Starting phenix.real_space_refine on Thu Mar 5 16:59:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fec_31552/03_2026/7fec_31552.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fec_31552/03_2026/7fec_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_31552/03_2026/7fec_31552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fec_31552/03_2026/7fec_31552.map" model { file = "/net/cci-nas-00/data/ceres_data/7fec_31552/03_2026/7fec_31552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fec_31552/03_2026/7fec_31552.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 5.34, per 1000 atoms: 0.22 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: 2.09 Conformation dependent library (CDL) restraints added in 1.3 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: 0.85 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: 5.56 Time building geometry restraints manager: 2.83 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: 0.08 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 6.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.080 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.210 ------------------------------------------------------------------------------- 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 : 14.43 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.020 0.001 ARG B 580 TYR 0.008 0.001 TYR I 420 PHE 0.007 0.001 PHE F 410 TRP 0.004 0.001 TRP D 445 HIS 0.006 0.001 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00443 (24471) covalent geometry : angle 0.83146 (33156) hydrogen bonds : bond 0.15337 ( 1134) hydrogen bonds : angle 7.47263 ( 3267) *********************** 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 : 0.765 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: 0.1855 time to fit residues: 109.2086 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 : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 0.0770 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 570 ASN A 608 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.217607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.171145 restraints weight = 27876.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.167579 restraints weight = 44997.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.170292 restraints weight = 40257.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.169999 restraints weight = 24111.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.170981 restraints weight = 22714.337| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24471 Z= 0.121 Angle : 0.581 5.846 33156 Z= 0.291 Chirality : 0.044 0.250 3924 Planarity : 0.004 0.034 4239 Dihedral : 4.193 20.017 3285 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.97 % Allowed : 7.08 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 3006 helix: 0.47 (0.14), residues: 1386 sheet: -0.82 (0.22), residues: 558 loop : -2.02 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 580 TYR 0.008 0.001 TYR D 556 PHE 0.030 0.001 PHE E 457 TRP 0.003 0.001 TRP E 445 HIS 0.008 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00283 (24471) covalent geometry : angle 0.58138 (33156) hydrogen bonds : bond 0.03905 ( 1134) hydrogen bonds : angle 4.84908 ( 3267) *********************** 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 361 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 335 time to evaluate : 0.969 Fit side-chains REVERT: E 480 MET cc_start: 0.8682 (mmm) cc_final: 0.7365 (tpt) REVERT: E 578 ILE cc_start: 0.8070 (mt) cc_final: 0.7804 (mt) REVERT: A 527 ARG cc_start: 0.7402 (mtt-85) cc_final: 0.6966 (mmt-90) REVERT: A 578 ILE cc_start: 0.7985 (mt) cc_final: 0.7784 (mt) REVERT: B 440 MET cc_start: 0.7152 (mtp) cc_final: 0.6754 (mtm) REVERT: B 480 MET cc_start: 0.8785 (mmm) cc_final: 0.7994 (tpt) REVERT: B 527 ARG cc_start: 0.7502 (mtt-85) cc_final: 0.6973 (mmt-90) REVERT: B 578 ILE cc_start: 0.8016 (mt) cc_final: 0.7739 (mt) REVERT: B 601 TYR cc_start: 0.7373 (p90) cc_final: 0.7104 (p90) REVERT: C 480 MET cc_start: 0.8814 (mmt) cc_final: 0.8461 (tpt) REVERT: C 578 ILE cc_start: 0.7998 (mt) cc_final: 0.7727 (mt) REVERT: C 601 TYR cc_start: 0.7443 (p90) cc_final: 0.7169 (p90) REVERT: D 578 ILE cc_start: 0.7961 (mt) cc_final: 0.7735 (mt) REVERT: F 556 TYR cc_start: 0.8588 (m-10) cc_final: 0.8290 (m-10) REVERT: F 578 ILE cc_start: 0.8051 (mt) cc_final: 0.7792 (mt) REVERT: G 440 MET cc_start: 0.7229 (mtm) cc_final: 0.6932 (mtm) REVERT: G 578 ILE cc_start: 0.7956 (mt) cc_final: 0.7700 (mt) REVERT: