Starting phenix.real_space_refine on Fri May 23 09:19:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fec_31552/05_2025/7fec_31552.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fec_31552/05_2025/7fec_31552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fec_31552/05_2025/7fec_31552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fec_31552/05_2025/7fec_31552.map" model { file = "/net/cci-nas-00/data/ceres_data/7fec_31552/05_2025/7fec_31552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fec_31552/05_2025/7fec_31552.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.063 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 108 5.16 5 C 15354 2.51 5 N 4140 2.21 5 O 4473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24075 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "A" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "B" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "C" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "D" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "F" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "G" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "H" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "I" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Time building chain proxies: 13.37, per 1000 atoms: 0.56 Number of scatterers: 24075 At special positions: 0 Unit cell: (178.78, 180.466, 79.2702, 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 108 16.00 O 4473 8.00 N 4140 7.00 C 15354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.97 Conformation dependent library (CDL) restraints added in 2.9 seconds 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5742 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 36 sheets defined 47.9% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'E' and resid 365 through 382 Processing helix chain 'E' and resid 437 through 440 Processing helix chain 'E' and resid 447 through 457 Processing helix chain 'E' and resid 465 through 479 removed outlier: 3.847A pdb=" N CYS E 474 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 484 removed outlier: 4.054A pdb=" N ILE E 484 " --> pdb=" O GLY E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 497 Processing helix chain 'E' and resid 500 through 511 Processing helix chain 'E' and resid 512 through 525 Processing helix chain 'E' and resid 532 through 544 Processing helix chain 'E' and resid 549 through 561 Processing helix chain 'E' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN E 570 " --> pdb=" O LEU E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 590 removed outlier: 4.073A pdb=" N GLU E 586 " --> pdb=" O GLY E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 620 Processing helix chain 'E' and resid 634 through 641 Processing helix chain 'A' and resid 365 through 382 Processing helix chain 'A' and resid 437 through 440 Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.846A pdb=" N CYS A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 4.054A pdb=" N ILE A 484 " --> pdb=" O GLY A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 497 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 532 through 544 Processing helix chain 'A' and resid 549 through 561 Processing helix chain 'A' and resid 561 through 570 removed outlier: 3.675A pdb=" N ASN A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 590 removed outlier: 4.074A pdb=" N GLU A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 620 Processing helix chain 'A' and resid 634 through 641 Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 437 through 440 Processing helix chain 'B' and resid 447 through 457 Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.846A pdb=" N CYS B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 484 removed outlier: 4.055A pdb=" N ILE B 484 " --> pdb=" O GLY B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 497 Processing helix chain 'B' and resid 500 through 511 Processing helix chain 'B' and resid 512 through 525 Processing helix chain 'B' and resid 532 through 544 Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 590 removed outlier: 4.072A pdb=" N GLU B 586 " --> pdb=" O GLY B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 620 Processing helix chain 'B' and resid 634 through 641 Processing helix chain 'C' and resid 365 through 382 Processing helix chain 'C' and resid 437 through 440 Processing helix chain 'C' and resid 447 through 457 Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.847A pdb=" N CYS C 474 " --> pdb=" O ALA C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 484 removed outlier: 4.054A pdb=" N ILE C 484 " --> pdb=" O GLY C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 497 Processing helix chain 'C' and resid 500 through 511 Processing helix chain 'C' and resid 512 through 525 Processing helix chain 'C' and resid 532 through 544 Processing helix chain 'C' and resid 549 through 561 Processing helix chain 'C' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 590 removed outlier: 4.072A pdb=" N GLU C 586 " --> pdb=" O GLY C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 620 Processing helix chain 'C' and resid 634 through 641 Processing helix chain 'D' and resid 365 through 382 Processing helix chain 'D' and resid 437 through 440 Processing helix chain 'D' and resid 447 through 457 Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.847A pdb=" N CYS D 474 " --> pdb=" O ALA D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 484 removed outlier: 4.054A pdb=" N ILE D 484 " --> pdb=" O GLY D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 497 Processing helix chain 'D' and resid 500 through 511 Processing helix chain 'D' and resid 512 through 525 Processing helix chain 'D' and resid 532 through 544 Processing helix chain 'D' and resid 549 through 561 Processing helix chain 'D' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN D 570 " --> pdb=" O LEU D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 590 removed outlier: 4.073A pdb=" N GLU D 586 " --> pdb=" O GLY D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 620 Processing helix chain 'D' and resid 634 