 " --> pdb=" O VAL D 674 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 583 through 584 removed outlier: 4.408A pdb=" N ALA D 583 " --> pdb=" O VAL D 610 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 266 through 269 removed outlier: 4.337A pdb=" N ASP E 313 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 310 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL E 361 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU E 312 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N HIS E 48 " --> pdb=" O PHE E 380 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE E 382 " --> pdb=" O HIS E 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 253 through 254 removed outlier: 4.488A pdb=" N VAL E 90 " --> pdb=" O GLU E 350 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AE8, first strand: chain 'E' and resid 280 through 281 Processing sheet with id=AE9, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AF1, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AF2, first strand: chain 'E' and resid 410 through 411 removed outlier: 6.946A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AF4, first strand: chain 'E' and resid 498 through 504 removed outlier: 3.971A pdb=" N HIS E 527 " --> pdb=" O VAL E 565 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 567 " --> pdb=" O HIS E 527 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 604 through 606 removed outlier: 6.413A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 609 through 610 Processing sheet with id=AF7, first strand: chain 'F' and resid 2 through 3 removed outlier: 4.566A pdb=" N ILE F 671 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL F 644 " --> pdb=" O TYR F 672 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL F 674 " --> pdb=" O VAL F 644 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU F 646 " --> pdb=" O VAL F 674 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA F 605 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N GLU F 498 " --> pdb=" O LEU F 604 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL F 606 " --> pdb=" O GLU F 498 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ASN F 500 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 266 through 269 removed outlier: 4.308A pdb=" N ASP F 313 " --> pdb=" O GLU F 269 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU F 310 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL F 361 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU F 312 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS F 48 " --> pdb=" O ILE F 382 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ALA F 384 " --> pdb=" O HIS F 48 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TYR F 50 " --> pdb=" O ALA F 384 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 253 through 254 Processing sheet with id=AG1, first strand: chain 'F' and resid 156 through 160 removed outlier: 3.626A pdb=" N GLU F 165 " --> pdb=" O SER F 158 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG F 163 " --> pdb=" O ASN F 160 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 280 through 281 Processing sheet with id=AG3, first strand: chain 'F' and resid 284 through 286 Processing sheet with id=AG4, first strand: chain 'F' and resid 389 through 391 Processing sheet with id=AG5, first strand: chain 'F' and resid 410 through 411 removed outlier: 7.489A pdb=" N GLN F 410 " --> pdb=" O LEU F 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'F' and resid 494 through 496 Processing sheet with id=AG7, first strand: chain 'F' and resid 609 through 610 Processing sheet with id=AG8, first strand: chain 'G' and resid 266 through 269 removed outlier: 4.266A pdb=" N ASP G 313 " --> pdb=" O GLU G 269 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 253 through 254 Processing sheet with id=AH1, first strand: chain 'G' and resid 156 through 160 Processing sheet with id=AH2, first strand: chain 'G' and resid 280 through 281 Processing sheet with id=AH3, first strand: chain 'G' and resid 284 through 286 Processing sheet with id=AH4, first strand: chain 'G' and resid 389 through 391 Processing sheet with id=AH5, first strand: chain 'G' and resid 410 through 411 removed outlier: 7.090A pdb=" N GLN G 410 " --> pdb=" O LEU G 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'G' and resid 494 through 496 Processing sheet with id=AH7, first strand: chain 'G' and resid 528 through 530 removed outlier: 4.445A pdb=" N ARG G 516 " --> pdb=" O GLU G 572 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N GLU G 498 " --> pdb=" O LEU G 604 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N VAL G 606 " --> pdb=" O GLU G 498 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASN G 500 " --> pdb=" O VAL G 606 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA G 605 " --> pdb=" O ILE G 645 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL G 644 " --> pdb=" O TYR G 672 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL G 674 " --> pdb=" O VAL G 644 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 646 " --> pdb=" O VAL G 674 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 609 through 610 2227 hydrogen bonds defined for protein. 