H 578 ILE cc_start: 0.8155 (mt) cc_final: 0.7852 (mt) REVERT: I 552 MET cc_start: 0.7859 (tpp) cc_final: 0.7432 (tpt) REVERT: I 578 ILE cc_start: 0.8038 (mt) cc_final: 0.7769 (mt) outliers start: 26 outliers final: 10 residues processed: 360 average time/residue: 0.1781 time to fit residues: 99.1335 Evaluate side-chains 302 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 292 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 401 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain G residue 615 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 190 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 274 optimal weight: 0.9980 chunk 260 optimal weight: 0.7980 chunk 221 optimal weight: 10.0000 chunk 182 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 102 optimal weight: 0.0980 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 570 ASN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 434 GLN ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN G 434 GLN ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.217881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.171521 restraints weight = 27949.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.169222 restraints weight = 40971.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.170943 restraints weight = 41314.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.171017 restraints weight = 24248.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.171793 restraints weight = 22281.657| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24471 Z= 0.117 Angle : 0.538 5.728 33156 Z= 0.270 Chirality : 0.043 0.197 3924 Planarity : 0.003 0.033 4239 Dihedral : 3.941 16.545 3285 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.60 % Allowed : 9.96 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.15), residues: 3006 helix: 0.80 (0.14), residues: 1386 sheet: -0.90 (0.22), residues: 576 loop : -1.92 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 580 TYR 0.007 0.001 TYR B 556 PHE 0.021 0.001 PHE F 457 TRP 0.004 0.001 TRP D 543 HIS 0.005 0.001 HIS C 608 Details of bonding type rmsd covalent geometry : bond 0.00282 (24471) covalent geometry : angle 0.53806 (33156) hydrogen bonds : bond 0.03580 ( 1134) hydrogen bonds : angle 4.53943 ( 3267) *********************** 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 373 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 330 time to evaluate : 0.921 Fit side-chains REVERT: E 527 ARG cc_start: 0.7340 (mtt-85) cc_final: 0.6871 (mmt-90) REVERT: E 578 ILE cc_start: 0.8069 (mt) cc_final: 0.7866 (mt) REVERT: E 648 ASP cc_start: 0.7393 (t0) cc_final: 0.7170 (t0) REVERT: A 552 MET cc_start: 0.7933 (tpp) cc_final: 0.7422 (tpt) REVERT: B 440 MET cc_start: 0.7211 (mtp) cc_final: 0.6920 (mtm) REVERT: B 518 GLU cc_start: 0.7976 (tt0) cc_final: 0.7677 (tm-30) REVERT: B 527 ARG cc_start: 0.7392 (mtt-85) cc_final: 0.6932 (mmt-90) REVERT: B 578 ILE cc_start: 0.8004 (mt) cc_final: 0.7777 (mt) REVERT: B 601 TYR cc_start: 0.7394 (p90) cc_final: 0.7103 (p90) REVERT: B 648 ASP cc_start: 0.7461 (t0) cc_final: 0.7225 (t0) REVERT: C 578 ILE cc_start: 0.7995 (mt) cc_final: 0.7777 (mt) REVERT: C 601 TYR cc_start: 0.7442 (p90) cc_final: 0.7151 (p90) REVERT: D 480 MET cc_start: 0.9143 (tpp) cc_final: 0.8464 (tpt) REVERT: D 527 ARG cc_start: 0.7482 (mtt-85) cc_final: 0.7062 (mmt-90) REVERT: D 578 ILE cc_start: 0.7917 (mt) cc_final: 0.7698 (mt) REVERT: D 648 ASP cc_start: 0.7546 (t0) cc_final: 0.7332 (t0) REVERT: D 664 GLN cc_start: 0.5811 (pm20) cc_final: 0.5553 (pm20) REVERT: F 527 ARG cc_start: 0.7319 (mtt-85) cc_final: 0.6982 (mmt-90) REVERT: F 556 TYR cc_start: 0.8603 (m-10) cc_final: 0.8213 (m-10) REVERT: F 578 ILE cc_start: 0.8058 (mt) cc_final: 0.7836 (mt) REVERT: F 613 LEU cc_start: 0.8387 (mp) cc_final: 0.8169 (mp) REVERT: F 648 ASP cc_start: 0.7485 (t0) cc_final: 0.7253 (t0) REVERT: F 664 GLN cc_start: 0.5669 (pm20) cc_final: 0.5461 (pm20) REVERT: G 440 MET cc_start: 0.7225 (mtm) cc_final: 0.6938 (mtm) REVERT: G 578 ILE cc_start: 0.7988 (mt) cc_final: 0.7772 (mt) REVERT: H 480 MET cc_start: 0.9145 (tpp) cc_final: 0.8747 (tpt) REVERT: H 527 ARG cc_start: 0.7417 (mtt-85) cc_final: 0.7103 (mmt-90) REVERT: H 578 ILE cc_start: 0.8154 (mt) cc_final: 0.7911 (mt) REVERT: H 648 ASP cc_start: 0.7527 (t0) cc_final: 0.7244 (t0) REVERT: H 664 GLN cc_start: 0.5848 (pm20) cc_final: 0.5548 (pm20) REVERT: I 578 ILE cc_start: 0.7991 (mt) cc_final: 0.7707 (mt) outliers start: 43 outliers final: 8 residues processed: 372 average time/residue: 0.1550 time to fit residues: 93.0146 Evaluate side-chains 309 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 301 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain H residue 615 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 ASN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** C 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 GLN ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.206217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.163822 restraints weight = 27434.