Starting phenix.real_space_refine on Sat Jun 28 17:39:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k93_36973/06_2025/8k93_36973.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k93_36973/06_2025/8k93_36973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k93_36973/06_2025/8k93_36973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k93_36973/06_2025/8k93_36973.map" model { file = "/net/cci-nas-00/data/ceres_data/8k93_36973/06_2025/8k93_36973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k93_36973/06_2025/8k93_36973.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.034 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 4 5.49 5 S 46 5.16 5 C 21150 2.51 5 N 6000 2.21 5 O 6270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33470 Number of models: 1 Model: "" Number of chains: 10 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: "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} Time building chain proxies: 19.52, per 1000 atoms: 0.58 Number of scatterers: 33470 At special positions: 0 Unit cell: (149.24, 139.4, 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 46 16.00 P 4 15.00 O 6270 8.00 N 6000 7.00 C 21150 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: 8.27 Conformation dependent library (CDL) restraints added in 5.1 seconds 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 60 sheets defined 54.8% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.75 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: 3.998A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 118 removed outlier: 4.427A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 154 Processing helix chain 'A' and resid 173 through 221 removed outlier: 5.488A pdb=" N ALA A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.773A 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 300 through 305 Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.539A pdb=" N GLU A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.706A pdb=" N GLY A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.747A 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 470 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 536 through 540 removed outlier: 3.892A pdb=" N GLN A 540 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 557 removed outlier: 3.712A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (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 651 No H-bonds generated for 'chain 'A' and resid 649 through 651' Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 removed outlier: 3.545A pdb=" N ALA A 680 " --> pdb=" O THR A 676 " (cutoff:3.500A) 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: 3.615A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN B 70 " --> pdb=" O TYR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 111 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 121 through 154 Processing helix chain 'B' and resid 173 through 221 removed outlier: 3.752A pdb=" N ARG B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (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 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 301 through 305 removed outlier: 3.612A pdb=" N ARG B 304 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 321 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.582A pdb=" N GLY B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 removed outlier: 3.842A 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 471 removed outlier: 4.019A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 541 removed outlier: 4.283A pdb=" N GLN B 540 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 541 " --> pdb=" O GLY B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 557 Processing helix chain 'B' and resid 584 through 597 Processing helix chain 'B' and resid 621 through 637 Processing helix chain 'B' and resid 649 through 654 removed outlier: 4.225A 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: 3.690A 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: 5.122A pdb=" N ALA C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 213 " --> pdb=" O TYR C 209 " (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: 4.173A pdb=" N GLY C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.752A 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 471 removed outlier: 3.965A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 536 through 539 removed outlier: 4.067A pdb=" N GLY C 539 " --> pdb=" O GLY C 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 536 through 539' Processing helix chain 'C' and resid 545 through 557 Processing helix chain 'C' and resid 585 through 597 Processing helix chain 'C' and resid 621 through 636 Processing helix chain 'C' and resid 649 through 654 removed outlier: 4.413A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) removed outlier: 3.761A 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: 3.713A 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 119 Processing helix chain 'D' and resid 121 through 154 Processing helix chain 'D' and resid 173 through 221 removed outlier: 3.669A pdb=" N ARG D 203 " --> pdb=" O ARG D 199 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.914A 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 314 through 320 Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 363 through 369 removed outlier: 3.994A pdb=" N GLY D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 380 removed outlier: 3.619A 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 451 Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.990A 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 531 through 535 Processing helix chain 'D' and resid 536 through 540 removed outlier: 3.521A pdb=" N GLY D 539 " --> pdb=" O GLY D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 557 removed outlier: 3.517A pdb=" N TYR D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) 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: 