Starting phenix.real_space_refine on Mon Jun 16 11:21:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7l_44315/06_2025/9b7l_44315.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7l_44315/06_2025/9b7l_44315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b7l_44315/06_2025/9b7l_44315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7l_44315/06_2025/9b7l_44315.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7l_44315/06_2025/9b7l_44315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7l_44315/06_2025/9b7l_44315.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 12089 2.51 5 N 3326 2.21 5 O 3715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19200 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3307 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 388} Chain breaks: 3 Chain: "B" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1384 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain breaks: 1 Chain: "C" Number of atoms: 4018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4018 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 470} Chain breaks: 1 Chain: "D" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3307 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 388} Chain breaks: 3 Chain: "E" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1375 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 165} Chain breaks: 1 Chain: "F" Number of atoms: 4018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4018 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 470} Chain breaks: 1 Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 804 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.73, per 1000 atoms: 0.56 Number of scatterers: 19200 At special positions: 0 Unit cell: (156.228, 135.453, 102.213, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 3715 8.00 N 3326 7.00 C 12089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 111 " distance=2.02 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: 4.61 Conformation dependent library (CDL) restraints added in 2.5 seconds 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4464 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 53 sheets defined 7.2% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.648A pdb=" N SER A 358 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 355 through 359' Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.595A pdb=" N ILE A 566 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 568 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 removed outlier: 4.036A pdb=" N LEU B 435 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 removed outlier: 3.593A pdb=" N VAL B 473 " --> pdb=" O ASN B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 569 removed outlier: 3.537A pdb=" N ILE B 566 " --> pdb=" O GLU B 563 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR B 568 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.214A pdb=" N HIS C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.805A pdb=" N ASN C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 4.139A pdb=" N LEU C 435 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 554 through 556 No H-bonds generated for 'chain 'C' and resid 554 through 556' Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'D' and resid 288 through 293 removed outlier: 4.187A pdb=" N HIS D 292 " --> pdb=" O ARG D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 554 through 556 No H-bonds generated for 'chain 'D' and resid 554 through 556' Processing helix chain 'D' and resid 563 through 567 Processing helix chain 'E' and resid 563 through 567 Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 262 through 266 Processing helix chain 'F' and resid 288 through 293 removed outlier: 4.193A pdb=" N HIS F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 removed outlier: 3.961A pdb=" N ASN F 304 " --> pdb=" O ARG F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 removed outlier: 3.738A pdb=" N SER F 358 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA F 359 " --> pdb=" O LEU F 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 359' Processing helix chain 'F' and resid 396 through 400 Processing helix chain 'F' and resid 431 through 435 removed outlier: 3.991A pdb=" N LEU F 435 " --> pdb=" O LEU F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 496 Processing helix chain 'F' and resid 563 through 567 removed outlier: 3.625A pdb=" N ILE F 566 " --> pdb=" O GLU F 563 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'L' and resid 102 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 249 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 240 through 249 current: chain 'A' and resid 331 through 336 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 261 Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA4, first strand: chain 'A' and resid 479 through 480 removed outlier: 6.184A pdb=" N ILE A 479 " --> pdb=" O VAL A 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 490 Processing sheet with id=AA7, first strand: chain 'A' and resid 514 through 517 removed outlier: 4.003A pdb=" N GLY C 578 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AA9, first strand: chain 'A' and resid 578 through 581 removed outlier: 4.107A pdb=" N GLY A 578 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 619 through 621 removed outlier: 6.097A pdb=" N ALA A 620 " --> pdb=" O MET A 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 627 through 629 removed outlier: 3.842A pdb=" N MET C 605 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 445 through 449 removed outlier: 6.903A pdb=" N LYS B 462 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.473A pdb=" N ILE B 479 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 483 through 484 Processing sheet with id=AB6, first strand: chain 'B' and resid 488 through 490 Processing sheet with id=AB7, first strand: chain 'B' and resid 508 through 511 Processing sheet with id=AB8, first