6447 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: 9.42 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 13659 1.36 - 1.51: 10009 1.51 - 1.65: 16071 1.65 - 1.80: 53 1.80 - 1.95: 38 Bond restraints: 39830 Sorted by residual: bond pdb=" P TS6 G 801 " pdb=" S2P TS6 G 801 " ideal model delta sigma weight residual 2.275 1.946 0.329 2.00e-02 2.50e+03 2.71e+02 bond pdb=" P TS6 B 801 " pdb=" S2P TS6 B 801 " ideal model delta sigma weight residual 2.275 1.946 0.329 2.00e-02 2.50e+03 2.70e+02 bond pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.70e+02 bond pdb=" P TS6 F 801 " pdb=" S2P TS6 F 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.69e+02 ... (remaining 39825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 53821 3.46 - 6.92: 222 6.92 - 10.38: 6 10.38 - 13.85: 23 13.85 - 17.31: 10 Bond angle restraints: 54082 Sorted by residual: angle pdb=" O1P TS6 E 801 " pdb=" P TS6 E 801 " pdb=" S2P TS6 E 801 " ideal model delta sigma weight residual 98.15 115.46 -17.31 3.00e+00 1.11e-01 3.33e+01 angle pdb=" O1P TS6 G 801 " pdb=" P TS6 G 801 " pdb=" S2P TS6 G 801 " ideal model delta sigma weight residual 98.15 115.44 -17.29 3.00e+00 1.11e-01 3.32e+01 angle pdb=" O1P TS6 D 801 " pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 98.15 115.42 -17.27 3.00e+00 1.11e-01 3.32e+01 angle pdb=" O1P TS6 F 801 " pdb=" P TS6 F 801 " pdb=" S2P TS6 F 801 " ideal model delta sigma weight residual 98.15 115.42 -17.27 3.00e+00 1.11e-01 3.32e+01 angle pdb=" O1P TS6 C 801 " pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 98.15 115.35 -17.20 3.00e+00 1.11e-01 3.29e+01 ... (remaining 54077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 22094 17.93 - 35.86: 1509 35.86 - 53.80: 282 53.80 - 71.73: 168 71.73 - 89.66: 118 Dihedral angle restraints: 24171 sinusoidal: 9786 harmonic: 14385 Sorted by residual: dihedral pdb=" CA ALA D 508 " pdb=" C ALA D 508 " pdb=" N PRO D 509 " pdb=" CA PRO D 509 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ALA A 508 " pdb=" C ALA A 508 " pdb=" N PRO A 509 " pdb=" CA PRO A 509 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLU G 572 " pdb=" C GLU G 572 " pdb=" N GLN G 573 " pdb=" CA GLN G 573 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 24168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 5096 0.053 - 0.106: 774 0.106 - 0.159: 140 0.159 - 0.212: 14 0.212 - 0.265: 3 Chirality restraints: 6027 Sorted by residual: chirality pdb=" CG LEU B 188 " pdb=" CB LEU B 188 " pdb=" CD1 LEU B 188 " pdb=" CD2 LEU B 188 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA SER A 56 " pdb=" N SER A 56 " pdb=" C SER A 56 " pdb=" CB SER A 56 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA GLU F 61 " pdb=" N GLU F 61 " pdb=" C GLU F 61 " pdb=" CB GLU F 61 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 6024 not shown) Planarity restraints: 7217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 27 " 0.057 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO E 28 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO E 28 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 28 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 350 " -0.048 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO G 351 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO G 351 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 351 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 246 " 0.045 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO A 247 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " 0.038 5.00e-02 4.00e+02 ... (remaining 7214 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 412 2.66 - 3.22: 36161 3.22 - 3.78: 63202 3.78 - 4.34: 86387 4.34 - 4.90: 143956 Nonbonded interactions: 330118 Sorted by model distance: nonbonded pdb=" OG SER B 593 " pdb=" O LEU B 598 " model vdw 2.098 3.040 nonbonded pdb=" OG SER E 593 " pdb=" O LEU E 598 " model vdw 2.158 3.040 nonbonded pdb=" NH1 ARG E 36 " pdb=" OE2 GLU E 40 " model vdw 2.179 3.120 nonbonded pdb=" NH1 ARG A 114 " pdb=" O LEU B 188 " model vdw 2.183 3.120 nonbonded pdb=" OG1 THR D 676 " pdb=" OE1 GLU D 678 " model vdw 2.187 3.040 ... (remaining 330113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 35.450 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 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: 40.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.006 0.329 39830 Z= 0.308 Angle : 0.739 17.306 54082 Z= 0.410 Chirality : 0.041 0.265 6027 Planarity : 0.005 0.085 7217 Dihedral : 15.378 89.659 14931 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.23 % Rotamer: Outliers : 0.18 % Allowed : 0.15 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 aren not related in a simple way. whole: 1.02 (0.12), residues: 5019 helix: 1.76 (0.10), residues: 2534 sheet: -0.32 (0.19), residues: 679 loop : -0.41 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 36 TYR 0.024 0.002 TYR D 271 PHE 0.029 0.002 PHE G 218 TRP 0.035 0.001 TRP A 205 HIS 0.012 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00580 (39830) covalent geometry : angle 0.73874 (54082) hydrogen bonds : bond 0.12334 ( 2227) hydrogen bonds : angle 5.94553 ( 6447) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 382 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: B 57 