4.122A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 654 " --> pdb=" O LEU D 651 " (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: 3.632A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 121 through 154 Processing helix chain 'E' and resid 173 through 221 removed outlier: 3.832A pdb=" N ARG E 203 " --> pdb=" O ARG E 199 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 4.040A 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 297 Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 314 through 321 Processing helix chain 'E' and resid 322 through 333 Processing helix chain 'E' and resid 363 through 369 removed outlier: 3.859A pdb=" N GLY E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 380 removed outlier: 4.067A pdb=" N SER E 377 " --> pdb=" O ASP E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 408 Processing helix chain 'E' and resid 412 through 428 Processing helix chain 'E' and resid 436 through 452 Processing helix chain 'E' and resid 456 through 471 removed outlier: 4.104A 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 535 through 540 removed outlier: 3.910A pdb=" N GLN E 540 " --> pdb=" O LEU E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 557 Processing helix chain 'E' and resid 585 through 597 Processing helix chain 'E' and resid 621 through 637 Processing helix chain 'E' and resid 649 through 654 removed outlier: 4.342A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 654 " --> pdb=" O LEU E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 667 Processing helix chain 'E' and resid 676 through 686 Processing helix chain 'E' and resid 694 through 719 Processing helix chain 'F' and resid 4 through 9 removed outlier: 3.501A pdb=" N LEU F 8 " --> pdb=" O SER F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.721A pdb=" N THR F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 119 removed outlier: 4.310A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASN F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 154 Processing helix chain 'F' and resid 173 through 221 removed outlier: 4.887A pdb=" N ALA F 206 " --> pdb=" O ARG F 202 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN F 212 " --> pdb=" O HIS F 208 " (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 251 removed outlier: 3.986A pdb=" N ARG F 251 " --> pdb=" O ALA F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 278 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 301 through 305 removed outlier: 3.517A pdb=" N ALA F 305 " --> pdb=" O VAL F 302 " (cutoff:3.500A) 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: 3.688A pdb=" N GLY F 369 " --> pdb=" O GLU F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 379 removed outlier: 3.932A 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 470 Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 535 through 540 Processing helix chain 'F' and resid 544 through 557 removed outlier: 3.516A pdb=" N THR F 548 " --> pdb=" O LYS F 544 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR F 557 " --> pdb=" O LEU F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 597 Processing helix chain 'F' and resid 621 through 637 Processing helix chain 'F' and resid 650 through 654 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 sheet with id=AA1, first strand: chain 'A' and resid 266 through 269 removed outlier: 4.582A pdb=" N ASP A 313 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 310 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 361 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A 312 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 49 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N HIS A 48 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE A 382 " --> pdb=" O HIS A 48 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 50 " --> pdb=" O ILE A 382 " (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 157 Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 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 494 through 496 Processing sheet with id=AA8, first strand: chain 'A' and resid 529 through 530 removed outlier: 6.513A pdb=" N ILE A 529 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N PHE A 571 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N GLU A 498 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL A 606 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN A 500 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA A 605 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 644 " --> pdb=" O TYR A 672 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 674 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 646 " --> pdb=" O VAL A 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 609 through 610 Processing sheet with id=AB1, first strand: chain 'B' and resid 266 through 269 removed outlier: 4.317A pdb=" N ASP B 313 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 310 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL B 361 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU B 312 " --> pdb=" O VAL B 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 253 through 254 Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 157 Processing sheet with id=AB4, first strand: chain 'B' and resid 280 through 281 Processing sheet with id=AB5, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AB6, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AB7, first strand: chain 'B' and resid 410 through 411 removed outlier: 7.198A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AB9, first strand: chain 'B' and resid 528 through 530 removed outlier: 6.810A pdb=" N ILE B 529 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N PHE B 571 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG B 516 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TRP B 511 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N GLU B 498 