through 641 Processing helix chain 'F' and resid 365 through 382 Processing helix chain 'F' and resid 437 through 440 Processing helix chain 'F' and resid 447 through 457 Processing helix chain 'F' and resid 465 through 479 removed outlier: 3.846A pdb=" N CYS F 474 " --> pdb=" O ALA F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 484 removed outlier: 4.055A pdb=" N ILE F 484 " --> pdb=" O GLY F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 497 Processing helix chain 'F' and resid 500 through 511 Processing helix chain 'F' and resid 512 through 525 Processing helix chain 'F' and resid 532 through 544 Processing helix chain 'F' and resid 549 through 561 Processing helix chain 'F' and resid 561 through 570 removed outlier: 3.675A pdb=" N ASN F 570 " --> pdb=" O LEU F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 590 removed outlier: 4.073A pdb=" N GLU F 586 " --> pdb=" O GLY F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 620 Processing helix chain 'F' and resid 634 through 641 Processing helix chain 'G' and resid 365 through 382 Processing helix chain 'G' and resid 437 through 440 Processing helix chain 'G' and resid 447 through 457 Processing helix chain 'G' and resid 465 through 479 removed outlier: 3.847A pdb=" N CYS G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 484 removed outlier: 4.055A pdb=" N ILE G 484 " --> pdb=" O GLY G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 497 Processing helix chain 'G' and resid 500 through 511 Processing helix chain 'G' and resid 512 through 525 Processing helix chain 'G' and resid 532 through 544 Processing helix chain 'G' and resid 549 through 561 Processing helix chain 'G' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN G 570 " --> pdb=" O LEU G 566 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 590 removed outlier: 4.073A pdb=" N GLU G 586 " --> pdb=" O GLY G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 620 Processing helix chain 'G' and resid 634 through 641 Processing helix chain 'H' and resid 365 through 382 Processing helix chain 'H' and resid 437 through 440 Processing helix chain 'H' and resid 447 through 457 Processing helix chain 'H' and resid 465 through 479 removed outlier: 3.846A pdb=" N CYS H 474 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 484 removed outlier: 4.055A pdb=" N ILE H 484 " --> pdb=" O GLY H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 497 Processing helix chain 'H' and resid 500 through 511 Processing helix chain 'H' and resid 512 through 525 Processing helix chain 'H' and resid 532 through 544 Processing helix chain 'H' and resid 549 through 561 Processing helix chain 'H' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN H 570 " --> pdb=" O LEU H 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 590 removed outlier: 4.073A pdb=" N GLU H 586 " --> pdb=" O GLY H 582 " (cutoff:3.500A) Processing helix chain 'H' and resid 605 through 620 Processing helix chain 'H' and resid 634 through 641 Processing helix chain 'I' and resid 365 through 382 Processing helix chain 'I' and resid 437 through 440 Processing helix chain 'I' and resid 447 through 457 Processing helix chain 'I' and resid 465 through 479 removed outlier: 3.847A pdb=" N CYS I 474 " --> pdb=" O ALA I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 480 through 484 removed outlier: 4.054A pdb=" N ILE I 484 " --> pdb=" O GLY I 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 485 through 497 Processing helix chain 'I' and resid 500 through 511 Processing helix chain 'I' and resid 512 through 525 Processing helix chain 'I' and resid 532 through 544 Processing helix chain 'I' and resid 549 through 561 Processing helix chain 'I' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN I 570 " --> pdb=" O LEU I 566 " (cutoff:3.500A) Processing helix chain 'I' and resid 582 through 590 removed outlier: 4.073A pdb=" N GLU I 586 " --> pdb=" O GLY I 582 " (cutoff:3.500A) Processing helix chain 'I' and resid 605 through 620 Processing helix chain 'I' and resid 634 through 641 Processing sheet with id=AA1, first strand: chain 'E' and resid 389 through 392 removed outlier: 6.871A pdb=" N LEU E 353 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU E 391 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU E 355 " --> pdb=" O GLU E 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU E 404 " --> pdb=" O PRO E 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY E 441 " --> pdb=" O LEU E 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR E 420 " --> pdb=" O LEU E 446 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 651 through 653 removed outlier: 6.645A pdb=" N ILE E 628 " --> pdb=" O LEU E 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE E 578 " --> pdb=" O VAL E 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER E 668 " --> pdb=" O ILE E 578 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG E 580 " --> pdb=" O SER E 668 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 593 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 392 removed outlier: 6.870A pdb=" N LEU A 353 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU A 391 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 355 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 404 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY A 441 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 420 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.645A pdb=" N ILE A 628 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE A 578 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 668 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG A 580 " --> pdb=" O SER A 668 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA9, first strand: chain 'B' and resid 389 through 392 removed outlier: 6.871A pdb=" N LEU B 353 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU B 391 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 355 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 404 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY B 441 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 420 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 