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.160639 restraints weight = 45350.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.162687 restraints weight = 42536.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.162359 restraints weight = 25049.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.163250 restraints weight = 23178.101| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 24471 Z= 0.221 Angle : 0.645 7.599 33156 Z= 0.321 Chirality : 0.047 0.291 3924 Planarity : 0.004 0.031 4239 Dihedral : 4.209 16.106 3285 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.09 % Allowed : 10.92 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.15), residues: 3006 helix: 0.57 (0.14), residues: 1386 sheet: -0.95 (0.21), residues: 576 loop : -2.07 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 580 TYR 0.011 0.002 TYR D 420 PHE 0.031 0.002 PHE G 457 TRP 0.007 0.001 TRP B 445 HIS 0.007 0.002 HIS H 564 Details of bonding type rmsd covalent geometry : bond 0.00556 (24471) covalent geometry : angle 0.64534 (33156) hydrogen bonds : bond 0.04268 ( 1134) hydrogen bonds : angle 4.93870 ( 3267) *********************** 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 375 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 319 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 480 MET cc_start: 0.8685 (mmm) cc_final: 0.7810 (tpt) REVERT: E 669 ILE cc_start: 0.7561 (mm) cc_final: 0.7227 (mt) REVERT: A 614 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.6994 (pm20) REVERT: A 669 ILE cc_start: 0.7527 (mm) cc_final: 0.7166 (mt) REVERT: B 440 MET cc_start: 0.7330 (mtp) cc_final: 0.7018 (mtm) REVERT: B 527 ARG cc_start: 0.7385 (mtt-85) cc_final: 0.7147 (mtt-85) REVERT: B 614 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7186 (pm20) REVERT: B 664 GLN cc_start: 0.5859 (pm20) cc_final: 0.5650 (pm20) REVERT: C 400 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6218 (pt) REVERT: C 420 TYR cc_start: 0.6823 (m-80) cc_final: 0.6149 (m-80) REVERT: C 614 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7181 (pm20) REVERT: C 664 GLN cc_start: 0.5977 (pm20) cc_final: 0.5755 (pm20) REVERT: C 669 ILE cc_start: 0.7644 (mm) cc_final: 0.7346 (mt) REVERT: D 614 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6989 (pm20) REVERT: D 669 ILE cc_start: 0.7741 (mm) cc_final: 0.7458 (mt) REVERT: F 556 TYR cc_start: 0.8620 (m-10) cc_final: 0.8300 (m-10) REVERT: F 664 GLN cc_start: 0.5943 (pm20) cc_final: 0.5690 (pm20) REVERT: F 669 ILE cc_start: 0.7569 (mm) cc_final: 0.7263 (mt) REVERT: G 440 MET cc_start: 0.7340 (mtm) cc_final: 0.7059 (mtm) REVERT: G 605 SER cc_start: 0.6079 (OUTLIER) cc_final: 0.5834 (p) REVERT: G 614 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7061 (pm20) REVERT: G 669 ILE cc_start: 0.7600 (mm) cc_final: 0.7314 (mt) REVERT: H 527 ARG cc_start: 0.7300 (mtt-85) cc_final: 0.7006 (mmt-90) REVERT: H 614 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: H 648 ASP cc_start: 0.7503 (t0) cc_final: 0.7241 (t0) REVERT: H 669 ILE cc_start: 0.7626 (mm) cc_final: 0.7358 (mt) REVERT: I 400 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6049 (pt) REVERT: I 527 ARG cc_start: 0.7173 (mtt-85) cc_final: 0.6781 (mmt-90) REVERT: I 648 ASP cc_start: 0.7417 (t0) cc_final: 0.7190 (t0) REVERT: I 669 ILE cc_start: 0.7552 (mm) cc_final: 0.7210 (mt) outliers start: 56 outliers final: 25 residues processed: 374 average time/residue: 0.1489 time to fit residues: 91.7458 Evaluate side-chains 336 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 302 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 614 GLN Chi-restraints excluded: chain E residue 657 LEU 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 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 400 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 381 THR 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 614 GLN 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 657 