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N VAL B 606 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASN B 500 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 605 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN B 642 " --> pdb=" O HIS B 670 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR B 672 " --> pdb=" O GLN B 642 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL B 644 " --> pdb=" O TYR B 672 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL B 674 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 609 through 610 Processing sheet with id=AC2, first strand: chain 'C' and resid 2 through 3 removed outlier: 4.776A pdb=" N ILE C 671 " --> pdb=" O LEU C 3 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 9.825A pdb=" N GLU C 498 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL C 606 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASN C 500 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS C 527 " --> pdb=" O VAL C 565 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 266 through 269 removed outlier: 4.461A pdb=" N ASP C 313 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU C 310 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL C 361 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU C 312 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N HIS C 48 " --> pdb=" O PHE C 380 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 88 through 93 Processing sheet with id=AC5, first strand: chain 'C' and resid 156 through 159 removed outlier: 3.546A pdb=" N GLU C 165 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 280 through 281 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: 7.315A 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 583 through 584 removed outlier: 4.376A pdb=" N ALA C 583 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 266 through 269 removed outlier: 4.118A pdb=" N ASP D 313 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU D 310 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL D 361 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU D 312 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA D 49 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLY D 362 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU D 51 " --> pdb=" O GLY D 362 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR D 50 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD5, first strand: chain 'D' and resid 156 through 157 Processing sheet with id=AD6, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AD7, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AD8, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AD9, first strand: chain 'D' and resid 410 through 411 removed outlier: 7.224A pdb=" N GLN D 410 " --> pdb=" O LEU D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AE2, first strand: chain 'D' and resid 528 through 530 removed outlier: 3.881A pdb=" N TRP D 511 " --> pdb=" O VAL D 505 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N LEU D 604 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN D 500 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 502 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL D 644 " --> pdb=" O TYR D 672 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL D 674 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU D 646 " --> pdb=" O VAL D 674 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 583 through 584 removed outlier: 4.552A pdb=" N ALA D 583 " --> pdb=" O VAL D 610 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA D 609 " --> pdb=" O LEU D 617 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 266 through 268 removed outlier: 6.042A pdb=" N LEU E 310 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL E 361 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU E 312 " --> pdb=" O VAL E 361 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 253 through 254 Processing sheet with id=AE6, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.695A pdb=" N SER E 158 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU E 165 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AE8, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AE9, first strand: chain 'E' and resid 410 through 411 removed outlier: 7.262A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AF2, first strand: chain 'E' and resid 498 through 504 removed outlier: 3.758A pdb=" N HIS E 527 " --> pdb=" O VAL E 565 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE E 567 " --> pdb=" O HIS E 527 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 583 through 584 removed outlier: 4.550A pdb=" N ALA E 583 " --> pdb=" O VAL E 610 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 604 through 606 removed outlier: 6.506A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL E 644 " --> pdb=" O TYR E 672 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL E 674 " --> pdb=" O VAL E 644 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU E 646 " --> pdb=" O VAL E 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'F' and resid 266 through 269 removed outlier: 4.181A pdb=" N ASP F 313 " --> pdb=" O GLU F 269 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU F 310 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL F 361 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU F 312 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N HIS F 48 " --> pdb=" O PHE F 380 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 382 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 253 through 254 Processing sheet with id=AF7, first strand: chain 'F' and resid 156 through 157 Processing sheet with id=AF8, first strand: chain 'F' and resid 280 through 281 Processing sheet with id=AF9, first strand: chain 'F' and resid 284 through 286 Processing sheet with id=AG1, first strand: chain 'F' and resid 389 through 391 Processing sheet with id=AG2, first strand: chain 'F' and resid 410 through 411 removed outlier: 7.126A pdb=" N GLN F 410 " --> pdb=" O LEU F 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'F' and resid 494 through 495 Processing sheet with id=AG4, first strand: chain 'F' and resid 498 through 505 removed outlier: 3.971A pdb=" N TRP F 511 " --> pdb=" O VAL F 505 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 604 through 606 removed outlier: 6.062A pdb=" N ALA F 605 " --> pdb=" O ILE F 645 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 609 through 610 1890 hydrogen bonds defined for protein. 