651 through 653 removed outlier: 6.645A pdb=" N ILE B 628 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE B 578 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER B 668 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG B 580 " --> pdb=" O SER B 668 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 593 through 596 Processing sheet with id=AB4, first strand: chain 'C' and resid 389 through 392 removed outlier: 6.871A pdb=" N LEU C 353 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU C 391 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU C 355 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 404 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY C 441 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 420 " --> pdb=" O LEU C 446 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 651 through 653 removed outlier: 6.646A pdb=" N ILE C 628 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE C 578 " --> pdb=" O VAL C 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER C 668 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG C 580 " --> pdb=" O SER C 668 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 593 through 596 Processing sheet with id=AB8, first strand: chain 'D' and resid 389 through 392 removed outlier: 6.870A pdb=" N LEU D 353 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU D 391 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU D 355 " --> pdb=" O GLU D 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU D 404 " --> pdb=" O PRO D 408 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY D 441 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR D 420 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 651 through 653 removed outlier: 6.646A pdb=" N ILE D 628 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE D 578 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER D 668 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG D 580 " --> pdb=" O SER D 668 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 593 through 596 Processing sheet with id=AC3, first strand: chain 'F' and resid 389 through 392 removed outlier: 6.870A pdb=" N LEU F 353 " --> pdb=" O ASN F 389 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU F 391 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU F 355 " --> pdb=" O GLU F 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU F 404 " --> pdb=" O PRO F 408 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY F 441 " --> pdb=" O LEU F 436 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR F 420 " --> pdb=" O LEU F 446 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 651 through 653 removed outlier: 6.644A pdb=" N ILE F 628 " --> pdb=" O LEU F 652 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE F 578 " --> pdb=" O VAL F 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER F 668 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG F 580 " --> pdb=" O SER F 668 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 593 through 596 Processing sheet with id=AC7, first strand: chain 'G' and resid 389 through 392 removed outlier: 6.870A pdb=" N LEU G 353 " --> pdb=" O ASN G 389 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU G 391 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU G 355 " --> pdb=" O GLU G 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU G 404 " --> pdb=" O PRO G 408 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY G 441 " --> pdb=" O LEU G 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR G 420 " --> pdb=" O LEU G 446 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 651 through 653 removed outlier: 6.646A pdb=" N ILE G 628 " --> pdb=" O LEU G 652 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE G 578 " --> pdb=" O VAL G 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER G 668 " --> pdb=" O ILE G 578 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG G 580 " --> pdb=" O SER G 668 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 593 through 596 Processing sheet with id=AD2, first strand: chain 'H' and resid 389 through 392 removed outlier: 6.870A pdb=" N LEU H 353 " --> pdb=" O ASN H 389 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU H 391 " --> pdb=" O LEU H 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU H 355 " --> pdb=" O GLU H 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU H 404 " --> pdb=" O PRO H 408 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY H 441 " --> pdb=" O LEU H 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR H 420 " --> pdb=" O LEU H 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 651 through 653 removed outlier: 6.644A pdb=" N ILE H 628 " --> pdb=" O LEU H 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE H 578 " --> pdb=" O VAL H 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER H 668 " --> pdb=" O ILE H 578 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG H 580 " --> pdb=" O SER H 668 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 593 through 596 Processing sheet with id=AD6, first strand: chain 'I' and resid 389 through 392 removed outlier: 6.870A pdb=" N LEU I 353 " --> pdb=" O ASN I 389 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU I 391 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU I 355 " --> pdb=" O GLU I 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU I 404 " --> pdb=" O PRO I 408 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY I 441 " --> pdb=" O LEU I 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR I 420 " --> pdb=" O LEU I 446 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 651 through 653 removed outlier: 6.645A pdb=" N ILE I 628 " --> pdb=" O LEU I 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE I 578 " --> pdb=" O VAL I 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER I 668 " --> pdb=" O ILE I 578 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG I 580 " --> pdb=" O SER I 668 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 593 through 596 1134 hydrogen bonds defined for protein. 3267 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: 7.65 Time building geometry restraints manager: 6.