LEU Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain H residue 615 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 152 optimal weight: 2.9990 chunk 237 optimal weight: 0.4980 chunk 247 optimal weight: 0.9990 chunk 102 optimal weight: 0.0070 chunk 93 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 199 optimal weight: 0.0980 chunk 198 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 overall best weight: 0.4600 ------------------------------------------------------------------------------- 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 434 GLN ** 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 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.213558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.172460 restraints weight = 27034.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.170431 restraints weight = 36686.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.171835 restraints weight = 38112.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.171595 restraints weight = 25089.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.172559 restraints weight = 22584.200| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24471 Z= 0.105 Angle : 0.546 8.638 33156 Z= 0.272 Chirality : 0.043 0.237 3924 Planarity : 0.003 0.029 4239 Dihedral : 3.765 15.971 3285 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.09 % Allowed : 11.74 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.15), residues: 3006 helix: 1.00 (0.14), residues: 1395 sheet: -0.94 (0.21), residues: 576 loop : -1.72 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 580 TYR 0.005 0.001 TYR A 556 PHE 0.023 0.001 PHE G 457 TRP 0.005 0.001 TRP E 445 HIS 0.003 0.001 HIS I 608 Details of bonding type rmsd covalent geometry : bond 0.00243 (24471) covalent geometry : angle 0.54585 (33156) hydrogen bonds : bond 0.03326 ( 1134) hydrogen bonds : angle 4.46356 ( 3267) *********************** 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 374 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 318 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: E 518 GLU cc_start: 0.7845 (tt0) cc_final: 0.7582 (tm-30) REVERT: E 527 ARG cc_start: 0.7205 (mtt-85) cc_final: 0.6687 (mmt-90) REVERT: E 614 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: E 634 THR cc_start: 0.7532 (p) cc_final: 0.7286 (t) REVERT: E 669 ILE cc_start: 0.7508 (mm) cc_final: 0.7161 (mt) REVERT: A 634 THR cc_start: 0.7540 (p) cc_final: 0.7194 (t) REVERT: A 669 ILE cc_start: 0.7568 (mm) cc_final: 0.7221 (mt) REVERT: B 440 MET cc_start: 0.7216 (mtp) cc_final: 0.6971 (mtm) REVERT: B 518 GLU cc_start: 0.7918 (tt0) cc_final: 0.7652 (tm-30) REVERT: B 527 ARG cc_start: 0.7316 (mtt-85) cc_final: 0.6910 (mmt-90) REVERT: B 614 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: B 669 ILE cc_start: 0.7672 (mm) cc_final: 0.7331 (mt) REVERT: C 420 TYR cc_start: 0.6712 (m-80) cc_final: 0.6093 (m-80) REVERT: C 518 GLU cc_start: 0.7768 (tt0) cc_final: 0.7566 (tm-30) REVERT: C 614 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7044 (pm20) REVERT: C 664 GLN cc_start: 0.5666 (pm20) cc_final: 0.5281 (pm20) REVERT: C 669 ILE cc_start: 0.7701 (mm) cc_final: 0.7417 (mt) REVERT: D 480 MET cc_start: 0.9141 (tpp) cc_final: 0.8690 (tpt) REVERT: D 527 ARG cc_start: 0.7328 (mtt-85) cc_final: 0.6914 (mmt-90) REVERT: D 614 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: D 634 THR cc_start: 0.7511 (p) cc_final: 0.7194 (t) REVERT: D 669 ILE cc_start: 0.7731 (mm) cc_final: 0.7450 (mt) REVERT: F 527 ARG cc_start: 0.7205 (mtt-85) cc_final: 0.6927 (mmt-90) REVERT: F 556 TYR cc_start: 0.8503 (m-10) cc_final: 0.8152 (m-10) REVERT: F 634 THR cc_start: 0.7612 (p) cc_final: 0.7347 (t) REVERT: F 669 ILE cc_start: 0.7589 (mm) cc_final: 0.7277 (mt) REVERT: G 440 MET cc_start: 0.7218 (mtm) cc_final: 0.6921 (mtm) REVERT: G 527 ARG cc_start: 0.7195 (mtt-85) cc_final: 0.6949 (mmt-90) REVERT: G 605 SER cc_start: 0.5936 (OUTLIER) cc_final: 0.5730 (p) REVERT: G 669 ILE cc_start: 0.7533 (mm) cc_final: 0.7267 (mt) REVERT: H 518 GLU cc_start: 0.7872 (tt0) cc_final: 0.7543 (tm-30) REVERT: H 614 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: H 664 GLN cc_start: 0.5776 (pm20) cc_final: 0.5482 (pm20) REVERT: H 669 ILE cc_start: 0.7630 (mm) cc_final: 0.7347 (mt) REVERT: I 527 ARG cc_start: 0.7093 (mtt-85) cc_final: 0.6786 (mmt-90) REVERT: I 614 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: I 669 ILE cc_start: 0.7519 (mm) cc_final: 0.7191 (mt) outliers start: 56 outliers final: 18 