Starting phenix.real_space_refine on Thu Sep 18 17:06:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7l_44315/09_2025/9b7l_44315.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7l_44315/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b7l_44315/09_2025/9b7l_44315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7l_44315/09_2025/9b7l_44315.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b7l_44315/09_2025/9b7l_44315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7l_44315/09_2025/9b7l_44315.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.80, per 1000 atoms: 0.25 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: 1.74 Conformation dependent library (CDL) restraints added in 755.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.57 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: 3.24 Time building geometry restraints manager: 2.34 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: 0.500 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: 0.290 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 18.540 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:9.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.060 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.14), 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 ARG 0.016 0.002 ARG C 488 TYR 0.051 0.003 TYR H 69 PHE 0.034 0.003 PHE C 367 TRP 0.032 0.003 TRP C 281 HIS 0.021 0.003 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00850 (19751) covalent geometry : angle 1.02302 (26903) SS BOND : bond 0.00644 ( 2) SS BOND : angle 1.64016 ( 4) hydrogen bonds : bond 0.21258 ( 225) hydrogen bonds : angle 8.59839 ( 453) *********************** 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 : 0.562 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: 0.6155 time to fit residues: 224.1453 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 : 0.758 ------------------------------------------------------------------------------- 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 216 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 608 GLN 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.087077 restraints weight = 31374.673| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.63 r_work: 0.2892 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19753 Z= 0.128 Angle : 0.584 8.375 26907 Z= 0.310 Chirality : 0.043 0.149 2788 Planarity : 0.004 0.042 3571 Dihedral : 6.322 58.224 2669 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.23 % Allowed : 6.55 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (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 ARG 0.008 0.001 ARG A 550 TYR 0.024 0.002 TYR H 69 PHE 0.016 0.002 PHE C 367 TRP 0.015 0.002 TRP B 509 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00282 (19751) covalent geometry : angle 0.58336 (26903) SS BOND : bond 0.00801 ( 2) SS BOND : angle 1.52674 ( 4) hydrogen bonds : bond 0.03457 ( 225) hydrogen bonds : angle 6.52074 ( 453) *********************** 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 271 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 0.727 Fit side-chains REVERT: A 529 GLU cc_start: 0.7526 (tp30) cc_final: 0.7221 (tt0) REVERT: B 514 ARG cc_start: 0.7612 (mtm180) cc_final: 0.5763 (mmt180) REVERT: B 529 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6355 (tp30) REVERT: C 238 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7674 (ptt-90) REVERT: C 258 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7504 (mmtt) REVERT: C 398 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7113 (mp0) REVERT: C 406 ARG cc_start: 0.7020 (mtt180) cc_final: 0.4887 (ptt-90) REVERT: C 452 ASN cc_start: 0.8043 (m110) cc_final: 0.7568 (m-40) REVERT: C 588 GLN cc_start: 0.7663 (mp-120) cc_final: 0.7259 (mp10) REVERT: D 312 ARG cc_start: 0.7597 (mtt90) cc_final: 0.7308 (mtt-85) REVERT: D 321 GLN cc_start: 0.7848 (mt0) cc_final: 0.7538 (mt0) REVERT: D 529 GLU cc_start: 0.6677 (tp30) cc_final: 0.6042 (tp30) REVERT: D 531 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6887 (mt-10) REVERT: D 562 ASN cc_start: 0.6775 (p0) cc_final: 0.6388 (p0) REVERT: E 493 VAL cc_start: 0.7552 (m) cc_final: 0.7231 (t) REVERT: E 565 GLU cc_start: 0.7940 (mp0) cc_final: 0.7148 (pt0) REVERT: F 235 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8607 (mt) REVERT: F 324 GLU cc_start: 0.7167 (pt0) cc_final: 0.6612 (pp20) REVERT: F 347 ASP cc_start: 0.7818 (t0) cc_final: 0.7284 (p0) REVERT: F 404 MET cc_start: 0.8064 (mtp) cc_final: 0.7823 (mtp) REVERT: H 123 ASP cc_start: 0.8264 (p0) cc_final: 0.7244 (p0) outliers start: 47 outliers final: 23 residues