5451 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: 16.24 Time building geometry restraints manager: 9.86 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: 11715 1.36 - 1.51: 8927 1.51 - 1.65: 13414 1.65 - 1.80: 52 1.80 - 1.95: 24 Bond restraints: 34132 Sorted by residual: bond pdb=" P TS6 C 801 " pdb=" S2P TS6 C 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 D 801 " pdb=" S2P TS6 D 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 E 801 " pdb=" S2P TS6 E 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 B 801 " pdb=" S2P TS6 B 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.68e+02 bond pdb=" O4P TS6 C 801 " pdb=" P TS6 C 801 " ideal model delta sigma weight residual 1.516 1.613 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 34127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 46111 3.48 - 6.95: 210 6.95 - 10.43: 6 10.43 - 13.90: 11 13.90 - 17.38: 6 Bond angle restraints: 46344 Sorted by residual: angle pdb=" O PRO C 54 " pdb=" C PRO C 54 " pdb=" N PRO C 55 " ideal model delta sigma weight residual 121.31 118.24 3.07 4.60e-01 4.73e+00 4.46e+01 angle pdb=" N ARG A 203 " pdb=" CA ARG A 203 " pdb=" C ARG A 203 " ideal model delta sigma weight residual 114.62 107.66 6.96 1.14e+00 7.69e-01 3.73e+01 angle pdb=" O1P TS6 D 801 " pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 98.15 115.53 -17.38 3.00e+00 1.11e-01 3.36e+01 angle pdb=" O1P TS6 E 801 " pdb=" P TS6 E 801 " pdb=" S2P TS6 E 801 " ideal model delta sigma weight residual 98.15 115.42 -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 98.15 115.40 -17.25 3.00e+00 1.11e-01 3.31e+01 ... (remaining 46339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 18725 17.93 - 35.86: 1415 35.86 - 53.79: 308 53.79 - 71.73: 158 71.73 - 89.66: 112 Dihedral angle restraints: 20718 sinusoidal: 8388 harmonic: 12330 Sorted by residual: 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 180.00 157.60 22.40 0 5.00e+00 4.00e-02 2.01e+01 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 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA LEU D 411 " pdb=" C LEU D 411 " pdb=" N THR D 412 " pdb=" CA THR D 412 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 20715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4186 0.049 - 0.098: 811 0.098 - 0.147: 149 0.147 - 0.196: 16 0.196 - 0.245: 4 Chirality restraints: 5166 Sorted by residual: chirality pdb=" CA LEU D 360 " pdb=" N LEU D 360 " pdb=" C LEU D 360 " pdb=" CB LEU D 360 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA VAL D 361 " pdb=" N VAL D 361 " pdb=" C VAL D 361 " pdb=" CB VAL D 361 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA SER D 56 " pdb=" N SER D 56 " pdb=" C SER D 56 " pdb=" CB SER D 56 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 5163 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 246 " 0.079 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO C 247 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO C 247 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 247 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 522 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO C 523 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 523 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 523 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 350 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO C 351 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 351 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 351 " -0.033 5.00e-02 4.00e+02 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 237 2.64 - 3.20: 30069 3.20 - 3.77: 53450 3.77 - 4.33: 72153 4.33 - 4.90: 121623 Nonbonded interactions: 277532 Sorted by model distance: nonbonded pdb=" OG SER C 593 " pdb=" O LEU C 598 " model vdw 2.070 3.040 nonbonded pdb=" NH2 ARG A 516 " pdb=" OD2 ASP B 611 " model vdw 2.156 3.120 nonbonded pdb=" NH2 ARG C 516 " pdb=" OD2 ASP D 611 " model vdw 2.172 3.120 nonbonded pdb=" OE2 GLU A 475 " pdb=" NH2 ARG A 513 " model vdw 2.211 3.120 nonbonded pdb=" OG1 THR A 18 " pdb=" OE1 GLU A 19 " model vdw 2.219 3.040 ... (remaining 277527 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 719) selection = (chain 'C' and resid 1 through 719) selection = (chain 'D' and resid 1 through 719) selection = (chain 'E' and resid 1 through 719) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.330 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 80.550 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 34132 Z= 0.293 Angle : 0.728 17.380 46344 Z= 0.404 Chirality : 0.041 0.245 5166 Planarity : 0.005 0.119 6186 Dihedral : 16.127 89.657 12798 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.30 % Favored : 96.56 % Rotamer: Outliers : 0.09 % Allowed : 0.38 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.13), residues: 4302 helix: 1.98 (0.11), residues: 2173 sheet: -0.33 (0.22), residues: 532 loop : -0.27 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 290 HIS 0.006 0.001 HIS E 560 PHE 0.026 0.002 PHE D 352 TYR 0.023 0.002 TYR B 209 ARG 0.012 0.001 ARG D 328 Details of bonding type rmsd hydrogen bonds : bond 0.13001 ( 1890) hydrogen bonds : angle 6.01392 ( 5451) covalent geometry : bond 0.00587 (34132) covalent geometry : angle 0.72828 (46344) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 251 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.5682 (mtm) cc_final: 0.5458 (mtt) REVERT: A 606 VAL cc_start: 0.9032 (t) cc_final: 0.8751 (m) REVERT: B 9 GLU cc_start: 0.7884 (tp30) cc_final: 0.7514 (tp30) REVERT: B 57 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8432 (tt) REVERT: B 91 LEU cc_start: 0.7931 (mm) cc_final: 0.7459 (pp) REVERT: B 689 MET cc_start: 0.7794 (mtp) cc_final: 0.7575 (mtp) REVERT: B 708 ARG cc_start: 0.7329 (ttm-80) cc_final: 0.6918 (ttm-80) REVERT: C 57 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8491 (tt) REVERT: C 117 GLU cc_start: 0.6680 (mp0) cc_final: 0.6396 (mp0) REVERT: D 57 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8371 (tt) REVERT: E 208 HIS cc_start: 0.7967 (t-90) cc_final: 0.6762 (t70) REVERT: F 426 MET cc_start: 0.7491 (ttp) cc_final: 0.7155 (ttt) REVERT: F 433 MET cc_start: 0.8403 (ptm) cc_final: 0.8156 (ptp) REVERT: F 520 ARG cc_start: 0.5607 (tpp-160) cc_final: 0.5225 (tpp-160) REVERT: F 595 ILE cc_start: 0.7833 (mm) cc_final: 0.7459 (mm) outliers start: 3 outliers final: 0 residues processed: 254 average time/residue: 0.4785 time to fit residues: 198.0569 Evaluate side-chains 164 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 3.614 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 5.9990 chunk 322 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 333 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 386 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 ASN C 332 ASN D 396 ASN ** E 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS F 543 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.164007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.106097 restraints weight = 51405.918| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.17 r_work: 0.3219 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34132 Z= 0.120 Angle : 0.534 11.734 46344 Z= 0.269 Chirality : 0.038 0.168 5166 Planarity : 0.004 0.055 6186 Dihedral : 4.249 45.252 4806 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.51 % Rotamer: Outliers : 0.56 % Allowed : 5.41 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.13), residues: 4302 helix: 2.08 (0.11), residues: 2199 sheet: -0.39 (0.21), residues: 577 loop : -0.18 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 205 HIS 0.006 0.001 HIS F 208 PHE 0.029 0.001 PHE F 706 TYR 0.017 0.002 TYR C 50 ARG 0.006 0.000 ARG A 708 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 1890) hydrogen bonds : angle 4.82823 ( 5451) covalent geometry : bond 0.00264 (34132) covalent geometry : angle 0.53359 (46344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.5593 (mtm) cc_final: 0.5264 (ptp) REVERT: A 606 VAL cc_start: 0.8977 (t) cc_final: 0.8697 (m) REVERT: B 57 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8267 (tt) REVERT: C 57 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8197 (tt) REVERT: D 57 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8183 (tt) REVERT: E 43 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8510 (mp) REVERT: E 208 HIS cc_start: 0.7853 (t-90) cc_final: 0.6677 (t70) REVERT: F 426 MET cc_start: 0.7615 (ttp) cc_final: 0.7347 (ttm) REVERT: F 433 MET cc_start: 0.8046 (ptm) cc_final: 0.7772 (ptp) outliers start: 19 outliers final: 9 residues processed: 210 average time/residue: 0.4642 time to fit residues: 159.5828 Evaluate side-chains 170 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 3.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 107 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 370 optimal weight: 30.0000 chunk 240 optimal weight: 0.0970 chunk 215 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 HIS F 303 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.162450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109022 restraints weight = 51868.958| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.66 r_work: 0.3192 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34132 Z= 0.138 Angle : 0.518 11.155 46344 Z= 0.256 Chirality : 0.037 0.144 5166 Planarity : 0.004 0.053 6186 Dihedral : 4.131 47.818 4806 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % Rotamer: Outliers : 0.82 % Allowed : 7.50 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.13), residues: 4302 helix: 2.17 (0.11), residues: 2200 sheet: -0.41 (0.21), residues: 576 loop : -0.12 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 205 HIS 0.005 0.001 HIS F 208 PHE 0.015 0.001 PHE F 571 TYR 0.017 0.001 TYR E 50 ARG 0.007 0.000 ARG B 708 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 1890) hydrogen bonds : angle 4.55478 ( 5451) covalent geometry : bond 0.00316 (34132) covalent geometry : angle 0.51770 (46344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.7498 (m-80) cc_final: 0.7232 (m-80) REVERT: A 97 GLN cc_start: 0.6738 (mt0) cc_final: 0.6245 (mm110) REVERT: A 606 VAL cc_start: 0.8984 (t) cc_final: 0.8679 (m) REVERT: B 57 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8361 (tt) REVERT: B 79 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7261 (pp) REVERT: B 544 LYS cc_start: 0.7630 (tttt) cc_final: 0.7409 (tmtt) REVERT: C 57 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8305 (tt) REVERT: C 689 MET cc_start: 0.6903 (mpp) cc_final: 0.6668 (mpp) REVERT: D 57 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8328 (tt) REVERT: E 43 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8608 (mp) REVERT: E 208 HIS cc_start: 0.7878 (t-90) cc_final: 0.6929 (t70) REVERT: E 698 LYS cc_start: 0.7647 (mtpp) cc_final: 0.7441 (mttp) REVERT: F 426 MET cc_start: 0.7588 (ttp) cc_final: 0.7362 (ttm) REVERT: F 433 MET cc_start: 0.8175 (ptm) cc_final: 0.7927 (ptp) outliers start: 28 outliers final: 16 residues processed: 201 average time/residue: 0.4577 time to fit residues: 150.7156 Evaluate side-chains 185 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 421 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 144 optimal weight: 0.0370 chunk 348 optimal weight: 1.9990 chunk 404 optimal weight: 30.0000 chunk 201 optimal weight: 