strand: chain 'B' and resid 593 through 596 removed outlier: 4.054A pdb=" N GLY B 578 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 231 through 235 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 238 through 249 current: chain 'C' and resid 331 through 336 Processing sheet with id=AC1, first strand: chain 'C' and resid 258 through 261 Processing sheet with id=AC2, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.499A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 445 through 451 removed outlier: 6.699A pdb=" N LYS C 462 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR C 450 " --> pdb=" O THR C 460 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AC5, first strand: chain 'C' and resid 488 through 490 Processing sheet with id=AC6, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AC7, first strand: chain 'C' and resid 619 through 621 removed outlier: 6.205A pdb=" N ALA C 620 " --> pdb=" O MET C 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 707 through 708 Processing sheet with id=AC9, first strand: chain 'D' and resid 240 through 249 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 240 through 249 current: chain 'D' and resid 331 through 336 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 258 through 261 Processing sheet with id=AD2, first strand: chain 'D' and resid 479 through 480 removed outlier: 6.173A pdb=" N ILE D 479 " --> pdb=" O VAL D 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 483 through 484 Processing sheet with id=AD4, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD5, first strand: chain 'D' and resid 514 through 517 removed outlier: 4.135A pdb=" N GLY F 578 " --> pdb=" O VAL F 596 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 542 through 544 Processing sheet with id=AD7, first strand: chain 'D' and resid 593 through 596 removed outlier: 3.884A pdb=" N GLY D 578 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 619 through 621 removed outlier: 6.081A pdb=" N ALA D 620 " --> pdb=" O MET D 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 627 through 629 removed outlier: 4.062A pdb=" N MET F 605 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE F 479 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 445 through 451 removed outlier: 5.693A pdb=" N LEU E 447 " --> pdb=" O SER E 464 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER E 464 " --> pdb=" O LEU E 447 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS E 449 " --> pdb=" O LYS E 462 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE E 451 " --> pdb=" O THR E 460 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR E 460 " --> pdb=" O ILE E 451 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 479 through 480 removed outlier: 6.261A pdb=" N ILE E 479 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET E 605 " --> pdb=" O PHE F 629 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 483 through 484 Processing sheet with id=AE4, first strand: chain 'E' and resid 488 through 490 Processing sheet with id=AE5, first strand: chain 'E' and resid 593 through 596 removed outlier: 3.962A pdb=" N GLY E 578 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 232 through 235 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 238 through 249 current: chain 'F' and resid 332 through 336 Processing sheet with id=AE7, first strand: chain 'F' and resid 258 through 261 Processing sheet with id=AE8, first strand: chain 'F' and resid 427 through 428 removed outlier: 6.346A pdb=" N ALA F 427 " --> pdb=" O ARG F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'F' and resid 445 through 451 removed outlier: 6.630A pdb=" N LYS F 462 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR F 450 " --> pdb=" O THR F 460 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 483 through 484 Processing sheet with id=AF2, first strand: chain 'F' and resid 488 through 490 Processing sheet with id=AF3, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AF4, first strand: chain 'F' and resid 619 through 621 Processing sheet with id=AF5, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.521A pdb=" N THR H 40 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 30 through 31 current: chain 'H' and resid 65 through 70 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 76 through 78 current: chain 'H' and resid 130 through 132 Processing sheet with id=AF7, first strand: chain 'L' and resid 29 through 32 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 29 through 32 current: chain 'L' and resid 67 through 70 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 67 through 70 current: chain 'L' and resid 120 through 122 No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'L' and resid 38 through 43 225 hydrogen bonds defined for protein. 453 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: 5.44 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5423 1.33 - 1.45: 4072 1.45 - 1.57: 10136 1.57 - 1.69: 0 1.69 - 1.82: 120 Bond restraints: 19751 Sorted by residual: bond pdb=" C TYR D 399 " pdb=" N PHE D 400 " ideal model delta sigma weight residual 1.331 1.215 0.116 2.07e-02 2.33e+03 3.16e+01 bond pdb=" C ILE F 566 " pdb=" O ILE F 566 " ideal model delta sigma weight residual 1.239 1.207 0.032 1.13e-02 7.83e+03 7.97e+00 bond pdb=" C TYR F 399 " pdb=" N PHE F 400 " ideal model delta sigma weight residual 1.331 1.276 0.055 2.07e-02 2.33e+03 7.10e+00 bond pdb=" CG GLN E 585 " pdb=" CD GLN E 585 " ideal model delta sigma weight residual 1.516 1.451 0.065 2.50e-02 1.60e+03 6.76e+00 bond pdb=" CG GLN B 585 " pdb=" CD GLN B 585 " ideal model delta sigma weight residual 1.516 1.451 0.065 2.50e-02 1.60e+03 6.70e+00 ... (remaining 19746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 26141 2.66 - 5.32: 668 5.32 - 7.99: 74 7.99 - 10.65: 14 10.65 - 13.31: 6 Bond angle restraints: 26903 Sorted by residual: angle pdb=" N GLY B 539 " pdb=" CA GLY B 539 " pdb=" C GLY B 539 " ideal model delta sigma weight residual 112.73 