Starting phenix.real_space_refine on Tue Aug 26 04:27:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k93_36973/08_2025/8k93_36973.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k93_36973/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k93_36973/08_2025/8k93_36973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k93_36973/08_2025/8k93_36973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k93_36973/08_2025/8k93_36973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k93_36973/08_2025/8k93_36973.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.034 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.19, per 1000 atoms: 0.24 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: 3.05 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.27 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: 8.17 Time building geometry restraints manager: 3.81 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: 0.02 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: 3.610 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: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.240 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.130 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (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 ARG 0.012 0.001 ARG D 328 TYR 0.023 0.002 TYR B 209 PHE 0.026 0.002 PHE D 352 TRP 0.016 0.002 TRP B 290 HIS 0.006 0.001 HIS E 560 Details of bonding type rmsd covalent geometry : bond 0.00587 (34132) covalent geometry : angle 0.72828 (46344) hydrogen bonds : bond 0.13001 ( 1890) hydrogen bonds : angle 6.01392 ( 5451) *********************** 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 : 1.142 Fit side-chains 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: 0.8157 (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: 0.1951 time to fit residues: 79.9617 Evaluate side-chains 162 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 20.0000 chunk 155 optimal weight: 30.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN D 396 ASN F 208 HIS ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.161004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.107692 restraints weight = 51773.101| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.49 r_work: 0.3196 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 34132 Z= 0.166 Angle : 0.558 11.496 46344 Z= 0.282 Chirality : 0.039 0.168 5166 Planarity : 0.005 0.055 6186 Dihedral : 4.305 47.009 4806 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 0.59 % Allowed : 5.58 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.13), residues: 4302 helix: 2.08 (0.11), residues: 2171 sheet: -0.47 (0.21), residues: 577 loop : -0.21 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 328 TYR 0.019 0.002 TYR E 50 PHE 0.030 0.001 PHE F 706 TRP 0.012 0.001 TRP C 205 HIS 0.006 0.001 HIS E 560 Details of bonding type rmsd covalent geometry : bond 0.00384 (34132) covalent geometry : angle 0.55836 (46344) hydrogen bonds : bond 0.04119 ( 1890) hydrogen bonds : angle 4.91953 ( 5451) *********************** 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 202 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: A 356 MET cc_start: 0.5667 (mtm) cc_final: 0.5299 (ptp) REVERT: B 57 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8353 (tt) REVERT: B 79 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7403 (pp) REVERT: C 57 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8324 (tt) REVERT: D 57 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8299 (tt) REVERT: D 221 PHE cc_start: 0.7645 (m-80) cc_final: 0.7425 (m-80) REVERT: D 254 LEU cc_start: 0.6935 (tp) cc_final: 0.6250 (pp) REVERT: E 43 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8646 (mp) REVERT: E 57 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8804 (tt) REVERT: E 208 HIS cc_start: 0.7880 (t-90) cc_final: 0.6684 (t70) REVERT: F 426 MET cc_start: 0.7613 (ttp) cc_final: 0.7345 (ttm) REVERT: F 433 MET cc_start: 0.8297 (ptm) cc_final: 0.8030 (ptp) outliers start: 20 outliers final: 10 residues processed: 199 average time/residue: 0.2207 time to fit residues: 71.0474 Evaluate side-chains 167 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 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 D residue 205 TRP Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 57 LEU 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 382 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 283 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 chunk 15 optimal weight: 50.0000 chunk 130 optimal weight: 0.9980 chunk 160 optimal weight: 50.0000 chunk 153 optimal weight: 9.9990 chunk 315 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 560 HIS C 48 HIS F 208 HIS F 303 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 = 0.4113 r_free = 0.4113 target = 0.158902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105290 