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8581 (tt) REVERT: C 689 MET cc_start: 0.8425 (mmp) cc_final: 0.8104 (mmt) REVERT: G 57 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8136 (tt) REVERT: G 708 ARG cc_start: 0.6837 (mmt-90) cc_final: 0.6436 (mmt180) outliers start: 7 outliers final: 3 residues processed: 384 average time/residue: 0.2560 time to fit residues: 152.8994 Evaluate side-chains 244 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 239 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 0.0370 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 0.0570 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN A 469 HIS ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN C 679 GLN D 97 GLN E 574 ASN F 540 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.155795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.112348 restraints weight = 51972.620| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.71 r_work: 0.3261 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 39830 Z= 0.116 Angle : 0.525 9.193 54082 Z= 0.264 Chirality : 0.038 0.178 6027 Planarity : 0.004 0.060 7217 Dihedral : 4.310 47.371 5610 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.35 % Favored : 97.57 % Rotamer: Outliers : 0.55 % Allowed : 4.51 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 aren not related in a simple way. whole: 1.29 (0.12), residues: 5019 helix: 1.99 (0.10), residues: 2555 sheet: -0.29 (0.20), residues: 630 loop : -0.29 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 120 TYR 0.016 0.002 TYR C 50 PHE 0.020 0.001 PHE A 221 TRP 0.016 0.001 TRP D 290 HIS 0.005 0.001 HIS C 560 Details of bonding type rmsd covalent geometry : bond 0.00252 (39830) covalent geometry : angle 0.52528 (54082) hydrogen bonds : bond 0.04069 ( 2227) hydrogen bonds : angle 4.81906 ( 6447) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 278 time to evaluate : 1.455 Fit side-chains REVERT: A 61 GLU cc_start: 0.8630 (tt0) cc_final: 0.8379 (pt0) REVERT: A 534 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6216 (tt0) REVERT: B 1 MET cc_start: 0.6421 (ptt) cc_final: 0.5988 (ptm) REVERT: B 57 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8403 (tt) REVERT: B 117 GLU cc_start: 0.6358 (pt0) cc_final: 0.6074 (mm-30) REVERT: B 439 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7847 (mm-30) REVERT: C 1 MET cc_start: 0.6638 (tpp) cc_final: 0.6283 (tpp) REVERT: D 114 ARG cc_start: 0.6556 (mmt180) cc_final: 0.6199 (mtt180) REVERT: E 378 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: G 57 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8211 (tt) REVERT: G 203 ARG cc_start: 0.7062 (ttt180) cc_final: 0.6808 (tpt-90) REVERT: G 426 MET cc_start: 0.8895 (mtp) cc_final: 0.8616 (mtp) REVERT: G 708 ARG cc_start: 0.6936 (mmt-90) cc_final: 0.6373 (mmt180) outliers start: 22 outliers final: 10 residues processed: 292 average time/residue: 0.2252 time to fit residues: 106.3016 Evaluate side-chains 254 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 241 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 378 GLU Chi-restraints excluded: chain E residue 574 ASN Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 99 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 383 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 158 optimal weight: 9.9990 chunk 247 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 381 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 479 optimal weight: 7.9990 chunk 384 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN A 527 HIS A 543 HIS ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN B 407 GLN E 100 HIS E 574 ASN F 357 GLN ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.148189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106652 restraints weight = 51932.039| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.38 r_work: 0.3145 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.104 39830 Z= 0.352 Angle : 0.696 10.358 54082 Z= 0.347 Chirality : 0.045 0.229 6027 Planarity : 0.006 0.065 7217 Dihedral : 4.680 55.707 5608 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % Rotamer: Outliers : 1.34 % Allowed : 6.78 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 aren not related in a simple way. whole: 0.83 (0.12), residues: 5019 helix: 1.57 (0.10), residues: 2555 sheet: -0.65 (0.19), residues: 637 loop : -0.38 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 513 TYR 0.035 0.003 TYR B 271 PHE 0.023 0.002 PHE E 352 TRP 0.021 0.002 TRP D 290 HIS 0.010 0.002 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00856 (39830) covalent geometry : angle 0.69582 (54082) hydrogen bonds : bond 0.04583 ( 2227) hydrogen bonds : angle 4.98472 ( 6447) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 238 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8059 (mm-30) REVERT: A 510 TYR cc_start: 0.7037 (m-10) cc_final: 0.6832 (m-10) REVERT: B 1 MET cc_start: 0.6527 (ptt) cc_final: 0.6106 (ptm) REVERT: C 1 MET cc_start: 0.6850 (tpp) cc_final: 0.6413 (tpp) REVERT: E 378 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: E 484 GLU cc_start: 0.7470 (mp0) cc_final: 0.7141 (mt-10) REVERT: E 695 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7974 (mp) REVERT: F 342 GLN cc_start: 0.6767 (mp-120) cc_final: 0.6326 (mp10) REVERT: F 554 ARG cc_start: 0.7785 (mtm180) cc_final: 0.7478 (mtm-85) REVERT: F 651 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8076 (mt) REVERT: G 77 ASP cc_start: 0.7495 (m-30) cc_final: 0.7294 (m-30) REVERT: G 151 GLN cc_start: 0.5563 (OUTLIER) cc_final: 0.4972 (mt0) REVERT: G 203 ARG cc_start: 0.7150 (ttt180) cc_final: 0.6858 (tpt-90) REVERT: G 665 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7750 (ttp80) REVERT: G 708 ARG cc_start: 0.7084 (mmt-90) cc_final: 0.6645 (mmt180) outliers start: 53 outliers final: 34 residues processed: 279 average time/residue: 0.2426 time to fit residues: 108.3436 Evaluate side-chains 252 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 205 TRP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 378 GLU Chi-restraints excluded: chain E residue 695 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 151 GLN Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 352 PHE Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 576 VAL Chi-restraints excluded: chain G residue 597 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 398 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 235 optimal weight: 7.9990 chunk 192 optimal weight: 0.3980 chunk 381 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 232 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 371 optimal weight: 0.4980 chunk 399 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 HIS ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 GLN D 60 HIS ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 679 GLN ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106593 restraints weight = 51939.332| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.40 r_work: 0.3192 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 39830 Z= 0.110 Angle : 0.511 14.754 54082 Z= 0.255 Chirality : 0.037 0.232 6027 Planarity : 0.004 0.058 7217 Dihedral : 4.270 52.286 5606 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.47 % Favored : 97.43 % Rotamer: Outliers : 1.13 % Allowed : 8.49 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 aren not related in a simple way. whole: 1.21 (0.12), residues: 5019 helix: 1.95 (0.10), residues: 2555 sheet: -0.56 (0.19), residues: 651 loop : -0.25 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 688 TYR 0.018 0.002 TYR G 557 PHE 0.015 0.001 PHE F 571 TRP 0.042 0.001 TRP F 205 HIS 0.004 0.000 HIS F 469 Details of bonding type rmsd covalent geometry : bond 0.00239 (39830) covalent geometry : angle 0.51140 (54082) hydrogen bonds : bond 0.03782 ( 2227) hydrogen bonds : angle 4.53313 ( 6447) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: B 1 MET cc_start: 0.6573 (ptt) cc_final: 0.6186 (ptm) REVERT: B 208 HIS cc_start: 0.7907 (t-90) cc_final: 0.7596 (t70) REVERT: C 1 MET cc_start: 0.6881 (tpp) cc_final: 0.6462 (tpp) REVERT: C 257 SER cc_start: 0.7764 (t) cc_final: 0.7153 (p) REVERT: C 342 GLN cc_start: 0.8440 (mp10) cc_final: 0.7906 (mp10) REVERT: D 57 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8479 (tt) REVERT: D 534 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6604 (mm-30) REVERT: E 484 GLU cc_start: 0.7621 (mp0) cc_final: 0.7292 (mt-10) REVERT: F 205 TRP cc_start: 0.7986 (m100) cc_final: 0.7776 (m100) REVERT: F 646 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8748 (pp) REVERT: F 651 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8079 (mt) REVERT: G 151 GLN cc_start: 0.5519 (OUTLIER) cc_final: 0.4987 (mt0) REVERT: G 203 ARG cc_start: 0.7138 (ttt180) cc_final: 0.6889 (tpt-90) REVERT: G 708 ARG cc_start: 0.7104 (mmt-90) cc_final: 0.6544 (mtm-85) outliers start: 45 outliers final: 21 residues processed: 299 average time/residue: 0.2285 time to fit residues: 110.7660 Evaluate side-chains 254 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 151 GLN Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 352 PHE Chi-restraints excluded: chain G residue 431 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 196 optimal weight: 9.9990 chunk 402 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 362 optimal weight: 5.9990 chunk 474 optimal weight: 0.7980 chunk 370 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 488 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN A 469 HIS ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.150902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107094 restraints weight = 51810.976| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.60 r_work: 0.3170 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 39830 Z= 0.192 Angle : 0.547 10.900 54082 Z= 0.271 Chirality : 0.039 0.236 6027 Planarity : 0.004 0.065 7217 Dihedral : 4.259 52.576 5606 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.09 % Rotamer: Outliers : 1.54 % Allowed : 8.89 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 aren not related in a simple way. whole: 1.23 (0.12), residues: 5019 helix: 1.98 (0.10), residues: 2548 sheet: -0.60 (0.19), residues: 651 loop : -0.24 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 114 TYR 0.019 0.002 TYR G 557 PHE 0.014 0.002 PHE D 629 TRP 0.015 0.001 TRP C 205 HIS 0.004 0.001 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00455 (39830) covalent geometry : angle 0.54667 (54082) hydrogen bonds : bond 0.03894 ( 2227) hydrogen bonds : angle 4.53699 ( 6447) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 237 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8014 (mm-30) REVERT: A 556 ARG cc_start: 0.7898 (tpp80) cc_final: 0.7537 (tpp80) REVERT: B 1 MET cc_start: 0.6492 (ptt) cc_final: 0.6101 (ptm) REVERT: B 208 HIS cc_start: 0.7886 (t-90) cc_final: 0.7539 (t70) REVERT: B 237 ARG cc_start: 0.7058 (ttm-80) cc_final: 0.6381 (ttm-80) REVERT: C 1 MET cc_start: 0.6832 (tpp) cc_final: 0.6387 (tpp) REVERT: C 257 SER cc_start: 0.7949 (t) cc_final: 0.7385 (p) REVERT: C 342 GLN cc_start: 0.8452 (mp10) cc_final: 0.7865 (mp10) REVERT: C 646 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8750 (pp) REVERT: D 57 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8444 (tt) REVERT: E 484 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7125 (mt-10) REVERT: F 342 GLN cc_start: 0.6738 (mp-120) cc_final: 0.6269 (mp10) REVERT: F 554 ARG cc_start: 0.7761 (mtm180) cc_final: 0.7534 (mtm-85) REVERT: F 646 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8682 (pp) REVERT: F 651 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8023 (mt) REVERT: G 86 ARG cc_start: 0.8132 (ppt170) cc_final: 0.7784 (ppt170) REVERT: G 151 GLN cc_start: 0.5584 (OUTLIER) cc_final: 0.5069 (mt0) REVERT: G 203 ARG cc_start: 0.7086 (ttt180) cc_final: 0.6786 (tpt-90) REVERT: G 708 ARG cc_start: 0.6993 (mmt-90) cc_final: 0.6444 (mtm-85) outliers start: 61 outliers final: 39 residues processed: 283 average time/residue: 0.2366 time to fit residues: 106.8287 Evaluate side-chains 267 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 711 GLU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 525 ARG Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 151 GLN Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 352 PHE Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 576 VAL Chi-restraints excluded: chain G residue 597 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 419 optimal weight: 2.9990 chunk 320 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 386 optimal weight: 0.9990 chunk 246 optimal weight: 0.2980 chunk 451 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 310 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 407 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 HIS ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.152903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109592 restraints weight = 51766.378| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.64 r_work: 0.3193 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 39830 Z= 0.120 Angle : 0.491 9.459 54082 Z= 0.244 Chirality : 0.037 0.207 6027 Planarity : 0.004 0.056 7217 Dihedral : 4.107 51.092 5606 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.41 % Favored : 97.51 % Rotamer: Outliers : 1.46 % Allowed : 9.27 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 aren not related in a simple way. whole: 1.38 (0.12), residues: 5019 helix: 2.12 (0.10), residues: 2555 sheet: -0.53 (0.20), residues: 651 loop : -0.21 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 179 TYR 0.016 0.001 TYR A 209 PHE 0.014 0.001 PHE F 571 TRP 0.015 0.001 TRP F 205 HIS 0.003 0.000 HIS F 469 Details of bonding type rmsd covalent geometry : bond 0.00275 (39830) covalent geometry : angle 0.49058 (54082) hydrogen bonds : bond 0.03604 ( 2227) hydrogen bonds : angle 4.34358 ( 6447) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: A 556 ARG cc_start: 0.7976 (tpp80) cc_final: 0.7434 (tpp80) REVERT: B 1 MET cc_start: 0.6446 (ptt) cc_final: 0.6068 (ptm) REVERT: B 57 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8505 (tt) REVERT: B 208 HIS cc_start: 0.7938 (t-90) cc_final: 0.7586 (t70) REVERT: B 237 ARG cc_start: 0.7079 (ttm-80) cc_final: 0.6430 (ttm-80) REVERT: C 1 MET cc_start: 0.6703 (tpp) cc_final: 0.6320 (tpp) REVERT: C 257 SER cc_start: 0.7869 (t) cc_final: 0.7289 (p) REVERT: C 342 GLN cc_start: 0.8442 (mp10) cc_final: 0.7862 (mp10) REVERT: C 542 PHE cc_start: 0.6416 (m-80) cc_final: 0.6202 (m-80) REVERT: D 57 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8437 (tt) REVERT: E 318 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8640 (mtmm) REVERT: E 484 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7017 (mt-10) REVERT: F 492 THR cc_start: 0.8831 (p) cc_final: 0.8419 (m) REVERT: F 646 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8667 (pp) REVERT: F 651 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7963 (mt) REVERT: G 117 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.5404 (mp0) REVERT: G 151 GLN cc_start: 0.5405 (OUTLIER) cc_final: 0.4944 (mt0) REVERT: G 203 ARG cc_start: 0.7101 (ttt180) cc_final: 0.6832 (tpt-90) REVERT: G 708 ARG cc_start: 0.7028 (mmt-90) cc_final: 0.6517 (mtm-85) outliers start: 58 outliers final: 36 residues processed: 290 average time/residue: 0.2182 time to fit residues: 102.9123 Evaluate side-chains 269 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 711 GLU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 151 GLN Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 352 PHE Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 