processed: 258 average time/residue: 0.6382 time to fit residues: 184.4098 Evaluate side-chains 211 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 120 optimal weight: 30.0000 chunk 59 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN C 403 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.083424 restraints weight = 31832.840| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.63 r_work: 0.2842 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1682 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= 0.252 Angle : 0.640 8.239 26907 Z= 0.341 Chirality : 0.046 0.199 2788 Planarity : 0.005 0.072 3571 Dihedral : 6.025 59.909 2637 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.80 % Allowed : 7.83 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.15), residues: 2398 helix: -3.58 (0.39), residues: 94 sheet: -0.13 (0.18), residues: 625 loop : -0.36 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 550 TYR 0.033 0.002 TYR H 69 PHE 0.017 0.002 PHE C 367 TRP 0.022 0.002 TRP B 509 HIS 0.016 0.002 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00593 (19751) covalent geometry : angle 0.63950 (26903) SS BOND : bond 0.00416 ( 2) SS BOND : angle 2.75673 ( 4) hydrogen bonds : bond 0.03711 ( 225) hydrogen bonds : angle 6.45789 ( 453) *********************** 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 246 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 0.604 Fit side-chains REVERT: A 529 GLU cc_start: 0.7572 (tp30) cc_final: 0.7189 (tt0) REVERT: B 514 ARG cc_start: 0.7593 (mtm180) cc_final: 0.5617 (mmt180) REVERT: C 238 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7759 (ptt-90) REVERT: C 258 LYS cc_start: 0.8372 (mtmt) cc_final: 0.7493 (mmtt) REVERT: C 398 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7208 (mp0) REVERT: C 406 ARG cc_start: 0.7338 (mtt180) cc_final: 0.4867 (ptt-90) REVERT: C 452 ASN cc_start: 0.7998 (m110) cc_final: 0.7542 (m-40) REVERT: C 691 ASN cc_start: 0.8279 (p0) cc_final: 0.8012 (p0) REVERT: D 321 GLN cc_start: 0.7868 (mt0) cc_final: 0.7583 (mt0) REVERT: D 529 GLU cc_start: 0.6582 (tp30) cc_final: 0.5827 (tp30) REVERT: D 531 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: D 562 ASN cc_start: 0.6842 (p0) cc_final: 0.6391 (p0) REVERT: E 493 VAL cc_start: 0.7609 (m) cc_final: 0.7254 (t) REVERT: E 565 GLU cc_start: 0.7909 (mp0) cc_final: 0.7123 (pt0) REVERT: F 324 GLU cc_start: 0.7439 (pt0) cc_final: 0.6839 (pp20) REVERT: F 348 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8609 (m) REVERT: L 104 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7540 (pt0) outliers start: 59 outliers final: 36 residues processed: 233 average time/residue: 0.6271 time to fit residues: 163.1947 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 : 0.508 ------------------------------------------------------------------------------- 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 532 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 91 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 585 GLN F 259 GLN F 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.083813 restraints weight = 31616.298| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.65 r_work: 0.2855 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19753 Z= 0.169 Angle : 0.555 7.451 26907 Z= 0.294 Chirality : 0.043 0.160 2788 Planarity : 0.004 0.046 3571 Dihedral : 5.624 56.609 2635 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.85 % Allowed : 8.59 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.16), residues: 2398 helix: -3.60 (0.39), residues: 94 sheet: -0.04 (0.18), residues: 625 loop : -0.30 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 550 TYR 0.025 0.002 TYR H 69 PHE 0.012 0.002 PHE D 662 TRP 0.018 0.002 TRP B 509 HIS 0.009 0.002 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00392 (19751) covalent geometry : angle 0.55518 (26903) SS BOND : bond 0.00261 ( 2) SS BOND : angle 1.42540 ( 4) hydrogen bonds : bond 0.03016 ( 225) hydrogen bonds : angle 6.13239 ( 453) *********************** 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 247 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 187 time to evaluate : 0.835 Fit side-chains REVERT: A 529 GLU cc_start: 0.7450 (tp30) cc_final: 0.7158 (tt0) REVERT: B 514 ARG cc_start: 0.7579 (mtm180) cc_final: 0.5539 (mmt180) REVERT: B 529 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6424 (tp30) REVERT: C 258 LYS cc_start: 0.8347 (mtmt) cc_final: 0.7437 (mmtt) REVERT: C 406 ARG cc_start: 0.7358 (mtt180) cc_final: 0.4807 (ptt-90) REVERT: C 452 ASN cc_start: 0.7987 (m110) cc_final: 0.7556 (m-40) REVERT: C 588 GLN cc_start: 