restraints weight = 51959.062| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.30 r_work: 0.3168 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 34132 Z= 0.213 Angle : 0.567 11.089 46344 Z= 0.284 Chirality : 0.039 0.147 5166 Planarity : 0.004 0.055 6186 Dihedral : 4.299 51.133 4806 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 0.94 % Allowed : 7.79 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.13), residues: 4302 helix: 2.06 (0.11), residues: 2167 sheet: -0.63 (0.21), residues: 576 loop : -0.22 (0.16), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 328 TYR 0.022 0.002 TYR E 50 PHE 0.016 0.002 PHE C 630 TRP 0.010 0.001 TRP B 290 HIS 0.005 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00500 (34132) covalent geometry : angle 0.56728 (46344) hydrogen bonds : bond 0.03948 ( 1890) hydrogen bonds : angle 4.71111 ( 5451) *********************** 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: 32 poor density : 175 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.6807 (mt0) cc_final: 0.6327 (mm110) REVERT: A 356 MET cc_start: 0.5584 (mtm) cc_final: 0.5303 (ptp) REVERT: A 606 VAL cc_start: 0.9079 (t) cc_final: 0.8782 (m) REVERT: B 228 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7657 (mt) REVERT: C 57 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8378 (tt) REVERT: C 208 HIS cc_start: 0.7793 (t-90) cc_final: 0.7592 (t-90) REVERT: C 689 MET cc_start: 0.7082 (mpp) cc_final: 0.6811 (mpp) REVERT: D 221 PHE cc_start: 0.7815 (m-80) cc_final: 0.7552 (m-80) REVERT: E 43 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8616 (mp) REVERT: E 57 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8667 (tt) REVERT: F 426 MET cc_start: 0.7645 (ttp) cc_final: 0.7431 (ttm) REVERT: F 433 MET cc_start: 0.8341 (ptm) cc_final: 0.8098 (ptp) REVERT: F 636 LEU cc_start: 0.5921 (mm) cc_final: 0.5667 (mt) outliers start: 32 outliers final: 24 residues processed: 199 average time/residue: 0.1998 time to fit residues: 64.1333 Evaluate side-chains 178 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 228 LEU Chi-restraints excluded: chain B residue 256 THR 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 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 43 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 365 GLU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 208 HIS 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 328 optimal weight: 1.9990 chunk 303 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 417 optimal weight: 20.0000 chunk 371 optimal weight: 9.9990 chunk 65 optimal weight: 0.3980 chunk 372 optimal weight: 30.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.161536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103113 restraints weight = 51641.003| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.80 r_work: 0.3210 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1323 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= 0.131 Angle : 0.510 10.959 46344 Z= 0.253 Chirality : 0.037 0.140 5166 Planarity : 0.004 0.054 6186 Dihedral : 4.160 49.155 4806 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.58 % Favored : 97.35 % Rotamer: Outliers : 1.21 % Allowed : 9.20 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.13), residues: 4302 helix: 2.09 (0.11), residues: 2197 sheet: -0.59 (0.21), residues: 577 loop : -0.17 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 36 TYR 0.018 0.001 TYR E 50 PHE 0.014 0.001 PHE E 630 TRP 0.009 0.001 TRP B 205 HIS 0.008 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00298 (34132) covalent geometry : angle 0.50991 (46344) hydrogen bonds : bond 0.03624 ( 1890) hydrogen bonds : angle 4.50111 ( 5451) *********************** 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 217 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.7476 (m-80) cc_final: 0.7055 (m-80) REVERT: A 97 GLN cc_start: 0.6800 (mt0) cc_final: 0.6305 (mm110) REVERT: A 606 VAL cc_start: 0.9004 (t) cc_final: 0.8747 (m) REVERT: C 57 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8377 (tt) REVERT: C 208 HIS cc_start: 0.7806 (t-90) cc_final: 0.7589 (t-90) REVERT: C 371 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: C 689 MET cc_start: 0.7022 (mpp) cc_final: 0.6696 (mpp) REVERT: D 57 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8450 (tt) REVERT: D 200 ARG cc_start: 0.7643 (mmm160) cc_final: 0.7159 (mmm160) REVERT: D 221 PHE cc_start: 0.7737 (m-80) cc_final: 0.7497 (m-80) REVERT: E 43 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8651 (mp) REVERT: E 57 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8861 (tt) REVERT: F 426 MET cc_start: 0.7604 (ttp) cc_final: 0.7346 (ttm) REVERT: F 433 MET cc_start: 0.8258 (ptm) cc_final: 0.8029 (ptp) REVERT: F 636 LEU cc_start: 0.5901 (mm) cc_final: 0.5644 (mt) outliers start: 41 outliers final: 21 residues processed: 207 average time/residue: 0.1858 time to fit residues: 63.4265 Evaluate side-chains 180 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 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 193 GLU Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 417 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 365 GLU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 283 TYR 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 370 optimal weight: 9.9990 chunk 253 optimal weight: 5.9990 chunk 97 optimal weight: 0.0050 chunk 419 optimal weight: 0.9990 chunk 382 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 393 optimal weight: 7.