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4303 1.32 - 1.45: 5560 1.45 - 1.57: 14419 1.57 - 1.69: 0 1.69 - 1.81: 189 Bond restraints: 24471 Sorted by residual: bond pdb=" N VAL D 347 " pdb=" CA VAL D 347 " ideal model delta sigma weight residual 1.456 1.495 -0.038 8.70e-03 1.32e+04 1.96e+01 bond pdb=" N VAL F 347 " pdb=" CA VAL F 347 " ideal model delta sigma weight residual 1.456 1.493 -0.036 8.70e-03 1.32e+04 1.73e+01 bond pdb=" N VAL E 347 " pdb=" CA VAL E 347 " ideal model delta sigma weight residual 1.456 1.492 -0.036 8.70e-03 1.32e+04 1.72e+01 bond pdb=" N VAL I 347 " pdb=" CA VAL I 347 " ideal model delta sigma weight residual 1.456 1.492 -0.036 8.70e-03 1.32e+04 1.69e+01 bond pdb=" N VAL A 347 " pdb=" CA VAL A 347 " ideal model delta sigma weight residual 1.456 1.492 -0.036 8.70e-03 1.32e+04 1.67e+01 ... (remaining 24466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 31367 1.56 - 3.11: 1332 3.11 - 4.67: 308 4.67 - 6.22: 95 6.22 - 7.78: 54 Bond angle restraints: 33156 Sorted by residual: angle pdb=" N ALA B 418 " pdb=" CA ALA B 418 " pdb=" C ALA B 418 " ideal model delta sigma weight residual 107.99 115.38 -7.39 1.76e+00 3.23e-01 1.76e+01 angle pdb=" N ALA C 418 " pdb=" CA ALA C 418 " pdb=" C ALA C 418 " ideal model delta sigma weight residual 107.99 115.38 -7.39 1.76e+00 3.23e-01 1.76e+01 angle pdb=" N ALA E 418 " pdb=" CA ALA E 418 " pdb=" C ALA E 418 " ideal model delta sigma weight residual 107.99 115.37 -7.38 1.76e+00 3.23e-01 1.76e+01 angle pdb=" N ALA A 418 " pdb=" CA ALA A 418 " pdb=" C ALA A 418 " ideal model delta sigma weight residual 107.99 115.37 -7.38 1.76e+00 3.23e-01 1.76e+01 angle pdb=" N ALA F 418 " pdb=" CA ALA F 418 " pdb=" C ALA F 418 " ideal model delta sigma weight residual 107.99 115.37 -7.38 1.76e+00 3.23e-01 1.76e+01 ... (remaining 33151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 13429 16.79 - 33.58: 1359 33.58 - 50.37: 295 50.37 - 67.16: 1 67.16 - 83.95: 54 Dihedral angle restraints: 15138 sinusoidal: 6327 harmonic: 8811 Sorted by residual: dihedral pdb=" CA LEU D 662 " pdb=" C LEU D 662 " pdb=" N ILE D 663 " pdb=" CA ILE D 663 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA LEU B 662 " pdb=" C LEU B 662 " pdb=" N ILE B 663 " pdb=" CA ILE B 663 " ideal model delta harmonic sigma weight residual -180.00 -156.29 -23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA LEU G 662 " pdb=" C LEU G 662 " pdb=" N ILE G 663 " pdb=" CA ILE G 663 " ideal model delta harmonic sigma weight residual -180.00 -156.29 -23.71 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 15135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3247 0.061 - 0.123: 566 0.123 - 0.184: 53 0.184 - 0.246: 27 0.246 - 0.307: 31 Chirality restraints: 3924 Sorted by residual: chirality pdb=" CB ILE C 484 " pdb=" CA ILE C 484 " pdb=" CG1 ILE C 484 " pdb=" CG2 ILE C 484 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE G 484 " pdb=" CA ILE G 484 " pdb=" CG1 ILE G 484 " pdb=" CG2 ILE G 484 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE H 484 " pdb=" CA ILE H 484 " pdb=" CG1 ILE H 484 " pdb=" CG2 ILE H 484 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 3921 not shown) Planarity restraints: 4239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 610 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C THR C 610 " -0.037 2.00e-02 2.50e+03 pdb=" O THR C 610 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN C 611 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 610 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C THR A 610 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 610 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN A 611 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 610 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C THR B 610 " -0.037 2.00e-02 2.50e+03 pdb=" O THR B 610 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN B 611 " 0.012 2.00e-02 2.50e+03 ... (remaining 4236 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3285 2.75 - 3.29: 24205 3.29 - 3.83: 37983 3.83 - 4.36: 44508 4.36 - 4.90: 75304 Nonbonded interactions: 185285 Sorted by model distance: nonbonded pdb=" NE2 GLN A 417 " pdb=" OD2 ASP A 432 " model vdw 2.217 3.120 nonbonded pdb=" NE2 GLN B 417 " pdb=" OD2 ASP B 432 " model vdw 2.217 3.120 nonbonded pdb=" NE2 GLN G 417 " pdb=" OD2 ASP G 432 " model vdw 2.217 3.120 nonbonded pdb=" NE2 GLN H 417 " pdb=" OD2 ASP H 432 " model vdw 2.217 3.120 nonbonded pdb=" NE2 GLN E 417 " pdb=" OD2 ASP E 432 " model vdw 2.217 3.120 ... (remaining 185280 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: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 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: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 51.180 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.004 0.040 24471 Z= 0.233 Angle : 0.831 7.780 33156 Z= 0.481 Chirality : 0.056 0.307 3924 Planarity : 0.004 0.028 4239 Dihedral : 14.618 83.946 9396 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.14), residues: 3006 helix: -0.81 (0.13), residues: 1314 sheet: -0.94 (0.22), residues: 558 loop : -1.99 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 445 HIS 0.006 0.001 HIS A 564 PHE 0.007 0.001 PHE F 410 TYR 0.008 0.001 TYR I 420 ARG 0.020 0.001 ARG B 580 Details of bonding type rmsd hydrogen bonds : bond 0.15337 ( 1134) hydrogen bonds : angle 7.47263 ( 3267) covalent geometry : bond 0.00443 (24471) covalent geometry : angle 0.83146 (33156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 392 time to evaluate : 2.773 Fit side-chains REVERT: E 578 ILE cc_start: 0.7949 (mt) cc_final: 0.7607 (mt) REVERT: A 578 ILE cc_start: 0.7944 (mt) cc_final: 0.7583 (mt) REVERT: B 552 MET cc_start: 0.7763 (tpp) cc_final: 0.7476 (tpp) REVERT: B 578 ILE cc_start: 0.7880 (mt) cc_final: 0.7537 (mt) REVERT: B 601 TYR cc_start: 0.7468 (p90) cc_final: 0.7198 (p90) REVERT: C 420 TYR cc_start: 0.7004 (m-80) cc_final: 0.6569 (m-80) REVERT: C 518 GLU cc_start: 0.7812 (tt0) cc_final: 0.7584 (tm-30) REVERT: C 578 ILE cc_start: 0.7911 (mt) cc_final: 0.7525 (mt) REVERT: C 601 TYR cc_start: 