0.7514 (mp-120) cc_final: 0.7077 (mp10) REVERT: C 691 ASN cc_start: 0.8331 (p0) cc_final: 0.8018 (p0) REVERT: D 321 GLN cc_start: 0.7913 (mt0) cc_final: 0.7640 (mt0) REVERT: D 529 GLU cc_start: 0.6606 (tp30) cc_final: 0.5802 (tp30) REVERT: D 531 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7008 (mt-10) REVERT: D 562 ASN cc_start: 0.6779 (p0) cc_final: 0.6303 (p0) REVERT: D 664 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8175 (ttpp) REVERT: E 493 VAL cc_start: 0.7555 (m) cc_final: 0.7216 (t) REVERT: E 565 GLU cc_start: 0.7927 (mp0) cc_final: 0.7029 (pt0) REVERT: F 235 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8604 (mt) REVERT: F 259 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: F 324 GLU cc_start: 0.7481 (pt0) cc_final: 0.6855 (pp20) REVERT: F 348 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8698 (m) REVERT: F 404 MET cc_start: 0.8158 (mtp) cc_final: 0.7929 (mtt) REVERT: H 37 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8822 (tp) REVERT: H 75 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8185 (t0) REVERT: L 104 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7476 (pt0) outliers start: 60 outliers final: 34 residues processed: 234 average time/residue: 0.6126 time to fit residues: 161.1843 Evaluate side-chains 213 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 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 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 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 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 489 VAL Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 259 GLN 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 37 LEU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 104 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 218 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 195 optimal weight: 7.9990 chunk 223 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 F 233 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 = 0.3190 r_free = 0.3190 target = 0.100000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.083936 restraints weight = 31726.123| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.64 r_work: 0.2847 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19753 Z= 0.174 Angle : 0.551 6.799 26907 Z= 0.291 Chirality : 0.043 0.161 2788 Planarity : 0.004 0.045 3571 Dihedral : 5.530 58.942 2635 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.85 % Allowed : 9.25 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.16), residues: 2398 helix: -3.67 (0.38), residues: 94 sheet: -0.02 (0.19), residues: 626 loop : -0.27 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 550 TYR 0.024 0.002 TYR H 69 PHE 0.013 0.002 PHE F 535 TRP 0.018 0.002 TRP B 509 HIS 0.009 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00407 (19751) covalent geometry : angle 0.55065 (26903) SS BOND : bond 0.00297 ( 2) SS BOND : angle 1.30866 ( 4) hydrogen bonds : bond 0.02991 ( 225) hydrogen bonds : angle 6.02011 ( 453) *********************** 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 244 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 184 time to evaluate : 0.766 Fit side-chains REVERT: A 529 GLU cc_start: 0.7462 (tp30) cc_final: 0.6976 (tt0) REVERT: B 514 ARG cc_start: 0.7562 (mtm180) cc_final: 0.5526 (mmt180) REVERT: C 258 LYS cc_start: 0.8352 (mtmt) cc_final: 0.7436 (mmmt) REVERT: C 406 ARG cc_start: 0.7512 (mtt180) cc_final: 0.4829 (ptt-90) REVERT: C 452 ASN cc_start: 0.8000 (m110) cc_final: 0.7566 (m-40) REVERT: C 691 ASN cc_start: 0.8382 (p0) cc_final: 0.8059 (p0) REVERT: D 321 GLN cc_start: 0.7853 (mt0) cc_final: 0.7619 (mt0) REVERT: D 529 GLU cc_start: 0.6613 (tp30) cc_final: 0.5811 (tp30) REVERT: D 531 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7038 (mt-10) REVERT: D 562 ASN cc_start: 0.6798 (p0) cc_final: 0.6301 (p0) REVERT: D 664 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8148 (ttpp) REVERT: E 449 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8558 (ttpp) REVERT: E 493 VAL cc_start: 0.7547 (m) cc_final: 0.7197 (t) REVERT: E 565 GLU cc_start: 0.7880 (mp0) cc_final: 0.6999 (pt0) REVERT: F 235 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8622 (mt) REVERT: F 324 GLU cc_start: 0.7558 (pt0) cc_final: 0.6919 (pp20) REVERT: F 348 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8723 (m) REVERT: F 684 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: H 75 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8183 (t0) REVERT: H 108 ASP cc_start: 0.8975 (m-30) cc_final: 0.8755 (m-30) REVERT: L 104 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7459 (pt0) outliers start: 60 outliers final: 42 residues processed: 236 average time/residue: 0.6026 time to fit residues: 160.0312 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 : 0.752 ------------------------------------------------------------------------------- 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 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 489 VAL 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 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 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 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 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 H residue 35 VAL Chi-restraints excluded: chain H residue 69 TYR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 233 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 F 259 GLN L 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.099758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.083769 restraints weight = 31563.116| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.62 r_work: 0.2838 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19753 Z= 0.192 Angle : 0.560 6.318 26907 Z= 0.296 Chirality : 0.043 0.163 2788 Planarity : 0.004 0.047 3571 Dihedral : 5.510 54.208 2635 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.32 % Allowed : 9.07 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.16), residues: 2398 helix: -3.72 (0.38), residues: 94 sheet: 0.05 (0.19), residues: 622 loop : -0.31 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 550 TYR 0.026 0.002 TYR H 69 PHE 0.013 0.002 PHE F 535 TRP 0.018 0.002 TRP B 509 HIS 0.010 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00449 (19751) covalent geometry : angle 0.55950 (26903) SS BOND : bond 0.00330 ( 2) SS BOND : angle 1.28351 ( 4) hydrogen bonds : bond 0.03039 ( 225) hydrogen bonds : angle 6.00518 ( 453) *********************** 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 242 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 172 time to evaluate : 0.804 Fit side-chains REVERT: A 529 GLU cc_start: 0.7471 (tp30) cc_final: 0.7123 (tt0) REVERT: B 514 ARG cc_start: 0.7557 (mtm180) cc_final: 0.5499 (mmt180) REVERT: C 258 LYS cc_start: 0.8325 (mtmt) cc_final: 0.7415 (mmmt) REVERT: C 406 ARG cc_start: 0.7628 (mtt180) cc_final: 0.4728 (ptt-90) REVERT: C 691 ASN cc_start: 0.8378 (p0) cc_final: 0.8033 (p0) REVERT: D 321 GLN cc_start: 0.7885 (mt0) cc_final: 0.7651 (mt0) REVERT: D 529 GLU cc_start: 0.6595 (tp30) cc_final: 0.5827 (tp30) REVERT: D 531 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: D 562 ASN cc_start: 0.6882 (p0) cc_final: 0.6365 (p0) REVERT: D 664 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8146 (ttpp) REVERT: E 449 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8556 (ttpp) REVERT: E 493 VAL cc_start: 0.7510 (m) cc_final: 0.7156 (t) REVERT: E 565 GLU cc_start: 0.7848 (mp0) cc_final: 0.6923 (pt0) REVERT: F 235 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8657 (mt) REVERT: F 324 GLU cc_start: 0.7541 (pt0) cc_final: 0.6904 (pp20) REVERT: F 684 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: H 37 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8829 (tp) REVERT: H 75 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8164 (t0) REVERT: H 108 ASP cc_start: 0.8988 (m-30) cc_final: 0.8754 (m-30) REVERT: L 104 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7403 (pt0) outliers start: 70 outliers final: 46 residues processed: 234 average time/residue: 0.6445 time to fit residues: 169.3057 Evaluate side-chains 218 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 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 489 VAL 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 389 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 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 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 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 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 H residue 35 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 69 TYR 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 78 SER Chi-restraints excluded: chain L residue 104 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 44 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 overall best weight: 7.3188 ------------------------------------------------------------------------------- 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 C 588 GLN H 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.082981 restraints weight = 31738.847| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.62 r_work: 0.2823 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 19753 Z= 0.247 Angle : 0.601 6.512 26907 Z= 0.319 Chirality : 0.045 0.184 2788 Planarity : 0.005 0.051 3571 Dihedral : 5.707 54.318 2635 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.13 % Allowed : 9.