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.160166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108918 restraints weight = 51823.266| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.72 r_work: 0.3145 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 34132 Z= 0.169 Angle : 0.527 10.864 46344 Z= 0.260 Chirality : 0.038 0.162 5166 Planarity : 0.004 0.053 6186 Dihedral : 4.139 50.787 4806 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 1.50 % Allowed : 10.05 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.13), residues: 4302 helix: 2.11 (0.11), residues: 2195 sheet: -0.63 (0.21), residues: 577 loop : -0.12 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.019 0.002 TYR E 50 PHE 0.014 0.001 PHE E 630 TRP 0.009 0.001 TRP B 205 HIS 0.006 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00397 (34132) covalent geometry : angle 0.52701 (46344) hydrogen bonds : bond 0.03621 ( 1890) hydrogen bonds : angle 4.45190 ( 5451) *********************** 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 209 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.7083 (m-80) cc_final: 0.6748 (m-80) REVERT: A 365 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7864 (pm20) REVERT: A 606 VAL cc_start: 0.9048 (t) cc_final: 0.8772 (m) REVERT: B 646 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8992 (pp) REVERT: B 689 MET cc_start: 0.7271 (mtp) cc_final: 0.6839 (mmm) REVERT: C 57 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8386 (tt) REVERT: C 128 LYS cc_start: 0.7398 (tttm) cc_final: 0.7133 (tppt) REVERT: C 203 ARG cc_start: 0.6952 (ttm170) cc_final: 0.6743 (ptm160) REVERT: C 208 HIS cc_start: 0.7867 (t-90) cc_final: 0.7634 (t-90) REVERT: C 617 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8505 (mt) REVERT: C 689 MET cc_start: 0.7156 (mpp) cc_final: 0.6662 (mpp) REVERT: D 221 PHE cc_start: 0.7845 (m-80) cc_final: 0.7559 (m-80) REVERT: E 43 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8610 (mp) REVERT: E 57 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8651 (tt) REVERT: F 91 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8348 (tt) REVERT: F 426 MET cc_start: 0.7597 (ttp) cc_final: 0.7299 (ttm) REVERT: F 433 MET cc_start: 0.8276 (ptm) cc_final: 0.7929 (ptt) REVERT: F 636 LEU cc_start: 0.5956 (mm) cc_final: 0.5720 (mt) REVERT: F 648 GLU cc_start: 0.7700 (tt0) cc_final: 0.7430 (tm-30) outliers start: 51 outliers final: 28 residues processed: 199 average time/residue: 0.2312 time to fit residues: 75.4980 Evaluate side-chains 179 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 302 VAL 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 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 188 LEU 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 617 LEU 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 417 THR 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 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 226 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 422 optimal weight: 9.9990 chunk 373 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 347 optimal weight: 6.9990 chunk 312 optimal weight: 3.9990 chunk 267 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 GLN ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 GLN F 48 HIS F 208 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.157067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.108913 restraints weight = 51579.687| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.94 r_work: 0.3139 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 34132 Z= 0.280 Angle : 0.623 11.228 46344 Z= 0.309 Chirality : 0.041 0.161 5166 Planarity : 0.005 0.052 6186 Dihedral : 4.399 53.554 4806 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.37 % Favored : 96.56 % Rotamer: Outliers : 2.00 % Allowed : 10.70 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.13), residues: 4302 helix: 1.90 (0.11), residues: 2187 sheet: -0.88 (0.20), residues: 575 loop : -0.23 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 203 TYR 0.024 0.002 TYR E 50 PHE 0.020 0.002 PHE A 30 TRP 0.012 0.002 TRP B 290 HIS 0.006 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00666 (34132) covalent geometry : angle 0.62282 (46344) hydrogen bonds : bond 0.03991 ( 1890) hydrogen bonds : angle 4.67660 ( 5451) *********************** 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 219 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 151 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.7081 (m-80) cc_final: 0.6728 (m-80) REVERT: A 356 MET cc_start: 0.6374 (ptp) cc_final: 0.5883 (mtm) REVERT: A 365 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7754 (pm20) REVERT: A 606 VAL cc_start: 0.9165 (t) cc_final: 0.8857 (m) REVERT: A 611 ASP cc_start: 0.7276 (p0) cc_final: 0.6494 (t0) REVERT: B 315 LEU cc_start: 0.8507 (tt) cc_final: 0.8289 (tp) REVERT: B 646 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9061 (pp) REVERT: B 689 MET cc_start: 0.7443 (mtp) cc_final: 0.7142 (mmm) REVERT: C 17 SER cc_start: 0.7916 (p) cc_final: 0.7683 (t) REVERT: C 57 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8450 (tt) REVERT: C 114 ARG cc_start: 0.6579 (mmp80) cc_final: 0.6344 (mmt-90) REVERT: C 128 LYS cc_start: 0.7417 (tttm) cc_final: 0.7121 (tppt) REVERT: C 208 HIS cc_start: 0.7986 (t-90) cc_final: 0.7711 (t-90) REVERT: C 617 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8486 (mt) REVERT: C 689 MET cc_start: 0.7633 (mpp) cc_final: 0.7012 (mpp) REVERT: D 348 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6934 (tt0) REVERT: E 43 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8711 (mp) REVERT: E 646 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8664 (pp) REVERT: E 665 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8129 (mmm-85) REVERT: F 426 MET cc_start: 0.7601 (ttp) cc_final: 0.7288 (ttm) REVERT: F 636 LEU cc_start: 0.5928 (mm) cc_final: 0.5688 (mt) REVERT: F 648 GLU cc_start: 0.7710 (tt0) cc_final: 0.7284 (tm-30) outliers start: 68 outliers final: 39 residues processed: 209 average time/residue: 0.2301 time to fit residues: 78.3778 Evaluate side-chains 180 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 1.436 ------------------------------------------------------------------------------- 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 499 VAL Chi-restraints excluded: chain A residue 651 LEU 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 499 VAL 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 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 617 LEU Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 542 PHE 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 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 517 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 665 ARG Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 526 ASP 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 195 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 196 optimal weight: 0.6980 chunk 236 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 205 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.160084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.101841 restraints weight = 51664.734| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.77 r_work: 0.3184 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34132 Z= 0.131 Angle : 0.510 10.841 46344 Z= 0.252 Chirality : 0.037 0.206 5166 Planarity : 0.004 0.053 6186 Dihedral : 4.170 49.192 4806 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.37 % Favored : 97.56 % Rotamer: Outliers : 1.41 % Allowed : 11.70 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.13), residues: 4302 helix: 2.10 (0.11), residues: 2192 sheet: -0.86 (0.20), residues: 577 loop : -0.14 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 213 TYR 0.019 0.001 TYR E 50 PHE 0.032 0.001 PHE F 706 TRP 0.009 0.001 TRP F 290 HIS 0.003 0.001 HIS E 560 Details of bonding type rmsd covalent geometry : bond 0.00300 (34132) covalent geometry : angle 0.51039 (46344) hydrogen bonds : bond 0.03550 ( 1890) hydrogen bonds : angle 4.41932 ( 5451) *********************** 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 197 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 47 PHE cc_start: 0.7044 (m-80) cc_final: 0.6662 (m-80) REVERT: A 356 MET cc_start: 0.6435 (ptp) cc_final: 0.5781 (mtm) REVERT: A 365 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7805 (pm20) REVERT: A 606 VAL cc_start: 0.9140 (t) cc_final: 0.8880 (m) REVERT: B 646 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9051 (pp) REVERT: C 17 SER cc_start: 0.8086 (p) cc_final: 0.7814 (t) REVERT: C 57 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8280 (tt) REVERT: C 114 ARG cc_start: 0.6580 (mmp80) cc_final: 0.6287 (mmt-90) REVERT: C 128 LYS cc_start: 0.7377 (tttm) cc_final: 0.7099 (tppt) REVERT: C 203 ARG cc_start: 0.7145 (ttm170) cc_final: 0.6898 (ptm160) REVERT: C 208 HIS cc_start: 0.7992 (t-90) cc_final: 0.7700 (t-90) REVERT: C 371 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: C 617 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8577 (mt) REVERT: C 689 MET cc_start: 0.7415 (mpp) cc_final: 0.6804 (mpp) REVERT: D 57 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8682 (tt) REVERT: D 370 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8116 (mp) REVERT: E 43 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8625 (mp) REVERT: E 646 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8577 (pp) REVERT: E 665 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8246 (mmm-85) REVERT: F 91 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8470 (tt) REVERT: F 426 MET cc_start: 0.7547 (ttp) cc_final: 0.7322 (ttt) REVERT: F 636 LEU cc_start: 0.5958 (mm) cc_final: 0.5732 (mt) REVERT: F 648 GLU cc_start: 0.7712 (tt0) cc_final: 0.7390 (tm-30) outliers start: 48 outliers final: 32 residues processed: 188 average time/residue: 0.1990 time to fit residues: 62.0064 Evaluate side-chains 179 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 651 LEU 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 499 VAL 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 188 LEU Chi-restraints excluded: chain C residue 371 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 617 LEU Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 43 ILE 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 517 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 665 ARG 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 332 ASN Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 690 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 165 optimal weight: 10.0000 chunk 419 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 360 optimal weight: 0.1980 chunk 284 optimal weight: 10.0000 chunk 392 optimal weight: 6.9990 chunk 395 optimal weight: 1.9990 chunk 175 optimal weight: 0.0970 chunk 335 optimal weight: 8.9990 chunk 334 optimal weight: 5.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- 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** F 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.158513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.110266 restraints weight = 51669.216| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.92 r_work: 0.3175 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 34132 Z= 0.190 Angle : 0.543 11.022 46344 Z= 0.267 Chirality : 0.038 0.195 5166 Planarity : 0.004 0.053 6186 Dihedral : 4.197 51.508 4806 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.05 % Rotamer: Outliers : 1.73 % Allowed : 11.58 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.13), residues: 4302 helix: 2.07 (0.11), residues: 2192 sheet: -0.83 (0.21), residues: 579 loop : -0.15 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 213 TYR 0.019 0.002 TYR E 50 PHE 0.035 0.001 PHE F 706 TRP 0.009 0.001 TRP E 250 HIS 0.006 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00448 (34132) covalent geometry : angle 0.54257 (46344) hydrogen bonds : bond 0.03644 ( 1890) hydrogen bonds : angle 4.45898 ( 5451) *********************** 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 198 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 47 PHE cc_start: 0.7068 (m-80) cc_final: 0.6653 (m-80) REVERT: A 281 LEU cc_start: 0.8432 (mt) cc_final: 0.8111 (mt) REVERT: A 356 MET cc_start: 0.6294 (ptp) cc_final: 0.6002 (pmm) REVERT: A 365 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7768 (pm20) REVERT: A 606 VAL cc_start: 0.9108 (t) cc_final: 0.8847 (m) REVERT: A 611 ASP cc_start: 0.7392 (p0) cc_final: 0.6597 (t0) REVERT: B 315 LEU cc_start: 0.8465 (tt) cc_final: 0.8214 (tp) REVERT: B 646 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9054 (pp) REVERT: B 689 MET cc_start: 0.7409 (mtp) cc_final: 0.7075 (mmm) REVERT: C 17 SER cc_start: 0.8003 (p) cc_final: 0.7742 (t) REVERT: C 57 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8485 (tt) REVERT: C 114 ARG cc_start: 0.6651 (mmp80) cc_final: 0.6351 (mmt-90) REVERT: C 128 LYS cc_start: 0.7392 (tttm) cc_final: 0.7114 (tppt) REVERT: C 208 HIS cc_start: 0.7973 (t-90) cc_final: 0.7677 (t-90) REVERT: C 617 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8524 (mt) REVERT: C 689 MET cc_start: 0.7598 (mpp) cc_final: 0.6950 (mpp) REVERT: D 57 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8693 (tt) REVERT: D 348 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6907 (tt0) REVERT: D 370 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8223 (mp) REVERT: E 43 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8661 (mp) REVERT: E 646 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8647 (pp) REVERT: E 665 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8088 (mmm-85) REVERT: F 91 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8507 (tt) REVERT: F 426 MET cc_start: 0.7482 (ttp) cc_final: 0.7245 (ttt) REVERT: F 648 GLU cc_start: 0.7716 (tt0) cc_final: 0.7237 (tm-30) outliers start: 59 outliers final: 39 residues processed: 188 average