0.7980 chunk 350 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 303 optimal weight: 20.0000 chunk 197 optimal weight: 0.6980 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.163849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.103873 restraints weight = 51852.733| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.69 r_work: 0.3249 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34132 Z= 0.105 Angle : 0.488 10.659 46344 Z= 0.241 Chirality : 0.037 0.167 5166 Planarity : 0.004 0.055 6186 Dihedral : 4.014 47.610 4806 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 1.15 % Allowed : 8.58 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.13), residues: 4302 helix: 2.26 (0.11), residues: 2199 sheet: -0.37 (0.21), residues: 577 loop : -0.07 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 205 HIS 0.005 0.000 HIS F 208 PHE 0.024 0.001 PHE D 352 TYR 0.016 0.001 TYR C 557 ARG 0.007 0.000 ARG B 708 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 1890) hydrogen bonds : angle 4.36342 ( 5451) covalent geometry : bond 0.00233 (34132) covalent geometry : angle 0.48781 (46344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 3.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.6767 (mt0) cc_final: 0.6271 (mm110) REVERT: A 356 MET cc_start: 0.5718 (mtt) cc_final: 0.5427 (mtt) REVERT: A 516 ARG cc_start: 0.8312 (ttp80) cc_final: 0.7715 (ttt-90) REVERT: A 606 VAL cc_start: 0.8999 (t) cc_final: 0.8718 (m) REVERT: B 57 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8412 (tt) REVERT: C 57 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8168 (tt) REVERT: C 371 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: D 57 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8417 (tt) REVERT: E 43 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8592 (mp) REVERT: E 208 HIS cc_start: 0.7879 (t-90) cc_final: 0.6748 (t70) REVERT: F 426 MET cc_start: 0.7610 (ttp) cc_final: 0.7363 (ttm) REVERT: F 433 MET cc_start: 0.8271 (ptm) cc_final: 0.8053 (ptp) REVERT: F 636 LEU cc_start: 0.5916 (mm) cc_final: 0.5644 (mt) outliers start: 39 outliers final: 23 residues processed: 218 average time/residue: 0.4823 time to fit residues: 171.7674 Evaluate side-chains 183 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 3.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 117 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 409 optimal weight: 1.9990 chunk 398 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 375 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 167 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS E 357 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.157317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103200 restraints weight = 51835.601| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.07 r_work: 0.3111 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 34132 Z= 0.329 Angle : 0.660 10.540 46344 Z= 0.329 Chirality : 0.043 0.253 5166 Planarity : 0.005 0.057 6186 Dihedral : 4.385 54.221 4806 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 1.62 % Allowed : 9.73 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.13), residues: 4302 helix: 1.87 (0.11), residues: 2191 sheet: -0.73 (0.20), residues: 578 loop : -0.18 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 290 HIS 0.016 0.001 HIS F 208 PHE 0.023 0.002 PHE D 352 TYR 0.027 0.002 TYR C 420 ARG 0.014 0.001 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 1890) hydrogen bonds : angle 4.71921 ( 5451) covalent geometry : bond 0.00793 (34132) covalent geometry : angle 0.66013 (46344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 153 time to evaluate : 3.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7880 (pm20) REVERT: B 646 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9027 (pp) REVERT: C 57 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8425 (tt) REVERT: C 128 LYS cc_start: 0.7472 (tttm) cc_final: 0.7173 (tppt) REVERT: C 689 MET cc_start: 0.7401 (mpp) cc_final: 0.6852 (mpp) REVERT: E 43 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8712 (mp) REVERT: E 57 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8901 (tt) REVERT: F 91 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8390 (tt) REVERT: F 426 MET cc_start: 0.7618 (ttp) cc_final: 0.7318 (ttm) REVERT: F 433 MET cc_start: 0.8367 (ptm) cc_final: 0.8027 (ptt) REVERT: F 636 LEU cc_start: 0.5971 (mm) cc_final: 0.5730 (mt) outliers start: 55 outliers final: 32 residues processed: 197 average time/residue: 0.4783 time to fit residues: 155.0836 Evaluate side-chains 175 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 3.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 676 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 641 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 320 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 chunk 178 optimal weight: 0.8980 chunk 388 optimal weight: 5.9990 chunk 368 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 340 optimal weight: 10.0000 chunk 352 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.167157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.122156 restraints weight = 50988.143| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.58 r_work: 0.3308 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34132 Z= 0.111 Angle : 0.506 11.375 46344 Z= 0.250 Chirality : 0.037 0.200 5166 Planarity : 0.004 0.053 6186 Dihedral : 4.111 48.827 4806 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.25 % Favored : 97.68 % Rotamer: Outliers : 1.47 % Allowed : 10.41 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.13), residues: 4302 helix: 2.14 (0.11), residues: 2199 sheet: -0.63 (0.21), residues: 577 loop : -0.09 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 205 HIS 0.008 0.001 HIS F 208 PHE 0.022 0.001 PHE D 352 TYR 0.018 0.001 TYR E 50 ARG 0.007 0.000 ARG D 213 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 1890) hydrogen bonds : angle 4.39059 ( 5451) covalent geometry : bond 0.00245 (34132) covalent geometry : angle 0.50613 (46344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 3.