0.7573 (p90) cc_final: 0.7292 (p90) REVERT: D 440 MET cc_start: 0.7364 (mtm) cc_final: 0.7098 (mtm) REVERT: D 578 ILE cc_start: 0.7905 (mt) cc_final: 0.7534 (mt) REVERT: F 578 ILE cc_start: 0.7969 (mt) cc_final: 0.7622 (mt) REVERT: F 608 HIS cc_start: 0.7808 (m90) cc_final: 0.7470 (m90) REVERT: G 440 MET cc_start: 0.7230 (mtm) cc_final: 0.6901 (mtm) REVERT: G 578 ILE cc_start: 0.7944 (mt) cc_final: 0.7555 (mt) REVERT: H 578 ILE cc_start: 0.8039 (mt) cc_final: 0.7659 (mt) REVERT: I 552 MET cc_start: 0.7734 (tpp) cc_final: 0.7384 (tpp) REVERT: I 578 ILE cc_start: 0.7961 (mt) cc_final: 0.7559 (mt) outliers start: 9 outliers final: 0 residues processed: 397 average time/residue: 0.4099 time to fit residues: 241.2806 Evaluate side-chains 302 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 173 optimal weight: 20.0000 chunk 269 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 570 ASN ** A 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.210932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.169021 restraints weight = 27279.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.166788 restraints weight = 41642.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.168456 restraints weight = 41101.192| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24471 Z= 0.134 Angle : 0.592 5.816 33156 Z= 0.296 Chirality : 0.045 0.257 3924 Planarity : 0.004 0.033 4239 Dihedral : 4.254 20.146 3285 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.93 % Allowed : 7.20 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3006 helix: 0.38 (0.14), residues: 1386 sheet: -0.82 (0.22), residues: 558 loop : -2.07 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 543 HIS 0.010 0.001 HIS A 608 PHE 0.030 0.001 PHE H 457 TYR 0.009 0.001 TYR D 556 ARG 0.007 0.001 ARG H 580 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 1134) hydrogen bonds : angle 4.94747 ( 3267) covalent geometry : bond 0.00319 (24471) covalent geometry : angle 0.59245 (33156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 328 time to evaluate : 2.507 Fit side-chains REVERT: E 578 ILE cc_start: 0.8042 (mt) cc_final: 0.7824 (mt) REVERT: A 480 MET cc_start: 0.9147 (tpp) cc_final: 0.8874 (mmt) REVERT: A 527 ARG cc_start: 0.7381 (mtt-85) cc_final: 0.7001 (mmt-90) REVERT: B 440 MET cc_start: 0.7202 (mtp) cc_final: 0.6866 (mtm) REVERT: B 578 ILE cc_start: 0.7967 (mt) cc_final: 0.7742 (mt) REVERT: B 601 TYR cc_start: 0.7283 (p90) cc_final: 0.7037 (p90) REVERT: C 578 ILE cc_start: 0.7955 (mt) cc_final: 0.7747 (mt) REVERT: C 601 TYR cc_start: 0.7397 (p90) cc_final: 0.7156 (p90) REVERT: F 556 TYR cc_start: 0.8583 (m-10) cc_final: 0.8300 (m-10) REVERT: F 570 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7880 (p0) REVERT: F 578 ILE cc_start: 0.8006 (mt) cc_final: 0.7804 (mt) REVERT: G 440 MET cc_start: 0.7235 (mtm) cc_final: 0.6967 (mtm) REVERT: H 578 ILE cc_start: 0.8102 (mt) cc_final: 0.7873 (mt) REVERT: I 527 ARG cc_start: 0.7368 (mtt-85) cc_final: 0.6896 (mmt-90) REVERT: I 552 MET cc_start: 0.7863 (tpp) cc_final: 0.7465 (tpp) REVERT: I 578 ILE cc_start: 0.7978 (mt) cc_final: 0.7760 (mt) outliers start: 25 outliers final: 9 residues processed: 352 average time/residue: 0.3620 time to fit residues: 195.9465 Evaluate side-chains 299 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 289 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain H residue 615 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 236 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 253 optimal weight: 0.0570 chunk 288 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 ASN ** A 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.212925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.168274 restraints weight = 27817.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.165812 restraints weight = 44436.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.167232 restraints weight = 43411.018| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 24471 Z= 0.180 Angle : 0.597 5.970 33156 Z= 0.300 Chirality : 0.045 0.231 3924 Planarity : 0.004 0.036 4239 Dihedral : 4.206 17.217 3285 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.49 % Allowed : 9.92 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3006 helix: 0.48 (0.14), residues: 1377 sheet: -0.92 (0.22), residues: 576 loop : -2.16 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 543 HIS 0.006 0.001 HIS I 564 PHE 0.024 0.001 PHE D 457 TYR 0.010 0.001 TYR G 556 ARG 0.007 0.001 ARG A 580 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 1134) hydrogen bonds : angle 4.81477 ( 3267) covalent geometry : bond 0.00453 (24471) covalent geometry : angle 0.59656 (33156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 317 time to evaluate : 2.908 Fit side-chains REVERT: A 552 MET cc_start: 0.8027 (tpp) cc_final: 0.7620 (tpt) REVERT: B 440 MET cc_start: 0.7120 (mtp) cc_final: 0.6745 (mtm) REVERT: B 578 ILE cc_start: 0.8022 (mt) cc_final: 0.7800 (mt) REVERT: C 578 ILE cc_start: 0.8005 (mt) cc_final: 0.7786 (mt) REVERT: C 601 TYR cc_start: 0.7447 (p90) cc_final: 0.7155 (p90) REVERT: C 669 ILE cc_start: 0.7386 (mm) cc_final: 0.7078 (mt) REVERT: F 556 TYR cc_start: 0.8636 (m-10) cc_final: 0.8373 (m-10) REVERT: F 578 ILE cc_start: 0.8086 (mt) cc_final: 0.7867 (mt) REVERT: G 440 MET cc_start: 0.7299 (mtm) cc_final: 0.7010 (mtm) REVERT: H 578 ILE cc_start: 0.8131 (mt) cc_final: 0.7875 (mt) REVERT: H 664 GLN cc_start: 0.5991 (pm20) cc_final: 0.5675 (pm20) REVERT: H 669 ILE cc_start: 0.7492 (mm) cc_final: 0.7187 (mt) REVERT: I 552 MET cc_start: 0.8017 (tpp) cc_final: 0.7738 (tpp) REVERT: I 578 ILE cc_start: 0.7976 (mt) cc_final: 0.7720 (mt) outliers start: 40 outliers final: 14 residues processed: 356 average time/residue: 0.3300 time to fit residues: 187.9573 Evaluate side-chains 314 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 300 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain H residue 657 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 287 optimal weight: 0.9980 chunk 243 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 175 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 211 optimal weight: 0.7980 chunk 188 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 ASN ** A 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.213864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.4017 r_free = 0.4017 target = 0.164732 restraints weight = 28941.