125.61 -12.88 1.20e+00 6.94e-01 1.15e+02 angle pdb=" C GLY B 481 " pdb=" N PRO B 482 " pdb=" CA PRO B 482 " ideal model delta sigma weight residual 119.76 127.64 -7.88 1.03e+00 9.43e-01 5.85e+01 angle pdb=" N ILE B 440 " pdb=" CA ILE B 440 " pdb=" C ILE B 440 " ideal model delta sigma weight residual 108.36 119.17 -10.81 1.43e+00 4.89e-01 5.71e+01 angle pdb=" N GLY B 453 " pdb=" CA GLY B 453 " pdb=" C GLY B 453 " ideal model delta sigma weight residual 112.48 121.43 -8.95 1.21e+00 6.83e-01 5.47e+01 angle pdb=" N GLY D 267 " pdb=" CA GLY D 267 " pdb=" C GLY D 267 " ideal model delta sigma weight residual 111.02 124.33 -13.31 1.86e+00 2.89e-01 5.12e+01 ... (remaining 26898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 10948 17.42 - 34.83: 482 34.83 - 52.25: 72 52.25 - 69.66: 17 69.66 - 87.08: 18 Dihedral angle restraints: 11537 sinusoidal: 4535 harmonic: 7002 Sorted by residual: dihedral pdb=" CA ASN E 519 " pdb=" C ASN E 519 " pdb=" N PRO E 520 " pdb=" CA PRO E 520 " ideal model delta harmonic sigma weight residual 0.00 -24.83 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA TYR F 484 " pdb=" C TYR F 484 " pdb=" N ARG F 485 " pdb=" CA ARG F 485 " ideal model delta harmonic sigma weight residual -180.00 -157.51 -22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CB CYS L 42 " pdb=" SG CYS L 42 " pdb=" SG CYS L 111 " pdb=" CB CYS L 111 " ideal model delta sinusoidal sigma weight residual 93.00 55.26 37.74 1 1.00e+01 1.00e-02 2.01e+01 ... (remaining 11534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2367 0.089 - 0.177: 362 0.177 - 0.266: 54 0.266 - 0.355: 2 0.355 - 0.443: 3 Chirality restraints: 2788 Sorted by residual: chirality pdb=" CA ARG B 485 " pdb=" N ARG B 485 " pdb=" C ARG B 485 " pdb=" CB ARG B 485 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CA VAL L 73 " pdb=" N VAL L 73 " pdb=" C VAL L 73 " pdb=" CB VAL L 73 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA SER D 268 " pdb=" N SER D 268 " pdb=" C SER D 268 " pdb=" CB SER D 268 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 ... (remaining 2785 not shown) Planarity restraints: 3571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 69 " 0.025 2.00e-02 2.50e+03 2.11e-02 8.88e+00 pdb=" CG TYR H 69 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR H 69 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR H 69 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR H 69 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR H 69 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR H 69 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 69 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 566 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.43e+00 pdb=" C ILE F 566 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE F 566 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS F 567 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 290 " 0.020 2.00e-02 2.50e+03 2.04e-02 6.22e+00 pdb=" CG HIS C 290 " -0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS C 290 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS C 290 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS C 290 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS C 290 " 0.008 2.00e-02 2.50e+03 ... (remaining 3568 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 93 2.49 - 3.09: 13778 3.09 - 3.69: 30210 3.69 - 4.30: 47131 4.30 - 4.90: 76466 Nonbonded interactions: 167678 Sorted by model distance: nonbonded pdb=" ND1 HIS E 527 " pdb=" O GLU E 531 " model vdw 1.884 3.120 nonbonded pdb=" O TRP A 306 " pdb=" OG SER A 425 " model vdw 1.917 3.040 nonbonded pdb=" OE1 GLU E 529 " pdb=" NZ LYS E 567 " model vdw 1.934 3.120 nonbonded pdb=" CA SER D 483 " pdb=" CE MET D 524 " model vdw 2.043 3.890 nonbonded pdb=" OH TYR F 252 " pdb=" O ILE F 374 " model vdw 2.106 3.040 ... (remaining 167673 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 419 through 612) selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 41.920 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 : 0.008 0.116 19753 Z= 0.406 Angle : 1.023 13.310 26907 Z= 0.631 Chirality : 0.066 0.443 2788 Planarity : 0.005 0.052 3571 Dihedral : 10.979 87.081 7067 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.33 % Allowed : 2.52 % Favored : 96.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 2398 helix: -3.83 (0.34), residues: 94 sheet: -0.39 (0.17), residues: 666 loop : -0.68 (0.13), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 281 HIS 0.021 0.003 HIS C 290 PHE 0.034 0.003 PHE C 367 TYR 0.051 0.003 TYR H 69 ARG 0.016 0.002 ARG C 488 Details of bonding type rmsd hydrogen bonds : bond 0.21258 ( 225) hydrogen bonds : angle 8.59839 ( 453) SS BOND : bond 0.00644 ( 2) SS BOND : angle 1.64016 ( 4) covalent geometry : bond 0.00850 (19751) covalent geometry : angle 1.02302 (26903) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 302 time to evaluate : 2.286 Fit side-chains revert: symmetry clash REVERT: A 529 GLU cc_start: 0.7437 (tp30) cc_final: 0.7127 (tt0) REVERT: A 588 GLN cc_start: 0.7266 (mp10) cc_final: 0.6750 (mp10) REVERT: B 514 ARG cc_start: 0.7551 (mtm180) cc_final: 0.5857 (mmt180) REVERT: C 406 ARG cc_start: 0.7194 (mtt180) cc_final: 0.5242 (ptt-90) REVERT: C 419 ASN cc_start: 0.7652 (t0) cc_final: 0.7415 (t0) REVERT: D 321 GLN cc_start: 0.7813 (mt0) cc_final: 0.7610 (mt0) REVERT: E 461 LEU cc_start: 0.8988 (mm) cc_final: 0.8787 (mt) REVERT: E 493 VAL cc_start: 0.7554 (m) cc_final: 0.7315 (t) REVERT: E 565 GLU cc_start: 0.7729 (mp0) cc_final: 0.6978 (pt0) REVERT: F 235 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8463 (mt) REVERT: F 238 ARG cc_start: 0.7768 (mtm110) cc_final: 0.7468 (ptt90) REVERT: F 324 GLU cc_start: 0.7268 (pt0) cc_final: 0.6855 (pp20) REVERT: F 347 ASP cc_start: 0.7274 (t0) cc_final: 0.7016 (p0) REVERT: H 75 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7984 (t0) outliers start: 28 outliers final: 18 residues processed: 326 average time/residue: 1.4068 time to fit