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.16), residues: 2398 helix: -3.80 (0.37), residues: 95 sheet: -0.04 (0.20), residues: 600 loop : -0.37 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 550 TYR 0.029 0.002 TYR H 69 PHE 0.015 0.002 PHE D 662 TRP 0.019 0.002 TRP B 509 HIS 0.011 0.002 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00580 (19751) covalent geometry : angle 0.60102 (26903) SS BOND : bond 0.00377 ( 2) SS BOND : angle 1.43550 ( 4) hydrogen bonds : bond 0.03331 ( 225) hydrogen bonds : angle 6.18103 ( 453) *********************** 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 238 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 172 time to evaluate : 0.713 Fit side-chains REVERT: A 529 GLU cc_start: 0.7551 (tp30) cc_final: 0.7225 (tt0) REVERT: B 514 ARG cc_start: 0.7504 (mtm180) cc_final: 0.5437 (mmt180) REVERT: C 258 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7394 (mmmt) REVERT: C 691 ASN cc_start: 0.8420 (p0) cc_final: 0.8040 (p0) REVERT: D 321 GLN cc_start: 0.7894 (mt0) cc_final: 0.7649 (mt0) REVERT: D 529 GLU cc_start: 0.6575 (tp30) cc_final: 0.5777 (tp30) REVERT: D 531 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: D 562 ASN cc_start: 0.6916 (p0) cc_final: 0.6388 (p0) REVERT: D 664 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8199 (ttpp) REVERT: E 449 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8544 (ttpp) REVERT: E 493 VAL cc_start: 0.7556 (m) cc_final: 0.7222 (t) REVERT: E 565 GLU cc_start: 0.7849 (mp0) cc_final: 0.6938 (pt0) REVERT: F 235 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8677 (mt) REVERT: F 324 GLU cc_start: 0.7591 (pt0) cc_final: 0.6887 (pp20) REVERT: F 347 ASP cc_start: 0.8186 (t70) cc_final: 0.7984 (t0) REVERT: F 684 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: H 37 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8833 (tp) REVERT: H 108 ASP cc_start: 0.9039 (m-30) cc_final: 0.8728 (m-30) REVERT: L 104 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7477 (pt0) outliers start: 66 outliers final: 50 residues processed: 232 average time/residue: 0.6317 time to fit residues: 164.2285 Evaluate side-chains 224 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 167 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 489 VAL 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 389 VAL Chi-restraints excluded: chain C residue 412 GLN 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 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 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 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 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 H residue 21 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 37 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 113 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 chunk 40 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 673 GLN F 456 GLN L 102 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.084805 restraints weight = 31542.144| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.63 r_work: 0.2865 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19753 Z= 0.120 Angle : 0.508 5.903 26907 Z= 0.266 Chirality : 0.041 0.135 2788 Planarity : 0.004 0.051 3571 Dihedral : 5.155 55.884 2635 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.47 % Allowed : 10.63 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.16), residues: 2398 helix: -3.66 (0.38), residues: 100 sheet: 0.07 (0.19), residues: 622 loop : -0.30 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 550 TYR 0.017 0.001 TYR H 69 PHE 0.013 0.001 PHE D 629 TRP 0.013 0.001 TRP B 509 HIS 0.004 0.001 HIS H 118 Details of bonding type rmsd covalent geometry : bond 0.00277 (19751) covalent geometry : angle 0.50786 (26903) SS BOND : bond 0.00323 ( 2) SS BOND : angle 0.83966 ( 4) hydrogen bonds : bond 0.02605 ( 225) hydrogen bonds : angle 5.74463 ( 453) *********************** 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: 52 poor density : 180 time to evaluate : 0.792 Fit side-chains REVERT: A 529 GLU cc_start: 0.7576 (tp30) cc_final: 0.7183 (tt0) REVERT: B 514 ARG cc_start: 0.7543 (mtm180) cc_final: 0.5495 (mmt180) REVERT: C 258 LYS cc_start: 0.8260 (mtmt) cc_final: 0.7412 (mmmt) REVERT: C 588 GLN cc_start: 0.7550 (mp-120) cc_final: 0.6929 (mm110) REVERT: C 