time/residue: 0.1932 time to fit residues: 59.8045 Evaluate side-chains 180 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 651 LEU 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 499 VAL 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 188 LEU 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 617 LEU Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 496 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 255 LEU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 665 ARG 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 332 ASN Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 690 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 320 optimal weight: 0.5980 chunk 270 optimal weight: 1.9990 chunk 333 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 345 optimal weight: 3.9990 chunk 373 optimal weight: 20.0000 chunk 155 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 337 optimal weight: 6.9990 chunk 190 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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** C 396 ASN E 543 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.159640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.100934 restraints weight = 51460.934| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.84 r_work: 0.3190 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34132 Z= 0.117 Angle : 0.499 11.278 46344 Z= 0.245 Chirality : 0.037 0.141 5166 Planarity : 0.004 0.053 6186 Dihedral : 4.074 49.582 4806 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.51 % Rotamer: Outliers : 1.50 % Allowed : 11.70 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.13), residues: 4302 helix: 2.21 (0.11), residues: 2192 sheet: -0.75 (0.21), residues: 587 loop : -0.05 (0.17), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 213 TYR 0.017 0.001 TYR C 557 PHE 0.038 0.001 PHE F 706 TRP 0.009 0.001 TRP F 290 HIS 0.003 0.000 HIS E 560 Details of bonding type rmsd covalent geometry : bond 0.00265 (34132) covalent geometry : angle 0.49934 (46344) hydrogen bonds : bond 0.03413 ( 1890) hydrogen bonds : angle 4.31410 ( 5451) *********************** 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 205 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 47 PHE cc_start: 0.7103 (m-80) cc_final: 0.6678 (m-80) REVERT: A 281 LEU cc_start: 0.8505 (mt) cc_final: 0.8185 (mt) REVERT: A 356 MET cc_start: 0.6215 (ptp) cc_final: 0.5836 (pmm) REVERT: A 365 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7798 (pm20) REVERT: A 606 VAL cc_start: 0.8980 (t) cc_final: 0.8759 (m) REVERT: A 611 ASP cc_start: 0.7345 (p0) cc_final: 0.6525 (t0) REVERT: B 646 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8983 (pp) REVERT: B 689 MET cc_start: 0.7271 (mtp) cc_final: 0.6912 (mmm) REVERT: C 17 SER cc_start: 0.8051 (p) cc_final: 0.7768 (t) REVERT: C 57 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8209 (tt) REVERT: C 114 ARG cc_start: 0.6526 (mmp80) cc_final: 0.6247 (mmt-90) REVERT: C 128 LYS cc_start: 0.7383 (tttm) cc_final: 0.7107 (tppt) REVERT: C 200 ARG cc_start: 0.7480 (mmm160) cc_final: 0.7232 (mmm160) REVERT: C 203 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6643 (ptm160) REVERT: C 208 HIS cc_start: 0.8001 (t-90) cc_final: 0.7693 (t-90) REVERT: C 617 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8451 (mt) REVERT: C 689 MET cc_start: 0.7476 (mpp) cc_final: 0.6833 (mpp) REVERT: D 57 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8638 (tt) REVERT: D 200 ARG cc_start: 0.7692 (mmm160) cc_final: 0.7302 (mmm160) REVERT: D 348 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6756 (tt0) REVERT: D 370 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8162 (mp) REVERT: E 43 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8640 (mp) REVERT: E 646 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8545 (pp) REVERT: E 665 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8089 (mmm-85) REVERT: F 91 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8402 (tt) REVERT: F 426 MET cc_start: 0.7433 (ttp) cc_final: 0.7168 (ttt) REVERT: F 433 MET cc_start: 0.8185 (ptm) cc_final: 0.7964 (ptp) REVERT: F 648 GLU cc_start: 0.7678 (tt0) cc_final: 0.7367 (tm-30) outliers start: 51 outliers final: 32 residues processed: 194 average time/residue: 0.2003 time to fit residues: 63.3907 Evaluate side-chains 184 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 651 LEU 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 499 VAL 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 188 LEU Chi-restraints excluded: chain C residue 203 ARG 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 617 LEU Chi-restraints excluded: chain C residue 697 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 665 ARG Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 690 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 199 