residues processed: 371 average time/residue: 0.1498 time to fit residues: 90.4139 Evaluate side-chains 311 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 286 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 614 GLN Chi-restraints excluded: chain E residue 615 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 381 THR 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 401 THR Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 605 SER Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 629 VAL Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain I residue 614 GLN Chi-restraints excluded: chain I residue 615 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 139 optimal weight: 0.9980 chunk 272 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 181 optimal weight: 0.0570 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 284 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 171 optimal weight: 0.1980 chunk 208 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 434 GLN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 GLN ** 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.218385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171954 restraints weight = 27790.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.169286 restraints weight = 39170.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.171055 restraints weight = 39245.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.171106 restraints weight = 23999.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.171777 restraints weight = 22123.535| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24471 Z= 0.111 Angle : 0.576 13.618 33156 Z= 0.278 Chirality : 0.042 0.204 3924 Planarity : 0.003 0.032 4239 Dihedral : 3.625 16.110 3285 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.79 % Allowed : 12.49 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.15), residues: 3006 helix: 1.12 (0.14), residues: 1395 sheet: -0.86 (0.21), residues: 576 loop : -1.62 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 580 TYR 0.005 0.001 TYR H 420 PHE 0.026 0.001 PHE D 457 TRP 0.005 0.001 TRP I 654 HIS 0.004 0.001 HIS D 608 Details of bonding type rmsd covalent geometry : bond 0.00261 (24471) covalent geometry : angle 0.57628 (33156) hydrogen bonds : bond 0.03319 ( 1134) hydrogen bonds : angle 4.36744 ( 3267) *********************** 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 346 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 298 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 518 GLU cc_start: 0.7899 (tt0) cc_final: 0.7611 (tm-30) REVERT: E 527 ARG cc_start: 0.7252 (mtt-85) cc_final: 0.6804 (mmt-90) REVERT: E 634 THR cc_start: 0.7776 (p) cc_final: 0.7438 (t) REVERT: E 669 ILE cc_start: 0.7515 (mm) cc_final: 0.7168 (mt) REVERT: A 634 THR cc_start: 0.7664 (p) cc_final: 0.7294 (t) REVERT: A 669 ILE cc_start: 0.7602 (mm) cc_final: 0.7284 (mt) REVERT: B 440 MET cc_start: 0.7193 (mtp) cc_final: 0.6836 (mtm) REVERT: B 518 GLU cc_start: 0.7915 (tt0) cc_final: 0.7642 (tm-30) REVERT: B 527 ARG cc_start: 0.7312 (mtt-85) cc_final: 0.6997 (mmt-90) REVERT: B 614 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7102 (pm20) REVERT: B 669 ILE cc_start: 0.7705 (mm) cc_final: 0.7390 (mt) REVERT: C 420 TYR cc_start: 0.6833 (m-80) cc_final: 0.6129 (m-80) REVERT: C 518 GLU cc_start: 0.7810 (tt0) cc_final: 0.7543 (tm-30) REVERT: C 527 ARG cc_start: 0.7264 (mtt-85) cc_final: 0.6897 (mmt-90) REVERT: C 614 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7240 (pm20) REVERT: C 669 ILE cc_start: 0.7690 (mm) cc_final: 0.7408 (mt) REVERT: D 480 MET cc_start: 0.9117 (tpp) cc_final: 0.8701 (tpt) REVERT: D 527 ARG cc_start: 0.7437 (mtt-85) cc_final: 0.7025 (mmt-90) REVERT: D 614 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7028 (pm20) REVERT: D 634 THR cc_start: 0.7708 (p) cc_final: 0.7348 (t) REVERT: D 669 ILE cc_start: 0.7742 (mm) cc_final: 0.7442 (mt) REVERT: F 556 TYR cc_start: 0.8580 (m-10) cc_final: 0.8279 (m-10) REVERT: F 634 THR cc_start: 0.7803 (p) cc_final: 0.7149 (t) REVERT: F 669 ILE cc_start: 0.7612 (mm) cc_final: 0.7292 (mt) REVERT: G 605 SER cc_start: 0.6130 (OUTLIER) cc_final: 0.5881 (p) REVERT: G 634 THR cc_start: 0.7828 (p) cc_final: 0.7487 (t) REVERT: G 669 ILE cc_start: 0.7587 (mm) cc_final: 0.7331 (mt) REVERT: H 518 GLU cc_start: 0.7916 (tt0) cc_final: 0.7552 (tm-30) REVERT: H 614 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7058 (pm20) REVERT: H 664 GLN cc_start: 0.5706 (pm20) cc_final: 