691 ASN cc_start: 0.8392 (p0) cc_final: 0.8037 (p0) REVERT: D 321 GLN cc_start: 0.7847 (mt0) cc_final: 0.7611 (mt0) REVERT: D 529 GLU cc_start: 0.6619 (tp30) cc_final: 0.5861 (tp30) REVERT: D 531 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: D 562 ASN cc_start: 0.6839 (p0) cc_final: 0.6310 (p0) REVERT: D 664 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8018 (ttpp) REVERT: E 493 VAL cc_start: 0.7566 (m) cc_final: 0.7198 (t) REVERT: E 565 GLU cc_start: 0.7794 (mp0) cc_final: 0.6896 (pt0) REVERT: F 235 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8684 (mt) REVERT: F 324 GLU cc_start: 0.7559 (pt0) cc_final: 0.6895 (pp20) REVERT: F 684 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: H 37 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8798 (tp) REVERT: H 108 ASP cc_start: 0.8993 (m-30) cc_final: 0.8683 (m-30) REVERT: L 104 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7407 (pt0) outliers start: 52 outliers final: 35 residues processed: 225 average time/residue: 0.6329 time to fit residues: 159.9553 Evaluate side-chains 208 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 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 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 D residue 664 LYS Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 489 VAL 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 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 37 LEU 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 104 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 137 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 128 optimal weight: 0.0670 chunk 108 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 16 optimal weight: 50.0000 overall best weight: 7.0126 ------------------------------------------------------------------------------- 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 D 546 GLN D 673 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 = 0.3176 r_free = 0.3176 target = 0.099146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.083156 restraints weight = 31484.726| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.61 r_work: 0.2825 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 19753 Z= 0.236 Angle : 0.591 6.284 26907 Z= 0.312 Chirality : 0.044 0.176 2788 Planarity : 0.005 0.054 3571 Dihedral : 5.459 54.875 2633 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.37 % Allowed : 10.92 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.16), residues: 2398 helix: -3.50 (0.43), residues: 82 sheet: 0.01 (0.20), residues: 598 loop : -0.34 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 550 TYR 0.030 0.002 TYR H 69 PHE 0.015 0.002 PHE D 662 TRP 0.017 0.002 TRP B 509 HIS 0.009 0.002 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00556 (19751) covalent geometry : angle 0.59055 (26903) SS BOND : bond 0.00375 ( 2) SS BOND : angle 1.34574 ( 4) hydrogen bonds : bond 0.03237 ( 225) hydrogen bonds : angle 6.08423 ( 453) *********************** 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 219 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 0.533 Fit side-chains REVERT: A 529 GLU cc_start: 0.7520 (tp30) cc_final: 0.7165 (tt0) REVERT: B 514 ARG cc_start: 0.7509 (mtm180) cc_final: 0.5441 (mmt180) REVERT: C 238 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7883 (ptt-90) REVERT: C 258 LYS cc_start: 0.8320 (mtmt) cc_final: 0.7388 (mmmt) REVERT: C 691 ASN cc_start: 0.8447 (p0) cc_final: 0.8050 (p0) REVERT: D 321 GLN cc_start: 0.7896 (mt0) cc_final: 0.7659 (mt0) REVERT: D 529 GLU cc_start: 0.6651 (tp30) cc_final: 0.5864 (tp30) REVERT: D 531 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: D 562 ASN cc_start: 0.6880 (p0) cc_final: 0.6345 (p0) REVERT: D 664 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8177 (ttpp) REVERT: E 493 VAL cc_start: 0.7566 (m) cc_final: 0.7219 (t) REVERT: E 565 GLU cc_start: 0.7845 (mp0) cc_final: 0.6959 (pt0) REVERT: F 235 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8701 (mt) REVERT: F 324 GLU cc_start: 0.7594 (pt0) cc_final: 0.6886 (pp20) REVERT: F 684 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: H 37 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8835 (tp) REVERT: H 75 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8223 (t0) REVERT: H 108 ASP cc_start: 0.9048 (m-30) cc_final: 0.8740 (m-30) REVERT: L 104 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7435 (pt0) outliers start: 50 outliers final: 38 residues processed: 215 average time/residue: 0.6019 time to fit residues: 145.7290 Evaluate side-chains 213 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 