597 ASN Chi-restraints excluded: chain G residue 603 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 484 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 413 optimal weight: 9.9990 chunk 258 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 HIS ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.148814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105181 restraints weight = 52279.605| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.62 r_work: 0.3146 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 39830 Z= 0.253 Angle : 0.589 10.029 54082 Z= 0.292 Chirality : 0.040 0.245 6027 Planarity : 0.005 0.054 7217 Dihedral : 4.314 52.450 5606 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.05 % Favored : 96.87 % Rotamer: Outliers : 1.64 % Allowed : 9.75 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 aren not related in a simple way. whole: 1.19 (0.12), residues: 5019 helix: 1.94 (0.10), residues: 2548 sheet: -0.65 (0.19), residues: 651 loop : -0.24 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 114 TYR 0.021 0.002 TYR G 557 PHE 0.017 0.002 PHE G 352 TRP 0.025 0.002 TRP F 205 HIS 0.006 0.001 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00605 (39830) covalent geometry : angle 0.58897 (54082) hydrogen bonds : bond 0.04019 ( 2227) hydrogen bonds : angle 4.58394 ( 6447) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 223 time to evaluate : 1.176 Fit side-chains REVERT: A 37 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: A 556 ARG cc_start: 0.7917 (tpp80) cc_final: 0.7405 (tpp80) REVERT: B 1 MET cc_start: 0.6604 (ptt) cc_final: 0.6205 (ptm) REVERT: B 237 ARG cc_start: 0.7109 (ttm-80) cc_final: 0.6462 (ttm-80) REVERT: C 1 MET cc_start: 0.6860 (tpp) cc_final: 0.6421 (tpp) REVERT: C 257 SER cc_start: 0.8123 (t) cc_final: 0.7590 (p) REVERT: C 342 GLN cc_start: 0.8490 (mp10) cc_final: 0.7905 (mp10) REVERT: C 542 PHE cc_start: 0.6501 (m-80) cc_final: 0.6292 (m-80) REVERT: C 646 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8791 (pp) REVERT: D 57 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8503 (tt) REVERT: D 534 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6532 (mm-30) REVERT: E 484 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7098 (mt-10) REVERT: F 64 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7690 (mp) REVERT: F 205 TRP cc_start: 0.7904 (m100) cc_final: 0.7143 (m-10) REVERT: F 342 GLN cc_start: 0.6959 (mp-120) cc_final: 0.6411 (mp10) REVERT: F 554 ARG cc_start: 0.7845 (mtm180) cc_final: 0.7591 (mtm-85) REVERT: F 646 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8705 (pp) REVERT: F 651 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8076 (mt) REVERT: G 77 ASP cc_start: 0.7516 (m-30) cc_final: 0.7308 (m-30) REVERT: G 151 GLN cc_start: 0.5554 (OUTLIER) cc_final: 0.5085 (mt0) REVERT: G 203 ARG cc_start: 0.7094 (ttt180) cc_final: 0.6798 (tpt-90) REVERT: G 665 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7764 (ttp80) REVERT: G 708 ARG cc_start: 0.7010 (mmt-90) cc_final: 0.6531 (mtm-85) outliers start: 65 outliers final: 48 residues processed: 273 average time/residue: 0.2453 time to fit residues: 106.2140 Evaluate side-chains 268 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 205 TRP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 525 ARG Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 417 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 151 GLN Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 352 PHE Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 597 ASN Chi-restraints excluded: chain G residue 603 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 425 optimal weight: 7.9990 chunk 300 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 343 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 436 optimal weight: 1.9990 chunk 478 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 313 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103801 restraints weight = 52114.122| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.61 r_work: 0.3155 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 39830 Z= 0.193 Angle : 0.541 10.031 54082 Z= 0.270 Chirality : 0.039 0.243 6027 Planarity : 0.004 0.055 7217 Dihedral : 4.271 52.073 5606 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.83 % Favored : 97.07 % Rotamer: Outliers : 1.61 % Allowed : 10.08 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 aren not related in a simple way. whole: 1.22 (0.12), residues: 5019 helix: 1.98 (0.10), residues: 2548 sheet: -0.66 (0.19), residues: 651 loop : -0.23 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 139 TYR 0.019 0.002 TYR A 557 PHE 0.013 0.002 PHE C 629 TRP 0.015 0.001 TRP F 205 HIS 0.004 0.001 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00458 (39830) covalent geometry : angle 0.54116 (54082) hydrogen bonds : bond 0.03835 ( 2227) hydrogen bonds : angle 4.50010 ( 6447) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 229 time to evaluate : 1.614 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: A 556 ARG cc_start: 0.7948 (tpp80) cc_final: 0.7395 (tpp80) REVERT: A 659 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: B 1 MET cc_start: 0.6699 (ptt) cc_final: 0.6272 (ptm) REVERT: B 237 ARG cc_start: 0.7121 (ttm-80) cc_final: 0.6485 (ttm-80) REVERT: C 1 MET cc_start: 0.6864 (tpp) cc_final: 0.6421 (tpp) REVERT: C 257 SER cc_start: 0.8187 (t) cc_final: 0.7693 (p) REVERT: C 342 GLN cc_start: 0.8481 (mp10) cc_final: 0.7913 (mp10) REVERT: C 646 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8776 (pp) REVERT: D 57 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8465 (tt) REVERT: E 287 ARG cc_start: 0.6706 (ttm110) cc_final: 0.6445 (tpp80) REVERT: F 342 GLN cc_start: 0.7001 (mp-120) cc_final: 0.6443 (mp10) REVERT: F 554 ARG cc_start: 0.7859 (mtm180) cc_final: 0.7628 (mtm-85) REVERT: F 646 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8711 (pp) REVERT: F 651 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8078 (mt) REVERT: G 117 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.5511 (mp0) REVERT: G 151 GLN cc_start: 0.5497 (OUTLIER) cc_final: 0.5018 (mt0) REVERT: G 203 ARG cc_start: 0.7103 (ttt180) cc_final: 0.6818 (tpt-90) REVERT: G 665 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7737 (ttp80) REVERT: G 708 ARG cc_start: 0.6999 (mmt-90) cc_final: 0.6420 (mtm-85) outliers start: 64 outliers final: 47 residues processed: 279 average time/residue: 0.2898 time to fit residues: 129.1601 Evaluate side-chains 273 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 525 ARG Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 417 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 151 GLN Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 352 PHE Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 597 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 259 optimal weight: 0.9980 chunk 223 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 432 optimal weight: 3.9990 chunk 288 optimal weight: 0.9980 chunk 292 optimal weight: 0.9980 chunk 347 optimal weight: 0.7980 chunk 478 optimal weight: 10.0000 chunk 370 optimal weight: 30.0000 chunk 311 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 HIS ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 HIS D 573 GLN ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.152778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.110052 restraints weight = 51845.995| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.61 r_work: 0.3202 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 39830 Z= 0.111 Angle : 0.491 9.925 54082 Z= 0.244 Chirality : 0.037 0.231 6027 Planarity : 0.004 0.056 7217 Dihedral : 4.099 51.093 5606 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.65 % Favored : 97.27 % Rotamer: Outliers : 1.34 % Allowed : 10.48 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 aren not related in a simple way. whole: 1.47 (0.12), residues: 5019 helix: 2.21 (0.10), residues: 2548 sheet: -0.53 (0.20), residues: 651 loop : -0.16 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 114 TYR 0.016 0.001 TYR G 557 PHE 0.013 0.001 PHE F 571 TRP 0.032 0.001 TRP F 205 HIS 0.003 0.000 HIS F 469 Details of bonding type rmsd covalent geometry : bond 0.00248 (39830) covalent geometry : angle 0.49147 (54082) hydrogen bonds : bond 0.03556 ( 2227) hydrogen bonds : angle 4.29559 ( 6447) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 239 time to evaluate : 1.228 Fit side-chains REVERT: A 37 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8000 (mm-30) REVERT: A 659 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: B 1 MET cc_start: 0.6582 (ptt) cc_final: 0.6189 (ptm) REVERT: B 237 ARG cc_start: 0.7077 (ttm-80) cc_final: 0.6462 (ttm-80) REVERT: C 1 MET cc_start: 0.6760 (tpp) cc_final: 0.6371 (tpp) REVERT: C 257 SER cc_start: 0.8160 (t) cc_final: 0.7561 (p) REVERT: C 342 GLN cc_start: 0.8466 (mp10) cc_final: 0.7903 (mp10) REVERT: D 57 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8426 (tt) REVERT: D 682 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7817 (pt0) REVERT: E 40 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8220 (mt-10) REVERT: E 287 ARG cc_start: 0.6703 (ttm110) cc_final: 0.6425 (tpp80) REVERT: E 318 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8370 (mtmm) REVERT: E 696 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7614 (mm-40) REVERT: F 205 TRP cc_start: 0.7705 (m100) cc_final: 0.7197 (m-10) REVERT: F 342 GLN cc_start: 0.6948 (mp-120) cc_final: 0.6660 (mp10) REVERT: F 646 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8675 (pp) REVERT: F 651 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7988 (mt) REVERT: G 86 ARG cc_start: 0.8184 (ppt170) cc_final: 0.7082 (ttt90) REVERT: G 117 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5505 (mp0) REVERT: G 151 GLN cc_start: 0.5397 (OUTLIER) cc_final: 0.4998 (mt0) REVERT: G 203 ARG cc_start: 0.7112 (ttt180) cc_final: 0.6841 (tpt-90) REVERT: G 208 HIS cc_start: 0.6340 (t-90) cc_final: 0.6068 (m-70) REVERT: G 708 ARG cc_start: 0.7008 (mmt-90) cc_final: 0.6510 (mtm-85) outliers start: 53 outliers final: 35 residues processed: 278 average time/residue: 0.2273 time to fit residues: 102.8757 Evaluate side-chains 272 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 711 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 318 LYS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 151 GLN Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 352 PHE Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 597 ASN Chi-restraints excluded: chain G residue 603 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 361 optimal weight: 3.9990 chunk 359 optimal weight: 0.8980 chunk 424 optimal weight: 10.0000 chunk 463 optimal weight: 3.9990 chunk 418 optimal weight: 0.8980 chunk 473 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 453 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 210 optimal weight: 0.0870 chunk 122 optimal weight: 4.