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7901 (pm20) REVERT: C 57 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8700 (tt) REVERT: C 689 MET cc_start: 0.7565 (mpp) cc_final: 0.7105 (mpp) REVERT: D 57 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8765 (tt) REVERT: E 57 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8686 (tt) REVERT: E 646 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8474 (pp) REVERT: F 426 MET cc_start: 0.7390 (ttp) cc_final: 0.7124 (ttm) REVERT: F 636 LEU cc_start: 0.5862 (mm) cc_final: 0.5640 (mt) outliers start: 50 outliers final: 29 residues processed: 194 average time/residue: 0.4540 time to fit residues: 148.5047 Evaluate side-chains 172 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 3.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 22 optimal weight: 30.0000 chunk 342 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 chunk 317 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 221 optimal weight: 0.0970 chunk 93 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 396 ASN F 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.168054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.123715 restraints weight = 50987.978| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.57 r_work: 0.3330 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 34132 Z= 0.101 Angle : 0.490 11.909 46344 Z= 0.240 Chirality : 0.036 0.136 5166 Planarity : 0.004 0.054 6186 Dihedral : 3.963 48.490 4806 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.40 % Rotamer: Outliers : 1.23 % Allowed : 11.11 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.13), residues: 4302 helix: 2.30 (0.11), residues: 2192 sheet: -0.54 (0.21), residues: 585 loop : -0.02 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 205 HIS 0.004 0.000 HIS F 208 PHE 0.029 0.001 PHE F 706 TYR 0.016 0.001 TYR C 557 ARG 0.008 0.000 ARG D 213 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 1890) hydrogen bonds : angle 4.25146 ( 5451) covalent geometry : bond 0.00223 (34132) covalent geometry : angle 0.49040 (46344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8119 (ttt-90) REVERT: B 57 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8682 (tt) REVERT: C 57 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8563 (tt) REVERT: C 689 MET cc_start: 0.7636 (mpp) cc_final: 0.7177 (mpp) REVERT: D 57 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8772 (tt) REVERT: E 57 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8661 (tt) REVERT: E 111 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7400 (mm-30) REVERT: E 646 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8479 (pp) REVERT: F 636 LEU cc_start: 0.5792 (mm) cc_final: 0.5558 (mt) outliers start: 42 outliers final: 26 residues processed: 193 average time/residue: 0.4946 time to fit residues: 155.3295 Evaluate side-chains 177 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 311 optimal weight: 0.6980 chunk 349 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 402 optimal weight: 8.9990 chunk 394 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 404 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.165992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.120585 restraints weight = 50848.102| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.69 r_work: 0.3280 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34132 Z= 0.164 Angle : 0.523 11.448 46344 Z= 0.256 Chirality : 0.038 0.173 5166 Planarity : 0.004 0.053 6186 Dihedral : 4.020 50.468 4806 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 1.21 % Allowed : 11.38 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.13), residues: 4302 helix: 2.24 (0.11), residues: 2191 sheet: -0.60 (0.21), residues: 585 loop : 0.02 (0.17), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 205 HIS 0.003 0.001 HIS E 303 PHE 0.036 0.001 PHE F 706 TYR 0.018 0.002 TYR E 50 ARG 0.010 0.000 ARG D 213 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 1890) hydrogen bonds : angle 4.31871 ( 5451) covalent geometry : bond 0.00387 (34132) covalent geometry : angle 0.52260 (46344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 646 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9097 (pp) REVERT: C 57 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8740 (tt) REVERT: C 689 MET cc_start: 0.7530 (mpp) cc_final: 0.7067 (mpp) REVERT: C 706 PHE cc_start: 0.8274 (m-10) cc_final: 0.7924 (m-10) REVERT: D 57 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8846 (tt) REVERT: E 57 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8755 (tt) REVERT: E 111 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: E 646 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8505 (pp) REVERT: F 636 LEU cc_start: 0.5836 (mm) cc_final: 0.5625 (mt) outliers start: 41 outliers final: 28 residues processed: 176 average time/residue: 0.4684 time to fit residues: 137.8633 Evaluate side-chains 172 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 3.