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 407 optimal weight: 0.1980 chunk 237 optimal weight: 0.5980 chunk 291 optimal weight: 0.1980 chunk 271 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.161319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102598 restraints weight = 51820.177| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.62 r_work: 0.3243 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 34132 Z= 0.094 Angle : 0.490 13.230 46344 Z= 0.238 Chirality : 0.037 0.158 5166 Planarity : 0.004 0.054 6186 Dihedral : 3.941 48.387 4806 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.51 % Rotamer: Outliers : 1.29 % Allowed : 12.14 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.13), residues: 4302 helix: 2.35 (0.11), residues: 2191 sheet: -0.59 (0.21), residues: 590 loop : 0.01 (0.17), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 213 TYR 0.015 0.001 TYR E 557 PHE 0.039 0.001 PHE F 706 TRP 0.009 0.001 TRP F 290 HIS 0.006 0.000 HIS E 543 Details of bonding type rmsd covalent geometry : bond 0.00204 (34132) covalent geometry : angle 0.48958 (46344) hydrogen bonds : bond 0.03236 ( 1890) hydrogen bonds : angle 4.17896 ( 5451) ********************** 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 209 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.7106 (m-80) cc_final: 0.6673 (m-80) REVERT: A 281 LEU cc_start: 0.8515 (mt) cc_final: 0.8094 (mt) REVERT: A 516 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7754 (ttt-90) REVERT: A 611 ASP cc_start: 0.7366 (p0) cc_final: 0.6486 (t0) REVERT: B 57 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8441 (tt) REVERT: B 646 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9042 (pp) REVERT: B 689 MET cc_start: 0.7339 (mtp) cc_final: 0.6932 (mmm) REVERT: C 17 SER cc_start: 0.8152 (p) cc_final: 0.7907 (t) REVERT: C 57 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8335 (tt) REVERT: C 114 ARG cc_start: 0.6461 (mmp80) cc_final: 0.6186 (mpt-90) REVERT: C 128 LYS cc_start: 0.7295 (tttm) cc_final: 0.7029 (tppt) REVERT: C 208 HIS cc_start: 0.7975 (t-90) cc_final: 0.7678 (t-90) REVERT: C 689 MET cc_start: 0.7299 (mpp) cc_final: 0.6738 (mpp) REVERT: D 57 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8668 (tt) REVERT: D 200 ARG cc_start: 0.7619 (mmm160) cc_final: 0.7058 (mmm160) REVERT: D 348 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6820 (tt0) REVERT: D 370 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8276 (mp) REVERT: E 43 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8643 (mp) REVERT: E 646 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8570 (pp) REVERT: F 91 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8483 (tt) REVERT: F 426 MET cc_start: 0.7464 (ttp) cc_final: 0.7217 (ttt) REVERT: F 648 GLU cc_start: 0.7641 (tt0) cc_final: 0.7198 (tm-30) outliers start: 44 outliers final: 28 residues processed: 200 average time/residue: 0.1927 time to fit residues: 63.3416 Evaluate side-chains 186 residues out of total 3402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 12 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 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 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 79 LEU Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 255 LEU 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 F residue 91 LEU Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 632 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 391 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 356 optimal weight: 20.0000 chunk 389 optimal weight: 0.0030 chunk 56 optimal weight: 7.9990 chunk 259 optimal weight: 0.9990 chunk 218 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 ASN F 208 HIS F 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.159655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100439 restraints weight = 51419.054| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.61 r_work: 0.3211 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34132 Z= 0.141 Angle : 0.509 11.755 46344 Z= 0.248 Chirality : 0.037 0.198 5166 Planarity : 0.004 0.053 6186 Dihedral : 3.976 50.183 4806 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.56 % Favored : 97.37 % Rotamer: Outliers : 1.41 % Allowed : 12.05 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.13), residues: 4302 helix: 2.30 (0.11), residues: 2192 sheet: -0.66 (0.21), residues: 592 loop : 0.03 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 213 TYR 0.019 0.001 TYR C 557 PHE 0.040 0.001 PHE F 706 TRP 0.008 0.001 TRP F 511 HIS 0.007 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00328 (34132) covalent geometry : angle 0.50896 (46344) hydrogen bonds : bond 0.03353 ( 1890) hydrogen bonds : angle 4.23665 ( 5451) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8113.00 seconds wall clock time: 139 minutes 12.05 seconds (8352.05 seconds total)