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 322 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 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 D residue 664 LYS Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 580 VAL 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 F residue 580 VAL Chi-restraints excluded: chain F residue 654 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 37 LEU Chi-restraints excluded: chain H residue 69 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 124 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 220 optimal weight: 0.2980 chunk 204 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 230 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 673 GLN F 233 GLN L 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.086482 restraints weight = 31496.922| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.63 r_work: 0.2885 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19753 Z= 0.085 Angle : 0.483 5.831 26907 Z= 0.252 Chirality : 0.041 0.134 2788 Planarity : 0.004 0.059 3571 Dihedral : 4.710 53.248 2633 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.38 % Allowed : 12.06 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.16), residues: 2398 helix: -3.52 (0.39), residues: 100 sheet: 0.17 (0.20), residues: 602 loop : -0.18 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 550 TYR 0.011 0.001 TYR F 443 PHE 0.014 0.001 PHE D 629 TRP 0.011 0.001 TRP H 66 HIS 0.004 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00193 (19751) covalent geometry : angle 0.48279 (26903) SS BOND : bond 0.00361 ( 2) SS BOND : angle 0.66873 ( 4) hydrogen bonds : bond 0.02312 ( 225) hydrogen bonds : angle 5.49243 ( 453) ********************** 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 217 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.727 Fit side-chains REVERT: A 529 GLU cc_start: 0.7444 (tp30) cc_final: 0.7092 (tt0) REVERT: B 514 ARG cc_start: 0.7538 (mtm180) cc_final: 0.5506 (mmt180) REVERT: B 608 GLN cc_start: 0.8233 (mm110) cc_final: 0.7994 (mm110) REVERT: C 258 LYS cc_start: 0.8208 (mtmt) cc_final: 0.7393 (mmmt) REVERT: C 691 ASN cc_start: 0.8373 (p0) cc_final: 0.8049 (p0) REVERT: D 321 GLN cc_start: 0.7847 (mt0) cc_final: 0.7633 (mt0) REVERT: D 529 GLU cc_start: 0.6524 (tp30) cc_final: 0.5706 (tp30) REVERT: D 531 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: D 562 ASN cc_start: 0.6825 (p0) cc_final: 0.6309 (p0) REVERT: E 493 VAL cc_start: 0.7576 (m) cc_final: 0.7211 (t) REVERT: E 565 GLU cc_start: 0.7750 (mp0) cc_final: 0.6772 (tt0) REVERT: F 324 GLU cc_start: 0.7537 (pt0) cc_final: 0.6892 (pp20) REVERT: L 104 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7352 (pt0) outliers start: 29 outliers final: 21 residues processed: 213 average time/residue: 0.6296 time to fit residues: 150.1610 Evaluate side-chains 196 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 448 SER 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 448 SER Chi-restraints excluded: chain F residue 518 MET Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 42 CYS Chi-restraints excluded: chain L residue 104 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 130 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 194 optimal weight: 0.0870 chunk 53 optimal weight: 20.0000 chunk 214 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- 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 C 519 ASN C 588 GLN C 700 GLN D 673 GLN F 233 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.085318 restraints weight = 31483.763| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.63 r_work: 0.2867 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19753 Z= 0.129 Angle : 0.510 5.670 26907 Z= 0.266 Chirality : 0.041 0.131 2788 Planarity : 0.004 0.060 3571 Dihedral : 4.820 53.667 2632 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.47 % Allowed : 11.96 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.16), residues: 2398 helix: -3.22 (0.46), residues: 82 sheet: 0.20 (0.20), residues: 594 loop : -0.18 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 550 TYR 0.022 0.001 TYR H 69 PHE 0.013 0.001 PHE A 367 TRP 0.013 0.001 TRP B 509 HIS 0.004 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00300 (19751) covalent geometry : angle 0.50949 (26903) SS BOND : bond 0.00322 ( 2) SS BOND : angle 0.97948 ( 4) hydrogen bonds : bond 0.02602 ( 225) hydrogen bonds : angle 5.60307 ( 453) =============================================================================== Job complete usr+sys time: 5668.37 seconds wall clock time: 97 minutes 40.12 seconds (5860.12 seconds total)