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 247 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 395 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 421 optimal weight: 3.9990 chunk 389 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 362 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 713 HIS ** 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 = 0.4167 r_free = 0.4167 target = 0.164787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.119394 restraints weight = 50511.228| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.70 r_work: 0.3252 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 34132 Z= 0.163 Angle : 0.525 11.340 46344 Z= 0.258 Chirality : 0.038 0.197 5166 Planarity : 0.004 0.053 6186 Dihedral : 4.063 50.540 4806 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.63 % Favored : 97.30 % Rotamer: Outliers : 1.21 % Allowed : 11.41 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.13), residues: 4302 helix: 2.23 (0.11), residues: 2191 sheet: -0.64 (0.21), residues: 582 loop : -0.01 (0.17), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 205 HIS 0.003 0.001 HIS E 560 PHE 0.038 0.001 PHE F 706 TYR 0.020 0.002 TYR E 50 ARG 0.010 0.000 ARG D 213 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 1890) hydrogen bonds : angle 4.32558 ( 5451) covalent geometry : bond 0.00382 (34132) covalent geometry : angle 0.52519 (46344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 3.947 Fit side-chains revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8398 (mt) cc_final: 0.8081 (mt) REVERT: A 611 ASP cc_start: 0.6733 (p0) cc_final: 0.5865 (t0) REVERT: B 646 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9003 (pp) REVERT: C 57 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8641 (tt) REVERT: C 128 LYS cc_start: 0.7635 (ttmt) cc_final: 0.6667 (tppt) REVERT: C 689 MET cc_start: 0.7638 (mpp) cc_final: 0.7283 (mpp) REVERT: C 706 PHE cc_start: 0.8140 (m-10) cc_final: 0.7911 (m-10) REVERT: D 57 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8768 (tt) REVERT: E 57 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8682 (tt) REVERT: E 646 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8435 (pp) REVERT: E 665 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7542 (mmm-85) REVERT: F 636 LEU cc_start: 0.5804 (mm) cc_final: 0.5598 (mt) outliers start: 41 outliers final: 29 residues processed: 177 average time/residue: 0.4742 time to fit residues: 138.4368 Evaluate side-chains 170 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 665 ARG Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 277 optimal weight: 0.0770 chunk 285 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 394 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 312 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 276 optimal weight: 0.5980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN F 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.167608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.123099 restraints weight = 50875.809| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.62 r_work: 0.3323 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 34132 Z= 0.105 Angle : 0.493 11.454 46344 Z= 0.240 Chirality : 0.037 0.217 5166 Planarity : 0.004 0.054 6186 Dihedral : 3.951 48.861 4806 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 1.12 % Allowed : 11.61 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.13), residues: 4302 helix: 2.34 (0.11), residues: 2191 sheet: -0.56 (0.21), residues: 587 loop : 0.04 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 290 HIS 0.004 0.000 HIS F 208 PHE 0.040 0.001 PHE F 706 TYR 0.015 0.001 TYR C 557 ARG 0.011 0.000 ARG A 708 Details of bonding type rmsd hydrogen bonds : bond 0.03262 ( 1890) hydrogen bonds : angle 4.19778 ( 5451) covalent geometry : bond 0.00236 (34132) covalent geometry : angle 0.49309 (46344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8362 (mt) cc_final: 0.8047 (mt) REVERT: A 516 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8038 (ttt-90) REVERT: A 611 ASP cc_start: 0.6938 (p0) cc_final: 0.5967 (t0) REVERT: B 646 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9067 (pp) REVERT: C 57 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8559 (tt) REVERT: C 128 LYS cc_start: 0.7663 (ttmt) cc_final: 0.6626 (tppt) REVERT: C 689 MET cc_start: 0.7603 (mpp) cc_final: 0.7177 (mpp) REVERT: C 706 PHE cc_start: 0.8105 (m-10) cc_final: 0.7757 (m-10) REVERT: D 57 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8770 (tt) REVERT: D 200 ARG cc_start: 0.7668 (mmm160) cc_final: 0.7283 (mmm160) REVERT: E 57 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8682 (tt) REVERT: E 646 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8490 (pp) REVERT: E 665 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7930 (mmm-85) outliers start: 38 outliers final: 26 residues processed: 182 average time/residue: 0.4789 time to fit residues: 143.7663 Evaluate side-chains 176 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 665 ARG Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 613 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 295 optimal weight: 9.9990 chunk 333 optimal weight: 0.0870 chunk 330 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 356 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 421 optimal weight: 20.0000 chunk 384 optimal weight: 1.9990 chunk 334 optimal weight: 10.0000 chunk 242 optimal weight: 1.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 334 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 = 0.4174 r_free = 0.4174 target = 0.165430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.120199 restraints weight = 50398.314| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.64 r_work: 0.3272 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34132 Z= 0.145 Angle : 0.513 11.366 46344 Z= 0.250 Chirality : 0.037 0.195 5166 Planarity : 0.004 0.053 6186 Dihedral : 3.983 49.919 4806 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.33 % Rotamer: Outliers : 1.06 % Allowed : 11.76 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.13), residues: 4302 helix: 2.31 (0.11), residues: 2193 sheet: -0.49 (0.21), residues: 567 loop : 0.02 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 205 HIS 0.003 0.001 HIS D 469 PHE 0.040 0.001 PHE F 706 TYR 0.019 0.001 TYR C 557 ARG 0.012 0.000 ARG A 708 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 1890) hydrogen bonds : angle 4.23409 ( 5451) covalent geometry : bond 0.00339 (34132) covalent geometry : angle 0.51251 (46344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17800.88 seconds wall clock time: 304 minutes 22.25 seconds (18262.25 seconds total)