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 HIS A 560 HIS ** E 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.153031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109331 restraints weight = 51647.176| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.58 r_work: 0.3204 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39830 Z= 0.113 Angle : 0.492 17.913 54082 Z= 0.242 Chirality : 0.037 0.222 6027 Planarity : 0.004 0.072 7217 Dihedral : 4.031 51.300 5606 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 1.28 % Allowed : 10.58 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 aren not related in a simple way. whole: 1.55 (0.12), residues: 5019 helix: 2.26 (0.10), residues: 2555 sheet: -0.46 (0.20), residues: 651 loop : -0.12 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 114 TYR 0.016 0.001 TYR G 557 PHE 0.013 0.001 PHE F 571 TRP 0.034 0.001 TRP C 205 HIS 0.003 0.000 HIS F 469 Details of bonding type rmsd covalent geometry : bond 0.00255 (39830) covalent geometry : angle 0.49165 (54082) hydrogen bonds : bond 0.03491 ( 2227) hydrogen bonds : angle 4.24428 ( 6447) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8096 (mm-30) REVERT: A 85 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7682 (mm-30) REVERT: A 659 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: A 706 PHE cc_start: 0.7911 (m-10) cc_final: 0.7702 (m-10) REVERT: B 1 MET cc_start: 0.6620 (ptt) cc_final: 0.6205 (ptm) REVERT: B 237 ARG cc_start: 0.7114 (ttm-80) cc_final: 0.6499 (ttm-80) REVERT: C 1 MET cc_start: 0.6697 (tpp) cc_final: 0.6377 (tpp) REVERT: C 257 SER cc_start: 0.8134 (t) cc_final: 0.7538 (p) REVERT: C 342 GLN cc_start: 0.8472 (mp10) cc_final: 0.7928 (mp10) REVERT: D 57 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8465 (tt) REVERT: D 682 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7903 (pt0) REVERT: E 287 ARG cc_start: 0.6663 (ttm110) cc_final: 0.6392 (tpp80) REVERT: F 205 TRP cc_start: 0.7630 (m100) cc_final: 0.7174 (m-10) REVERT: F 342 GLN cc_start: 0.7048 (mp-120) cc_final: 0.6757 (mp10) REVERT: F 646 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8699 (pp) REVERT: F 651 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8049 (mt) REVERT: G 86 ARG cc_start: 0.8241 (ppt170) cc_final: 0.7144 (ttt90) REVERT: G 117 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5518 (mp0) REVERT: G 151 GLN cc_start: 0.5337 (OUTLIER) cc_final: 0.4939 (mt0) REVERT: G 203 ARG cc_start: 0.7139 (ttt180) cc_final: 0.6856 (tpt-90) REVERT: G 708 ARG cc_start: 0.7028 (mmt-90) cc_final: 0.6537 (mtm-85) outliers start: 51 outliers final: 36 residues processed: 270 average time/residue: 0.2654 time to fit residues: 115.9035 Evaluate side-chains 268 residues out of total 3969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 711 GLU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 151 GLN Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 352 PHE Chi-restraints excluded: chain G residue 597 ASN Chi-restraints excluded: chain G residue 603 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 371 optimal weight: 20.0000 chunk 295 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 447 optimal weight: 0.6980 chunk 288 optimal weight: 0.7980 chunk 257 optimal weight: 0.7980 chunk 473 optimal weight: 6.9990 chunk 348 optimal weight: 0.9980 chunk 266 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 398 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 HIS E 469 HIS E 653 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.153968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110389 restraints weight = 51621.701| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.58 r_work: 0.3222 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 39830 Z= 0.102 Angle : 0.484 15.381 54082 Z= 0.237 Chirality : 0.037 0.216 6027 Planarity : 0.004 0.056 7217 Dihedral : 3.963 50.651 5606 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.39 % Favored : 97.53 % Rotamer: Outliers : 1.13 % Allowed : 10.76 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 aren not related in a simple way. whole: 1.66 (0.12), residues: 5019 helix: 2.35 (0.10), residues: 2555 sheet: -0.41 (0.20), residues: 651 loop : -0.08 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 114 TYR 0.016 0.001 TYR G 557 PHE 0.013 0.001 PHE F 571 TRP 0.055 0.001 TRP B 205 HIS 0.003 0.000 HIS F 469 Details of bonding type rmsd covalent geometry : bond 0.00227 (39830) covalent geometry : angle 0.48392 (54082) hydrogen bonds : bond 0.03387 ( 2227) hydrogen bonds : angle 4.17637 ( 6447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10482.05 seconds wall clock time: 179 minutes 22.01 seconds (10762.01 seconds total)