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.155969 restraints weight = 32023.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.156267 restraints weight = 25189.576| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24471 Z= 0.128 Angle : 0.571 7.758 33156 Z= 0.281 Chirality : 0.044 0.208 3924 Planarity : 0.004 0.031 4239 Dihedral : 3.943 15.905 3285 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.94 % Allowed : 10.66 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3006 helix: 0.69 (0.14), residues: 1386 sheet: -0.94 (0.21), residues: 576 loop : -1.96 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 543 HIS 0.003 0.001 HIS H 608 PHE 0.032 0.001 PHE G 457 TYR 0.008 0.001 TYR A 556 ARG 0.005 0.000 ARG E 580 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 1134) hydrogen bonds : angle 4.61658 ( 3267) covalent geometry : bond 0.00308 (24471) covalent geometry : angle 0.57106 (33156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 320 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 527 ARG cc_start: 0.7376 (mtt-85) cc_final: 0.6885 (mmt-90) REVERT: E 648 ASP cc_start: 0.7460 (t0) cc_final: 0.7209 (t0) REVERT: E 664 GLN cc_start: 0.5634 (pm20) cc_final: 0.5374 (pm20) REVERT: E 669 ILE cc_start: 0.7167 (mm) cc_final: 0.6739 (mt) REVERT: A 527 ARG cc_start: 0.7336 (mtt-85) cc_final: 0.6912 (mmt-90) REVERT: A 614 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: A 664 GLN cc_start: 0.5564 (pm20) cc_final: 0.5360 (pm20) REVERT: A 669 ILE cc_start: 0.7124 (mm) cc_final: 0.6671 (mt) REVERT: B 433 SER cc_start: 0.8045 (p) cc_final: 0.7760 (t) REVERT: B 440 MET cc_start: 0.7032 (mtp) cc_final: 0.6792 (mtm) REVERT: B 518 GLU cc_start: 0.7959 (tt0) cc_final: 0.7648 (tm-30) REVERT: B 578 ILE cc_start: 0.7975 (mt) cc_final: 0.7669 (mt) REVERT: B 614 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: C 578 ILE cc_start: 0.7987 (mt) cc_final: 0.7720 (mt) REVERT: C 614 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: C 664 GLN cc_start: 0.5816 (pm20) cc_final: 0.5533 (pm20) REVERT: C 669 ILE cc_start: 0.7261 (mm) cc_final: 0.6924 (mt) REVERT: D 527 ARG cc_start: 0.7460 (mtt-85) cc_final: 0.6988 (mmt-90) REVERT: D 614 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7781 (pm20) REVERT: F 527 ARG cc_start: 0.7357 (mtt-85) cc_final: 0.7046 (mmt-90) REVERT: F 556 TYR cc_start: 0.8594 (m-10) cc_final: 0.8283 (m-10) REVERT: F 578 ILE cc_start: 0.8066 (mt) cc_final: 0.7781 (mt) REVERT: F 605 SER cc_start: 0.6304 (OUTLIER) cc_final: 0.6062 (p) REVERT: G 440 MET cc_start: 0.7197 (mtm) cc_final: 0.6871 (mtm) REVERT: G 605 SER cc_start: 0.6612 (OUTLIER) cc_final: 0.6382 (p) REVERT: G 614 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: H 527 ARG cc_start: 0.7364 (mtt-85) cc_final: 0.7030 (mmt-90) REVERT: H 578 ILE cc_start: 0.8135 (mt) cc_final: 0.7837 (mt) REVERT: H 614 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: H 648 ASP cc_start: 0.7584 (t0) cc_final: 0.7272 (t0) REVERT: H 669 ILE cc_start: 0.7136 (mm) cc_final: 0.6795 (mt) REVERT: I 400 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6315 (pt) REVERT: I 578 ILE cc_start: 0.7944 (mt) cc_final: 0.7648 (mt) REVERT: I 669 ILE cc_start: 0.7188 (mm) cc_final: 0.6785 (mt) outliers start: 52 outliers final: 18 residues processed: 371 average time/residue: 0.3131 time to fit residues: 188.2929 Evaluate side-chains 325 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 298 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 614 GLN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 614 GLN Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 605 SER Chi-restraints excluded: chain F residue 614 GLN Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 605 SER Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain I residue 400 LEU Chi-restraints excluded: chain I residue 614 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 293 optimal weight: 0.7980 chunk 222 optimal weight: 0.9990 chunk 205 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 ASN ** A 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 608 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.209377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.164158 restraints weight = 28149.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.161673 restraints weight = 46139.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.163846 restraints weight = 44998.283| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 24471 Z= 0.263 Angle : 0.677 7.084 33156 Z= 0.336 Chirality : 0.049 0.319 3924 Planarity : 0.004 0.029 4239 Dihedral : 4.342 17.159 3285 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.05 % Allowed : 12.27 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.15), residues: 3006 helix: 0.38 (0.14), residues: 1386 sheet: -0.79 (0.22), residues: 558 loop : -2.18 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 445 HIS 0.007 0.002 HIS H 564 PHE 0.023 0.002 PHE G 457 TYR 0.014 0.002 TYR H 420 ARG 0.004 0.001 ARG D 567 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 1134) hydrogen bonds : angle 5.02075 ( 3267) covalent geometry : bond 0.00662 (24471) covalent geometry : angle 0.67665 (33156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 314 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 614 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7141 (pm20) REVERT: E 664 GLN cc_start: 0.5831 (pm20) cc_final: 0.5580 (pm20) REVERT: E 669 ILE cc_start: 0.7670 (mm) cc_final: 0.7348 (mt) REVERT: A 527 ARG cc_start: 0.7383 (mtt-85) cc_final: 0.6952 (mmt-90) REVERT: A 614 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: A 669 ILE cc_start: 0.7682 (mm) cc_final: 0.7339 (mt) REVERT: B 614 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7264 (pm20) REVERT: B 669 ILE cc_start: 0.7882 (mm) cc_final: 0.7550 (mt) REVERT: C 420 TYR cc_start: 0.6908 (m-80) cc_final: 0.6250 (m-80) REVERT: C 614 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: C 669 ILE cc_start: 0.7856 (mm) cc_final: 0.7580 (mt) REVERT: D 614 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: D 669 ILE cc_start: 0.7859 (mm) cc_final: 0.7589 (mt) REVERT: F 556 TYR cc_start: 0.8665 (m-10) cc_final: 0.8413 (m-10) REVERT: F 605 SER cc_start: 0.5789 (OUTLIER) cc_final: 0.5578 (p) REVERT: F 669 ILE cc_start: 0.7610 (mm) cc_final: 0.7280 (mt) REVERT: G 440 MET cc_start: 0.7372 (mtm) cc_final: 0.7117 (mtm) REVERT: G 605 SER cc_start: 0.6071 (OUTLIER) cc_final: 0.5839 (p) REVERT: G 614 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7111 (pm20) REVERT: G 669 ILE cc_start: 0.7702 (mm) cc_final: 0.7449 (mt) REVERT: H 614 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7148 (pm20) REVERT: H 664 GLN cc_start: 0.6203 (pm20) cc_final: 0.5935 (pm20) REVERT: H 669 ILE cc_start: 0.7801 (mm) cc_final: 0.7541 (mt) REVERT: I 400 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6121 (pt) REVERT: I 527 ARG cc_start: 0.7271 (mtt-85) cc_final: 0.6846 (mmt-90) REVERT: I 669 ILE cc_start: 0.7719 (mm) cc_final: 0.7407 (mt) outliers start: 55 outliers final: 24 residues processed: 367 average time/residue: 0.3210 time to fit residues: 190.3119 Evaluate side-chains 332 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 298 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 614 GLN Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 614 GLN Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 605 SER Chi-restraints excluded: chain F residue 614 GLN Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 605 SER Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain H residue 657 LEU Chi-restraints excluded: chain I residue 400 LEU Chi-restraints excluded: chain I residue 614 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 256 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 248 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 213 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 ASN ** A 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.210314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.168393 restraints weight = 27198.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.165275 restraints weight = 44458.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.167431 restraints weight = 41272.750| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24471 Z= 0.130 Angle : 0.587 15.483 33156 Z= 0.288 Chirality : 0.044 0.291 3924 Planarity : 0.004 0.043 4239 Dihedral : 3.949 15.927 3285 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.05 % Allowed : 12.90 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3006 helix: 0.79 (0.14), residues: 1395 sheet: -0.97 (0.21), residues: 576 loop : -1.87 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 445 HIS 0.003 0.001 HIS D 608 PHE 0.029 0.001 PHE H 457 TYR 0.008 0.001 TYR G 556 ARG 0.010 0.000 ARG D 580 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 1134) hydrogen bonds : angle 4.58851 ( 3267) covalent geometry : bond 0.00313 (24471) covalent geometry : angle 0.58720 (33156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 316 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 480 MET cc_start: 0.8433 (tpt) cc_final: 0.7977 (tpt) REVERT: E 527 ARG cc_start: 0.7228 (mtt-85) cc_final: 0.6789 (mmt-90) REVERT: E 614 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7007 (pm20) REVERT: E 664 GLN cc_start: 0.5825 (pm20) cc_final: 0.5461 (pm20) REVERT: E 669 ILE cc_start: 0.7707 (mm) cc_final: 0.7427 (mt) REVERT: A 527 ARG cc_start: 0.7256 (mtt-85) cc_final: 0.6839 (mmt-90) REVERT: A 669 ILE cc_start: 0.7748 (mm) cc_final: 0.7450 (mt) REVERT: B 440 MET cc_start: 0.7075 (mtp) cc_final: 0.6791 (mtm) REVERT: B 518 GLU cc_start: 0.7885 (tt0) cc_final: 0.7675 (tm-30) REVERT: B 614 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7053 (pm20) REVERT: B 669 ILE cc_start: 0.7839 (mm) cc_final: 0.7518 (mt) REVERT: C 614 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7124 (pm20) REVERT: C 669 ILE cc_start: 0.7913 (mm) cc_final: 0.7659 (mt) REVERT: D 496 MET cc_start: 0.8233 (tpp) cc_final: 0.7970 (tpp) REVERT: D 527 ARG cc_start: 0.7357 (mtt-85) cc_final: 0.6896 (mmt-90) REVERT: D 614 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.6904 (pm20) REVERT: D 669 ILE cc_start: 0.7917 (mm) cc_final: 0.7643 (mt) REVERT: F 527 ARG cc_start: 0.7261 (mtt-85) cc_final: 0.6835 (mmt-90) REVERT: F 556 TYR cc_start: 0.8580 (m-10) cc_final: 0.8261 (m-10) REVERT: F 634 THR cc_start: 0.7690 (p) cc_final: 0.7073 (t) REVERT: F 669 ILE cc_start: 0.7536 (mm) cc_final: 0.7244 (mt) REVERT: G 440 MET cc_start: 0.7240 (mtm) cc_final: 0.6978 (mtm) REVERT: G 527 ARG cc_start: 0.7212 (mtt-85) cc_final: 0.6824 (mmt-90) REVERT: G 614 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6768 (pm20) REVERT: G 669 ILE cc_start: 0.7672 (mm) cc_final: 0.7455 (mt) REVERT: H 518 GLU cc_start: 0.7854 (tt0) cc_final: 0.7489 (tm-30) REVERT: H 527 ARG cc_start: 0.7307 (mtt-85) cc_final: 0.6827 (mmt-90) REVERT: H 664 GLN cc_start: 0.6016 (pm20) cc_final: 0.5631 (pm20) REVERT: H 669 ILE cc_start: 0.7800 (mm) cc_final: 0.7534 (mt) REVERT: I 400 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6147 (pt) REVERT: I 527 ARG cc_start: 0.7192 (mtt-85) cc_final: 0.6809 (mmt-90) REVERT: I 669 ILE cc_start: 0.7732 (mm) cc_final: 0.7422 (mt) outliers start: 55 outliers final: 21 residues processed: 368 average time/residue: 0.3537 time to fit residues: 206.7233 Evaluate side-chains 317 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 614 GLN Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 614 GLN Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain G residue 401 THR Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 629 VAL Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain I residue 400 LEU Chi-restraints excluded: chain I residue 614 GLN Chi-restraints excluded: chain I residue 615 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 233 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 226 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 247 optimal weight: 0.6980 chunk 140 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 ASN ** A 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 570 ASN ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 608 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.209431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.167236 restraints weight = 27394.