residues: 514.1102 Evaluate side-chains 211 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 725 ARG Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 575 GLU Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 104 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 217 optimal weight: 0.0570 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 HIS A 646 GLN A 651 ASN B 452 ASN B 456 GLN B 497 ASN C 403 GLN C 497 ASN C 519 ASN C 527 HIS C 608 GLN C 624 HIS C 646 GLN C 673 GLN D 590 GLN D 624 HIS D 646 GLN D 651 ASN D 673 GLN E 419 ASN E 430 GLN E 452 ASN E 512 ASN E 608 GLN F 452 ASN F 470 ASN F 562 ASN F 570 ASN F 608 GLN F 624 HIS F 646 GLN F 678 GLN F 700 GLN H 24 GLN L 26 GLN L 102 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.087076 restraints weight = 31572.101| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.63 r_work: 0.2891 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19753 Z= 0.129 Angle : 0.583 8.255 26907 Z= 0.310 Chirality : 0.043 0.148 2788 Planarity : 0.004 0.043 3571 Dihedral : 6.300 57.463 2669 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.23 % Allowed : 6.50 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 2398 helix: -3.54 (0.38), residues: 94 sheet: 0.04 (0.17), residues: 665 loop : -0.29 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 509 HIS 0.007 0.001 HIS C 290 PHE 0.016 0.002 PHE C 367 TYR 0.024 0.002 TYR H 69 ARG 0.008 0.001 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 225) hydrogen bonds : angle 6.50415 ( 453) SS BOND : bond 0.00780 ( 2) SS BOND : angle 1.48514 ( 4) covalent geometry : bond 0.00285 (19751) covalent geometry : angle 0.58299 (26903) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 2.197 Fit side-chains REVERT: A 529 GLU cc_start: 0.7522 (tp30) cc_final: 0.7212 (tt0) REVERT: B 514 ARG cc_start: 0.7571 (mtm180) cc_final: 0.5729 (mmt180) REVERT: B 529 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6367 (tp30) REVERT: C 238 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7658 (ptt-90) REVERT: C 258 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7504 (mmtt) REVERT: C 398 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7108 (mp0) REVERT: C 406 ARG cc_start: 0.7021 (mtt180) cc_final: 0.4880 (ptt-90) REVERT: C 419 ASN cc_start: 0.7963 (t0) cc_final: 0.7544 (t0) REVERT: C 452 ASN cc_start: 0.8042 (m110) cc_final: 0.7563 (m-40) REVERT: D 321 GLN cc_start: 0.7840 (mt0) cc_final: 0.7527 (mt0) REVERT: D 529 GLU cc_start: 0.6682 (tp30) cc_final: 0.6042 (tp30) REVERT: D 531 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: D 562 ASN cc_start: 0.6772 (p0) cc_final: 0.6385 (p0) REVERT: E 485 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7549 (ttt180) REVERT: E 493 VAL cc_start: 0.7548 (m) cc_final: 0.7225 (t) REVERT: E 565 GLU cc_start: 0.7940 (mp0) cc_final: 0.7143 (pt0) REVERT: F 235 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8599 (mt) REVERT: F 324 GLU cc_start: 0.7161 (pt0) cc_final: 0.6599 (pp20) REVERT: F 347 ASP cc_start: 0.7820 (t0) cc_final: 0.7280 (p0) REVERT: F 404 MET cc_start: 0.8065 (mtp) cc_final: 0.7828 (mtp) REVERT: H 123 ASP cc_start: 0.8264 (p0) cc_final: 0.7234 (p0) outliers start: 47 outliers final: 23 residues processed: 259 average time/residue: 1.3644 time to fit residues: 396.9121 Evaluate side-chains 210 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 45 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 142 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 chunk 238 optimal weight: 9.9990 chunk 170 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN C 403 GLN C 588 GLN C 651 ASN D 585 GLN D 663 ASN E 497 ASN F 229 HIS F 233 GLN F 673 GLN L 102 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.099635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.083595 restraints weight = 31472.152| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.62 r_work: 0.2853 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 19753 Z= 0.236 Angle : 0.624 8.201 26907 Z= 0.332 Chirality : 0.046 0.190 2788 Planarity : 0.005 0.064 3571 Dihedral : 5.934 59.958 2637 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.85 % Allowed : 7.93 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 2398 helix: -3.57 (0.39), residues: 94 sheet: -0.09 (0.18), residues: 625 loop : -0.33 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 509 HIS 0.015 0.002 HIS C 290 PHE 0.017 0.002 PHE C 367 TYR 0.032 0.002 TYR H 69 ARG 0.007 0.001 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 225) hydrogen bonds : angle 6.40657 ( 453) SS BOND : bond 0.00385 ( 2) SS BOND : angle 2.05899 ( 4) covalent geometry : bond 0.00554 (19751) covalent geometry : angle 0.62347 (26903) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 2.065 Fit side-chains REVERT: A 529 GLU cc_start: 0.7598 (tp30) cc_final: 0.7200 (tt0) REVERT: B 514 ARG cc_start: 0.7561 (mtm180) cc_final: 0.5601 (mmt180) REVERT: C 238 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7771 (ptt-90) REVERT: C 258 LYS cc_start: 0.8357 (mtmt) cc_final: 0.7489 (mmtt) REVERT: C 398 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7149 (mp0) REVERT: C 406 ARG cc_start: 0.7288 (mtt180) cc_final: 0.4819 (ptt-90) REVERT: C 419 ASN cc_start: 0.8049 (t0) cc_final: 0.7568 (t0) REVERT: C 452 ASN cc_start: 0.7993 (m110) cc_final: 0.7557 (m-40) REVERT: C 691 ASN cc_start: 0.8250 (p0) cc_final: 0.7949 (p0) REVERT: D 321 GLN cc_start: 0.7864 (mt0) cc_final: 0.7583 (mt0) REVERT: D 529 GLU cc_start: 0.6570 (tp30) cc_final: 0.5853 (tp30) REVERT: D 531 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7019 (mt-10) REVERT: D 562 ASN cc_start: 0.6794 (p0) cc_final: 0.6335 (p0) REVERT: E 493 VAL cc_start: 0.7592 (m) cc_final: 0.7232 (t) REVERT: E 565 GLU cc_start: 0.7920 (mp0) cc_final: 0.7128 (pt0) REVERT: F 324 GLU cc_start: 0.7406 (pt0) cc_final: 0.6814 (pp20) REVERT: F 348 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8611 (m) REVERT: L 104 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7535 (pt0) REVERT: L 127 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8027 (ttmm) outliers start: 60 outliers final: 35 residues processed: 232 average time/residue: 1.4070 time to fit residues: 365.6248 Evaluate side-chains 213 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 306 TRP Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 348 SER Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 69 TYR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 127 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 32 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN C 403 GLN C 588 GLN D 585 GLN F 651 ASN H 75 ASN L 102 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.082818 restraints weight = 31595.908| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.63 r_work: 0.2831 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 19753 Z= 0.238 Angle : 0.610 7.680 26907 Z= 0.325 Chirality : 0.045 0.190 2788 Planarity : 0.005 0.054 3571 Dihedral : 5.886 59.255 2635 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.04 % Allowed : 8.50 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2398 helix: -3.73 (0.38), residues: 95 sheet: -0.10 (0.18), residues: 621 loop : -0.38 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 509 HIS 0.012 0.002 HIS C 290 PHE 0.015 0.002 PHE F 535 TYR 0.030 0.002 TYR H 69 ARG 0.010 0.001 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 225) hydrogen bonds : angle 6.29456 ( 453) SS BOND : bond 0.00358 ( 2) SS BOND : angle 1.84379 ( 4) covalent geometry : bond 0.00557 (19751) covalent geometry : angle 0.60948 (26903) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 179 time to evaluate : 2.220 Fit side-chains REVERT: A 529 GLU cc_start: 0.7512 (tp30) cc_final: 0.7116 (tt0) REVERT: B 514 ARG cc_start: 0.7564 (mtm180) cc_final: 0.5502 (mmt180) REVERT: C 238 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7811 (ptt-90) REVERT: C 258 LYS cc_start: 0.8351 (mtmt) cc_final: 0.7458 (mmtt) REVERT: C 406 ARG cc_start: 0.7551 (mtt180) cc_final: 0.4816 (ptt-90) REVERT: C 419 ASN cc_start: 0.8080 (t0) cc_final: 0.7567 (t0) REVERT: C 452 ASN cc_start: 0.7997 (m110) cc_final: 0.7553 (m-40) REVERT: C 691 ASN cc_start: 0.8360 (p0) cc_final: 0.8016 (p0) REVERT: D 321 GLN cc_start: 0.7853 (mt0) cc_final: 0.7618 (mt0) REVERT: D 529 GLU cc_start: 0.6631 (tp30) cc_final: 0.5832 (tp30) REVERT: D 531 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7028 (mt-10) REVERT: D 562 ASN cc_start: 0.6845 (p0) cc_final: 0.6372 (p0) REVERT: D 664 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8241 (ttpp) REVERT: E 449 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8547 (ttpp) REVERT: E 493 VAL cc_start: 0.7518 (m) cc_final: 0.7193 (t) REVERT: E 565 GLU cc_start: 0.7900 (mp0) cc_final: 0.7032 (pt0) REVERT: F 235 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8600 (mt) REVERT: F 324 GLU cc_start: 0.7567 (pt0) cc_final: 0.6900 (pp20) REVERT: F 348 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8698 (m) REVERT: F 684 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: H 108 ASP cc_start: 0.8983 (m-30) cc_final: 0.8758 (m-30) REVERT: L 104 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: L 127 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8051 (ttmm) outliers start: 64 outliers final: 41 residues processed: 235 average time/residue: 1.3875 time to fit residues: 367.6243 Evaluate side-chains 220 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 306 TRP Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 348 SER Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 69 TYR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 127 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 133 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 190 optimal weight: 0.0040 chunk 218 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 overall best weight: 2.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A 673 GLN C 403 GLN C 588 GLN L 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.085373 restraints weight = 31543.378| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.63 r_work: 0.2868 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19753 Z= 0.111 Angle : 0.509 6.562 26907 Z= 0.267 Chirality : 0.041 0.136 2788 Planarity : 0.004 0.042 3571 Dihedral : 5.266 58.795 2635 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.33 % Allowed : 9.73 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2398 helix: -3.63 (0.38), residues: 100 sheet: 0.12 (0.19), residues: 618 loop : -0.26 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 509 HIS 0.005 0.001 HIS C 290 PHE 0.013 0.001 PHE D 629 TYR 0.019 0.001 TYR H 69 ARG 0.010 0.000 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.02621 ( 225) hydrogen bonds : angle 5.81393 ( 453) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.93268 ( 4) covalent geometry : bond 0.00253 (19751) covalent geometry : angle 0.50872 (26903) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 2.022 Fit side-chains REVERT: A 529 GLU cc_start: 0.7439 (tp30) cc_final: 0.6875 (tt0) REVERT: B 514 ARG cc_start: 0.7547 (mtm180) cc_final: 0.5526 (mmt180) REVERT: B 529 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6353 (tp30) REVERT: C 258 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7446 (mmtt) REVERT: C 398 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7186 (mp0) REVERT: C 406 ARG cc_start: 0.7546 (mtt180) cc_final: 0.4817 (ptt-90) REVERT: C 452 ASN cc_start: 0.8016 (m110) cc_final: 0.7571 (m-40) REVERT: C 691 ASN cc_start: 0.8340 (p0) cc_final: 0.8029 (p0) REVERT: D 321 GLN cc_start: 0.7904 (mt0) cc_final: 0.7637 (mt0) REVERT: D 529 GLU cc_start: 0.6584 (tp30) cc_final: 0.5801 (tp30) REVERT: D 531 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7033 (mt-10) REVERT: D 562 ASN cc_start: 0.6783 (p0) cc_final: 0.6292 (p0) REVERT: E 493 VAL cc_start: 0.7540 (m) cc_final: 0.7204 (t) REVERT: E 565 GLU cc_start: 0.7826 (mp0) cc_final: 0.6919 (pt0) REVERT: F 235 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8614 (mt) REVERT: F 324 GLU cc_start: 0.7554 (pt0) cc_final: 0.6918 (pp20) REVERT: F 348 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8722 (m) REVERT: H 75 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8170 (t0) REVERT: L 104 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7431 (pt0) outliers start: 49 outliers final: 31 residues processed: 231 average time/residue: 1.3835 time to fit residues: 358.6572 Evaluate side-chains 211 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 456 GLN Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 306 TRP Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 348 SER Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 104 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 152 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 70 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 209 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 159 optimal weight: 30.0000 chunk 102 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 overall best weight: 10.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A 673 GLN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN C 519 ASN C 588 GLN H 75 ASN L 102 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.082058 restraints weight = 31766.344| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.62 r_work: 0.2824 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 19753 Z= 0.329 Angle : 0.663 6.963 26907 Z= 0.353 Chirality : 0.048 0.218 2788 Planarity : 0.005 0.055 3571 Dihedral : 5.949 54.784 2635 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.18 % Allowed : 9.30 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2398 helix: -3.85 (0.36), residues: 95 sheet: -0.09 (0.19), residues: 599 loop : -0.40 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 509 HIS 0.014 0.002 HIS C 290 PHE 0.018 0.002 PHE D 535 TYR 0.037 0.003 TYR H 69 ARG 0.014 0.001 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 225) hydrogen bonds : angle 6.37294 ( 453) SS BOND : bond 0.00458 ( 2) SS BOND : angle 1.76211 ( 4) covalent geometry : bond 0.00776 (19751) covalent geometry : angle 0.66283 (26903) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 2.321 Fit side-chains REVERT: A 529 GLU cc_start: 0.7520 (tp30) cc_final: 0.7170 (tt0) REVERT: B 514 ARG cc_start: 0.7419 (mtm180) cc_final: 0.5389 (mmt180) REVERT: B 531 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: C 258 LYS cc_start: 0.8348 (mtmt) cc_final: 0.7459 (mmtt) REVERT: C 691 ASN cc_start: 0.8410 (p0) cc_final: 0.8003 (p0) REVERT: D 321 GLN cc_start: 0.7896 (mt0) cc_final: 0.7663 (mt0) REVERT: D 529 GLU cc_start: 0.6583 (tp30) cc_final: 0.5763 (tp30) REVERT: D 531 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: D 562 ASN cc_start: 0.6908 (p0) cc_final: 0.6397 (p0) REVERT: E 449 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8534 (ttpp) REVERT: E 493 VAL cc_start: 0.7604 (m) cc_final: 0.7300 (t) REVERT: E 500 GLU cc_start: 0.7938 (tp30) cc_final: 0.7703 (tp30) REVERT: E 565 GLU cc_start: 0.7902 (mp0) cc_final: 0.6977 (pt0) REVERT: F 235 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8678 (mt) REVERT: F 324 GLU cc_start: 0.7590 (pt0) cc_final: 0.6867 (pp20) REVERT: F 684 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: H 108 ASP cc_start: 0.9008 (m-30) cc_final: 0.8765 (m-30) REVERT: L 104 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: L 127 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8036 (ttmm) outliers start: 67 outliers final: 44 residues processed: 233 average time/residue: 1.3762 time to fit residues: 361.4234 Evaluate side-chains 220 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 306 TRP Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 69 TYR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 127 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 145 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 171 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A 673 GLN C 403 GLN C 588 GLN D 673 GLN F 233 GLN F 456 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.084978 restraints weight = 31190.553| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.62 r_work: 0.2852 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19753 Z= 0.119 Angle : 0.513 6.095 26907 Z= 0.270 Chirality : 0.041 0.137 2788 Planarity : 0.004 0.048 3571 Dihedral : 5.232 55.115 2635 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.28 % Allowed : 10.63 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.16), residues: 2398 helix: -3.68 (0.38), residues: 94 sheet: 0.06 (0.20), residues: 590 loop : -0.29 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 509 HIS 0.005 0.001 HIS C 290 PHE 0.013 0.001 PHE D 629 TYR 0.018 0.001 TYR H 69 ARG 0.013 0.001 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.02623 ( 225) hydrogen bonds : angle 5.82518 ( 453) SS BOND : bond 0.00303 ( 2) SS BOND : angle 0.84497 ( 4) covalent geometry : bond 0.00273 (19751) covalent geometry : angle 0.51303 (26903) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 178 time to evaluate : 2.197 Fit side-chains REVERT: A 529 GLU cc_start: 0.7533 (tp30) cc_final: 0.7162 (tt0) REVERT: B 514 ARG cc_start: 0.7524 (mtm180) cc_final: 0.5498 (mmt180) REVERT: B 529 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6588 (tt0) REVERT: C 238 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7871 (ptt-90) REVERT: C 258 LYS cc_start: 0.8264 (mtmt) cc_final: 0.7408 (mmtt) REVERT: C 406 ARG cc_start: 0.7764 (mtt180) cc_final: 0.4826 (ptt-90) REVERT: C 588 GLN cc_start: 0.7561 (mp-120) cc_final: 0.6902 (mm110) REVERT: C 691 ASN cc_start: 0.8368 (p0) cc_final: 0.8020 (p0) REVERT: D 321 GLN cc_start: 0.7862 (mt0) cc_final: 0.7631 (mt0) REVERT: D 529 GLU cc_start: 0.6644 (tp30) cc_final: 0.5867 (tp30) REVERT: D 531 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: D 562 ASN cc_start: 0.6809 (p0) cc_final: 0.6285 (p0) REVERT: E 493 VAL cc_start: 0.7543 (m) cc_final: 0.7195 (t) REVERT: E 500 GLU cc_start: 0.7884 (tp30) cc_final: 0.7539 (tp30) REVERT: E 565 GLU cc_start: 0.7866 (mp0) cc_final: 0.6934 (pt0) REVERT: F 235 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8672 (mt) REVERT: F 324 GLU cc_start: 0.7564 (pt0) cc_final: 0.6871 (pp20) REVERT: H 108 ASP cc_start: 0.8959 (m-30) cc_final: 0.8632 (m-30) REVERT: L 104 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7391 (pt0) REVERT: L 127 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.7987 (ttmm) outliers start: 48 outliers final: 30 residues processed: 217 average time/residue: 1.8783 time to fit residues: 464.9493 Evaluate side-chains 206 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 306 TRP Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 127 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 100 optimal weight: 1.9990 chunk 135 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 220 optimal weight: 0.3980 chunk 224 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN C 403 GLN C 519 ASN D 673 GLN F 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.086243 restraints weight = 31406.387| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.63 r_work: 0.2877 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19753 Z= 0.099 Angle : 0.484 5.794 26907 Z= 0.252 Chirality : 0.040 0.132 2788 Planarity : 0.004 0.050 3571 Dihedral : 4.780 54.040 2634 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.85 % Allowed : 11.34 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2398 helix: -3.55 (0.39), residues: 100 sheet: 0.27 (0.20), residues: 572 loop : -0.18 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 509 HIS 0.004 0.001 HIS C 290 PHE 0.012 0.001 PHE D 629 TYR 0.021 0.001 TYR B 484 ARG 0.014 0.000 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.02412 ( 225) hydrogen bonds : angle 5.52056 ( 453) SS BOND : bond 0.00286 ( 2) SS BOND : angle 0.78840 ( 4) covalent geometry : bond 0.00226 (19751) covalent geometry : angle 0.48415 (26903) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 2.422 Fit side-chains REVERT: A 529 GLU cc_start: 0.7567 (tp30) cc_final: 0.7183 (tt0) REVERT: B 514 ARG cc_start: 0.7497 (mtm180) cc_final: 0.5485 (mmt180) REVERT: B 529 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6463 (tt0) REVERT: B 608 GLN cc_start: 0.8256 (mm110) cc_final: 0.8003 (mm110) REVERT: C 258 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7438 (mmmt) REVERT: C 588 GLN cc_start: 0.7645 (mp-120) cc_final: 0.7009 (mm110) REVERT: C 691 ASN cc_start: 0.8383 (p0) cc_final: 0.8043 (p0) REVERT: D 321 GLN cc_start: 0.7814 (mt0) cc_final: 0.7610 (mt0) REVERT: D 529 GLU cc_start: 0.6592 (tp30) cc_final: 0.5803 (tp30) REVERT: D 531 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7036 (mt-10) REVERT: D 562 ASN cc_start: 0.6809 (p0) cc_final: 0.6286 (p0) REVERT: E 493 VAL cc_start: 0.7534 (m) cc_final: 0.7181 (t) REVERT: E 500 GLU cc_start: 0.7830 (tp30) cc_final: 0.7605 (tp30) REVERT: E 565 GLU cc_start: 0.7790 (mp0) cc_final: 0.6845 (tt0) REVERT: E 579 GLN cc_start: 0.8287 (mt0) cc_final: 0.8085 (mt0) REVERT: F 233 GLN cc_start: 0.8449 (mt0) cc_final: 0.8173 (tp40) REVERT: F 324 GLU cc_start: 0.7549 (pt0) cc_final: 0.6893 (pp20) REVERT: F 418 GLU cc_start: 0.7950 (pt0) cc_final: 0.7608 (tp30) REVERT: F 684 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8435 (tt0) REVERT: H 108 ASP cc_start: 0.8934 (m-30) cc_final: 0.8664 (m-30) REVERT: L 104 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: L 127 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.7900 (ttmm) outliers start: 39 outliers final: 25 residues processed: 226 average time/residue: 1.4609 time to fit residues: 370.3869 Evaluate side-chains 209 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 4.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 306 TRP Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 127 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 72 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 193 optimal weight: 0.0570 chunk 100 optimal weight: 20.0000 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A 673 GLN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN C 519 ASN C 700 GLN D 546 GLN D 673 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.084934 restraints weight = 31504.402| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.60 r_work: 0.2868 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19753 Z= 0.151 Angle : 0.522 5.902 26907 Z= 0.274 Chirality : 0.042 0.134 2788 Planarity : 0.004 0.055 3571 Dihedral : 4.943 55.248 2632 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.09 % Allowed : 11.44 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2398 helix: -3.52 (0.40), residues: 94 sheet: 0.15 (0.19), residues: 616 loop : -0.20 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 509 HIS 0.008 0.001 HIS C 290 PHE 0.012 0.001 PHE D 629 TYR 0.028 0.002 TYR B 484 ARG 0.015 0.001 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.02719 ( 225) hydrogen bonds : angle 5.71876 ( 453) SS BOND : bond 0.00294 ( 2) SS BOND : angle 1.08674 ( 4) covalent geometry : bond 0.00351 (19751) covalent geometry : angle 0.52185 (26903) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 2.003 Fit side-chains REVERT: A 529 GLU cc_start: 0.7486 (tp30) cc_final: 0.7129 (tt0) REVERT: B 514 ARG cc_start: 0.7500 (mtm180) cc_final: 0.5473 (mmt180) REVERT: B 529 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6494 (tt0) REVERT: B 608 GLN cc_start: 0.8248 (mm110) cc_final: 0.7983 (mm110) REVERT: C 238 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7818 (ptt-90) REVERT: C 258 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7403 (mmmt) REVERT: C 588 GLN cc_start: 0.7625 (mp-120) cc_final: 0.6999 (mm110) REVERT: C 691 ASN cc_start: 0.8373 (p0) cc_final: 0.8013 (p0) REVERT: D 321 GLN cc_start: 0.7866 (mt0) cc_final: 0.7648 (mt0) REVERT: D 529 GLU cc_start: 0.6661 (tp30) cc_final: 0.5900 (tp30) REVERT: D 531 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7056 (mt-10) REVERT: D 562 ASN cc_start: 0.6844 (p0) cc_final: 0.6321 (p0) REVERT: E 493 VAL cc_start: 0.7553 (m) cc_final: 0.7188 (t) REVERT: E 500 GLU cc_start: 0.7855 (tp30) cc_final: 0.7514 (tp30) REVERT: E 565 GLU cc_start: 0.7802 (mp0) cc_final: 0.6848 (tt0) REVERT: F 324 GLU cc_start: 0.7557 (pt0) cc_final: 0.6904 (pp20) REVERT: F 418 GLU cc_start: 0.7986 (pt0) cc_final: 0.7643 (tp30) REVERT: F 684 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8446 (tt0) REVERT: H 75 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8207 (t0) REVERT: H 108 ASP cc_start: 0.8976 (m-30) cc_final: 0.8684 (m-30) REVERT: L 104 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7405 (pt0) REVERT: L 127 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.7956 (ttmm) outliers start: 44 outliers final: 32 residues processed: 211 average time/residue: 1.6278 time to fit residues: 384.8069 Evaluate side-chains 212 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 456 GLN Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 306 TRP Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 518 MET Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 127 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 150 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 161 optimal weight: 20.0000 chunk 56 optimal weight: 0.0060 chunk 110 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 52 optimal weight: 0.0170 chunk 235 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 overall best weight: 3.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN D 673 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.085025 restraints weight = 31405.674| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.61 r_work: 0.2857 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19753 Z= 0.134 Angle : 0.513 5.821 26907 Z= 0.268 Chirality : 0.041 0.131 2788 Planarity : 0.004 0.058 3571 Dihedral : 4.885 55.261 2632 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.09 % Allowed : 11.53 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2398 helix: -3.29 (0.45), residues: 82 sheet: 0.19 (0.20), residues: 614 loop : -0.22 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 509 HIS 0.006 0.001 HIS C 290 PHE 0.012 0.001 PHE D 629 TYR 0.023 0.001 TYR B 484 ARG 0.016 0.001 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.02623 ( 225) hydrogen bonds : angle 5.68596 ( 453) SS BOND : bond 0.00298 ( 2) SS BOND : angle 0.98287 ( 4) covalent geometry : bond 0.00311 (19751) covalent geometry : angle 0.51264 (26903) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 3.018 Fit side-chains REVERT: A 529 GLU cc_start: 0.7488 (tp30) cc_final: 0.7128 (tt0) REVERT: B 514 ARG cc_start: 0.7482 (mtm180) cc_final: 0.5482 (mmt180) REVERT: B 529 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6420 (tt0) REVERT: B 608 GLN cc_start: 0.8224 (mm110) cc_final: 0.7949 (mm110) REVERT: C 238 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7834 (ptt-90) REVERT: C 258 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7398 (mmmt) REVERT: C 691 ASN cc_start: 0.8354 (p0) cc_final: 0.8002 (p0) REVERT: D 321 GLN cc_start: 0.7837 (mt0) cc_final: 0.7627 (mt0) REVERT: D 529 GLU cc_start: 0.6645 (tp30) cc_final: 0.5842 (tp30) REVERT: D 531 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: D 562 ASN cc_start: 0.6836 (p0) cc_final: 0.6315 (p0) REVERT: E 493 VAL cc_start: 0.7533 (m) cc_final: 0.7158 (t) REVERT: E 500 GLU cc_start: 0.7862 (tp30) cc_final: 0.7528 (tp30) REVERT: E 565 GLU cc_start: 0.7748 (mp0) cc_final: 0.6788 (tt0) REVERT: F 324 GLU cc_start: 0.7561 (pt0) cc_final: 0.6902 (pp20) REVERT: F 418 GLU cc_start: 0.7980 (pt0) cc_final: 0.7638 (tp30) REVERT: F 684 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8444 (tt0) REVERT: H 75 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8177 (t0) REVERT: H 108 ASP cc_start: 0.8976 (m-30) cc_final: 0.8685 (m-30) REVERT: L 104 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: L 127 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.7926 (ttmm) outliers start: 44 outliers final: 32 residues processed: 213 average time/residue: 1.7438 time to fit residues: 418.3691 Evaluate side-chains 210 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 TRP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 456 GLN Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain D residue 306 TRP Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 448 SER Chi-restraints excluded: chain F residue 518 MET Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 127 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 8 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 224 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN C 588 GLN D 673 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.083918 restraints weight = 31674.459| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.63 r_work: 0.2833 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19753 Z= 0.185 Angle : 0.553 6.031 26907 Z= 0.291 Chirality : 0.043 0.149 2788 Planarity : 0.004 0.059 3571 Dihedral : 5.161 55.254 2632 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.99 % Allowed : 11.72 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2398 helix: -3.36 (0.45), residues: 82 sheet: 0.13 (0.19), residues: 614 loop : -0.28 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 509 HIS 0.006 0.001 HIS A 290 PHE 0.016 0.002 PHE D 367 TYR 0.029 0.002 TYR H 69 ARG 0.016 0.001 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.02961 ( 225) hydrogen bonds : angle 5.89879 ( 453) SS BOND : bond 0.00319 ( 2) SS BOND : angle 1.17796 ( 4) covalent geometry : bond 0.00432 (19751) covalent geometry : angle 0.55294 (26903) =============================================================================== Job complete usr+sys time: 13185.25 seconds wall clock time: 229 minutes 35.67 seconds (13775.67 seconds total)