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.164388 restraints weight = 43613.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.166188 restraints weight = 42767.558| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24471 Z= 0.148 Angle : 0.595 15.514 33156 Z= 0.295 Chirality : 0.044 0.250 3924 Planarity : 0.004 0.036 4239 Dihedral : 3.928 15.299 3285 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.72 % Allowed : 13.83 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3006 helix: 0.83 (0.14), residues: 1395 sheet: -0.95 (0.21), residues: 576 loop : -1.82 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 543 HIS 0.006 0.001 HIS I 608 PHE 0.025 0.001 PHE H 457 TYR 0.008 0.001 TYR H 420 ARG 0.007 0.000 ARG D 590 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 1134) hydrogen bonds : angle 4.58114 ( 3267) covalent geometry : bond 0.00364 (24471) covalent geometry : angle 0.59489 (33156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 298 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 527 ARG cc_start: 0.7181 (mtt-85) cc_final: 0.6671 (mmt-90) REVERT: E 664 GLN cc_start: 0.5675 (pm20) cc_final: 0.5416 (pm20) REVERT: E 669 ILE cc_start: 0.7763 (mm) cc_final: 0.7494 (mt) REVERT: A 669 ILE cc_start: 0.7863 (mm) cc_final: 0.7580 (mt) REVERT: B 440 MET cc_start: 0.7132 (mtp) cc_final: 0.6858 (mtm) REVERT: B 518 GLU cc_start: 0.7933 (tt0) cc_final: 0.7698 (tm-30) REVERT: B 614 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6992 (pm20) REVERT: B 669 ILE cc_start: 0.7861 (mm) cc_final: 0.7545 (mt) REVERT: C 420 TYR cc_start: 0.6703 (m-80) cc_final: 0.6209 (m-80) REVERT: C 480 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8423 (tpt) REVERT: C 614 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7085 (pm20) REVERT: C 669 ILE cc_start: 0.7954 (mm) cc_final: 0.7725 (mt) REVERT: D 614 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: D 669 ILE cc_start: 0.7913 (mm) cc_final: 0.7675 (mt) REVERT: F 556 TYR cc_start: 0.8600 (m-10) cc_final: 0.8278 (m-10) REVERT: F 669 ILE cc_start: 0.7658 (mm) cc_final: 0.7382 (mt) REVERT: G 440 MET cc_start: 0.7260 (mtm) cc_final: 0.6972 (mtm) REVERT: G 496 MET cc_start: 0.7914 (ttm) cc_final: 0.7594 (tpp) REVERT: G 527 ARG cc_start: 0.7222 (mtt-85) cc_final: 0.6841 (mmt-90) REVERT: G 614 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6835 (pm20) REVERT: G 633 ASP cc_start: 0.7490 (t70) cc_final: 0.7260 (t0) REVERT: G 634 THR cc_start: 0.7835 (p) cc_final: 0.7571 (t) REVERT: G 669 ILE cc_start: 0.7708 (mm) cc_final: 0.7506 (mt) REVERT: H 518 GLU cc_start: 0.7826 (tt0) cc_final: 0.7508 (tm-30) REVERT: H 614 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.6975 (pm20) REVERT: H 669 ILE cc_start: 0.7810 (mm) cc_final: 0.7536 (mt) REVERT: I 400 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6188 (pt) REVERT: I 669 ILE cc_start: 0.7768 (mm) cc_final: 0.7510 (mt) outliers start: 46 outliers final: 30 residues processed: 341 average time/residue: 0.3465 time to fit residues: 185.1749 Evaluate side-chains 317 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 570 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 614 GLN Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain F residue 614 GLN Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 401 THR Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 629 VAL Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 613 LEU Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain H residue 657 LEU Chi-restraints excluded: chain I residue 400 LEU Chi-restraints excluded: chain I residue 614 GLN Chi-restraints excluded: chain I residue 615 LEU Chi-restraints excluded: chain I residue 657 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.222 > 50: distance: 4 - 9: 19.304 distance: 9 - 10: 15.451 distance: 9 - 15: 16.320 distance: 10 - 11: 28.274 distance: 10 - 13: 7.794 distance: 11 - 12: 25.406 distance: 11 - 16: 25.870 distance: 13 - 14: 35.248 distance: 14 - 15: 23.938 distance: 16 - 17: 16.069 distance: 17 - 18: 21.629 distance: 17 - 20: 18.504 distance: 18 - 19: 24.408 distance: 18 - 21: 22.336 distance: 21 - 22: 13.189 distance: 22 - 23: 9.534 distance: 22 - 25: 16.682 distance: 23 - 24: 9.178 distance: 23 - 30: 5.082 distance: 25 - 26: 20.271 distance: 26 - 27: 15.345 distance: 27 - 28: 20.517 distance: 27 - 29: 15.303 distance: 30 - 31: 7.878 distance: 31 - 32: 34.378 distance: 31 - 34: 12.701 distance: 32 - 33: 20.214 distance: 32 - 35: 6.576 distance: 35 - 36: 11.615 distance: 36 - 37: 25.565 distance: 36 - 39: 5.459 distance: 37 - 38: 26.143 distance: 37 - 43: 24.993 distance: 39 - 40: 11.809 distance: 40 - 41: 37.565 distance: 40 - 42: 13.139 distance: 43 - 44: 15.068 distance: 44 - 45: 12.334 distance: 44 - 47: 19.307 distance: 45 - 55: 19.441 distance: 46 - 127: 6.423 distance: 48 - 49: 13.280 distance: 48 - 50: 20.458 distance: 49 - 51: 14.568 distance: 50 - 52: 23.239 distance: 51 - 53: 14.121 distance: 52 - 53: 17.329 distance: 53 - 54: 19.265 distance: 55 - 56: 8.442 distance: 55 - 157: 17.474 distance: 56 - 57: 15.301 distance: 56 - 59: 16.044 distance: 57 - 58: 36.226 distance: 57 - 63: 23.668 distance: 58 - 154: 20.796 distance: 59 - 60: 23.310 distance: 60 - 61: 22.863 distance: 60 - 62: 36.201 distance: 63 - 64: 12.004 distance: 63 - 110: 13.797 distance: 64 - 65: 23.915 distance: 64 - 67: 13.795 distance: 65 - 66: 24.558 distance: 65 - 71: 32.764 distance: 66 - 107: 30.903 distance: 67 - 68: 25.068 distance: 68 - 69: 31.179 distance: 68 - 70: 34.914 distance: 71 - 72: 19.996 distance: 72 - 73: 19.338 distance: 72 - 75: 13.798 distance: 73 - 74: 25.495 distance: 73 - 79: 31.882 distance: 75 - 76: 29.111 distance: 75 - 77: 18.137 distance: 76 - 78: 25.139 distance: 79 - 80: 18.863 distance: 80 - 81: 37.806 distance: 81 - 82: 27.245 distance: 81 - 83: 29.574