0.5422 (pm20) REVERT: H 669 ILE cc_start: 0.7617 (mm) cc_final: 0.7329 (mt) REVERT: I 527 ARG cc_start: 0.7170 (mtt-85) cc_final: 0.6877 (mmt-90) REVERT: I 669 ILE cc_start: 0.7612 (mm) cc_final: 0.7266 (mt) outliers start: 48 outliers final: 26 residues processed: 344 average time/residue: 0.1516 time to fit residues: 84.0364 Evaluate side-chains 306 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 275 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 400 LEU 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 A residue 657 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 434 GLN 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 381 THR 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 G residue 434 GLN Chi-restraints excluded: chain G residue 605 SER Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 629 VAL Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain H residue 615 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 199 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 280 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 7 optimal weight: 0.2980 chunk 177 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN ** 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 434 GLN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 570 ASN I 434 GLN ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 608 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.212678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.169932 restraints weight = 27202.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.167068 restraints weight = 44682.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.169308 restraints weight = 38613.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.168639 restraints weight = 26827.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.169733 restraints weight = 24444.721| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2304 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= 0.126 Angle : 0.585 15.037 33156 Z= 0.281 Chirality : 0.043 0.181 3924 Planarity : 0.004 0.037 4239 Dihedral : 3.636 15.452 3285 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.79 % Allowed : 13.57 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 3006 helix: 1.13 (0.14), residues: 1395 sheet: -0.89 (0.21), residues: 576 loop : -1.54 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 580 TYR 0.007 0.001 TYR G 556 PHE 0.017 0.001 PHE G 457 TRP 0.005 0.001 TRP I 654 HIS 0.004 0.001 HIS I 608 Details of bonding type rmsd covalent geometry : bond 0.00304 (24471) covalent geometry : angle 0.58530 (33156) hydrogen bonds : bond 0.03374 ( 1134) hydrogen bonds : angle 4.37554 ( 3267) *********************** 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 339 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 291 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 518 GLU cc_start: 0.8005 (tt0) cc_final: 0.7678 (tm-30) REVERT: E 614 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: E 634 THR cc_start: 0.7658 (p) cc_final: 0.7340 (t) REVERT: E 669 ILE cc_start: 0.7682 (mm) cc_final: 0.7363 (mt) REVERT: A 527 ARG cc_start: 0.7105 (mtt-85) cc_final: 0.6728 (mmt-90) REVERT: A 669 ILE cc_start: 0.7698 (mm) cc_final: 0.7396 (mt) REVERT: B 440 MET cc_start: 0.7222 (mtp) cc_final: 0.6895 (mtm) REVERT: B 518 GLU cc_start: 0.7890 (tt0) cc_final: 0.7586 (tm-30) REVERT: B 614 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: B 669 ILE cc_start: 0.7805 (mm) cc_final: 0.7494 (mt) REVERT: C 420 TYR cc_start: 0.6823 (m-80) cc_final: 0.6071 (m-80) REVERT: C 480 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8258 (tpt) REVERT: C 518 GLU cc_start: 0.7788 (tt0) cc_final: 0.7574 (tm-30) REVERT: C 527 ARG cc_start: 0.7247 (mtt-85) cc_final: 0.6863 (mmt-90) REVERT: C 614 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7069 (pm20) REVERT: C 669 ILE cc_start: 0.7791 (mm) cc_final: 0.7574 (mt) REVERT: D 480 MET cc_start: 0.9122 (tpp) cc_final: 0.8773 (tpt) REVERT: D 527 ARG cc_start: 0.7426 (mtt-85) cc_final: 0.7022 (mmt-90) REVERT: D 614 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6804 (pm20) REVERT: D 633 ASP cc_start: 0.7471 (t0) cc_final: 0.7189 (t0) REVERT: D 669 ILE cc_start: 0.7847 (mm) cc_final: 0.7587 (mt) REVERT: F 480 MET cc_start: 0.8861 (tpt) cc_final: 0.8548 (tpt) REVERT: F 527 ARG cc_start: 0.7183 (mtt-85) cc_final: 0.6883 (mmt-90) REVERT: F 552 MET cc_start: 0.7840 (tpp) cc_final: 0.7534 (tpp) REVERT: F 556 TYR cc_start: 0.8605 (m-10) cc_final: 0.8209 (m-10) REVERT: F 669 ILE cc_start: 0.7679 (mm) cc_final: 0.7388 (mt) REVERT: G 527 ARG cc_start: 0.7158 (mtt-85) cc_final: 0.6863 (mmt-90) REVERT: G 605 SER cc_start: 0.5948 (OUTLIER) cc_final: 0.5705 (p) REVERT: G 634 THR cc_start: 0.7735 (p) cc_final: 0.7432 (t) REVERT: G 669 ILE cc_start: 0.7659 (mm) cc_final: 0.7430 (mt) REVERT: H 518 GLU cc_start: 0.7943 (tt0) cc_final: 0.7516 (tm-30) REVERT: H 664 GLN cc_start: 0.5746 (pm20) cc_final: 0.5410 (pm20) REVERT: H 669 ILE cc_start: 0.7689 (mm) cc_final: 0.7432 (mt) REVERT: I 400 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6178 (pt) REVERT: I 434 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.6260 (pm20) REVERT: I 669 ILE cc_start: 0.7714 (mm) cc_final: 0.7363 (mt) outliers start: 48 outliers final: 29 residues processed: 336 average time/residue: 0.1508 time to fit residues: 81.5408 Evaluate side-chains 310 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 273 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 434 GLN Chi-restraints excluded: chain E residue 570 ASN 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 400 LEU Chi-restraints excluded: chain A residue 570 ASN 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 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 381 THR 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 434 GLN 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 G residue 605 SER 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 434 GLN Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain I residue 400 LEU Chi-restraints excluded: chain I residue 434 GLN Chi-restraints excluded: chain I residue 614 GLN Chi-restraints excluded: chain I residue 615 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 137 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 179 optimal weight: 0.5980 chunk 292 optimal weight: 10.0000 chunk 283 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 240 optimal weight: 0.0050 chunk 264 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 185 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 GLN ** 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 434 GLN ** 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 434 GLN ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 GLN ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 GLN ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 570 ASN I 434 GLN ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 608 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.219101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.172770 restraints weight = 27849.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.169919 restraints weight = 41083.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.171810 restraints weight = 39543.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.171845 restraints weight = 24141.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.172502 restraints weight = 22302.408| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2411 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= 0.113 Angle : 0.577 13.578 33156 Z= 0.280 Chirality : 0.042 0.170 3924 Planarity : 0.004 0.040 4239 Dihedral : 3.579 15.978 3285 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.83 % Allowed : 13.83 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3006 helix: 1.26 (0.14), residues: 1395 sheet: -0.91 (0.21), residues: 576 loop : -1.46 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 580 TYR 0.005 0.001 TYR D 420 PHE 0.018 0.001 PHE D 637 TRP 0.005 0.001 TRP I 654 HIS 0.004 0.001 HIS I 608 Details of bonding type rmsd covalent geometry : bond 0.00267 (24471) covalent geometry : angle 0.57661 (33156) hydrogen bonds : bond 0.03299 ( 1134) hydrogen bonds : angle 4.31719 ( 3267) *********************** REFINEMENT MACRO_CYCLE 8 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 347 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 298 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 480 MET cc_start: 0.9039 (tpt) cc_final: 0.7914 (tpt) REVERT: E 518 GLU cc_start: 0.7891 (tt0) cc_final: 0.7588 (tm-30) REVERT: E 527 ARG cc_start: 0.7186 (mtt-85) cc_final: 0.6747 (mmt-90) REVERT: E 613 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7978 (mp) REVERT: E 614 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7055 (pm20) REVERT: E 634 THR cc_start: 0.7772 (p) cc_final: 0.7429 (t) REVERT: E 669 ILE cc_start: 0.7658 (mm) cc_final: 0.7321 (mt) REVERT: A 527 ARG cc_start: 0.7125 (mtt-85) cc_final: 0.6761 (mmt-90) REVERT: A 669 ILE cc_start: 0.7691 (mm) cc_final: 0.7365 (mt) REVERT: B 440 MET cc_start: 0.7181 (mtp) cc_final: 0.6795 (mtm) REVERT: B 518 GLU cc_start: 0.7912 (tt0) cc_final: 0.7620 (tm-30) REVERT: B 527 ARG cc_start: 0.7141 (mtt-85) cc_final: 0.6807 (mmt-90) REVERT: B 614 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7087 (pm20) REVERT: B 669 ILE cc_start: 0.7757 (mm) cc_final: 0.7444 (mt) REVERT: C 420 TYR cc_start: 0.6846 (m-80) cc_final: 0.6117 (m-80) REVERT: C 518 GLU cc_start: 0.7785 (tt0) cc_final: 0.7534 (tm-30) REVERT: C 527 ARG cc_start: 0.7234 (mtt-85) cc_final: 0.6874 (mmt-90) REVERT: C 614 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: C 669 ILE cc_start: 0.7750 (mm) cc_final: 0.7504 (mt) REVERT: D 614 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7032 (pm20) REVERT: D 669 ILE cc_start: 0.7835 (mm) cc_final: 0.7562 (mt) REVERT: F 480 MET cc_start: 0.8807 (tpt) cc_final: 0.8498 (tpt) REVERT: F 527 ARG cc_start: 0.7246 (mtt-85) cc_final: 0.6929 (mmt-90) REVERT: F 552 MET cc_start: 0.7808 (tpp) cc_final: 0.7548 (tpp) REVERT: F 556 TYR cc_start: 0.8613 (m-10) cc_final: 0.8203 (m-10) REVERT: F 669 ILE cc_start: 0.7638 (mm) cc_final: 0.7313 (mt) REVERT: G 434 GLN cc_start: 0.6418 (OUTLIER) cc_final: 0.6182 (pm20) REVERT: G 527 ARG cc_start: 0.7181 (mtt-85) cc_final: 0.6877 (mmt-90) REVERT: G 634 THR cc_start: 0.7778 (p) cc_final: 0.7509 (t) REVERT: G 669 ILE cc_start: 0.7638 (mm) cc_final: 0.7388 (mt) REVERT: H 518 GLU cc_start: 0.7951 (tt0) cc_final: 0.7520 (tm-30) REVERT: H 614 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7099 (pm20) REVERT: H 669 ILE cc_start: 0.7671 (mm) cc_final: 0.7399 (mt) REVERT: I 400 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6209 (pt) REVERT: I 434 GLN cc_start: 0.6323 (OUTLIER) cc_final: 0.6071 (pm20) REVERT: I 527 ARG cc_start: 0.7136 (mtt-85) cc_final: 0.6776 (mmt-90) REVERT: I 614 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6921 (pm20) REVERT: I 669 ILE cc_start: 0.7686 (mm) cc_final: 0.7389 (mt) outliers start: 49 outliers final: 29 residues processed: 344 average time/residue: 0.1617 time to fit residues: 89.2971 Evaluate side-chains 318 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 434 GLN Chi-restraints excluded: chain E residue 570 ASN 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 400 LEU Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 434 GLN 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 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 434 GLN 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 G residue 387 GLU Chi-restraints excluded: chain G residue 434 GLN Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 434 GLN Chi-restraints excluded: chain H residue 570 ASN Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain H residue 615 LEU Chi-restraints excluded: chain I residue 400 LEU Chi-restraints excluded: chain I residue 434 GLN Chi-restraints excluded: chain I residue 614 GLN Chi-restraints excluded: chain I residue 615 LEU Chi-restraints excluded: chain I residue 629 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 59 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 215 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 296 optimal weight: 7.9990 chunk 254 optimal weight: 0.6980 chunk 186 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 434 GLN ** 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 434 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.214110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.172362 restraints weight = 27291.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.169436 restraints weight = 41112.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.170790 restraints weight = 39339.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.170606 restraints weight = 22568.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.171469 restraints weight = 20547.699| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2445 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= 0.118 Angle : 0.578 12.947 33156 Z= 0.282 Chirality : 0.043 0.154 3924 Planarity : 0.004 0.039 4239 Dihedral : 3.590 17.587 3285 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.83 % Allowed : 13.94 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 3006 helix: 1.30 (0.14), residues: 1395 sheet: -0.92 (0.21), residues: 576 loop : -1.39 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 580 TYR 0.006 0.001 TYR D 420 PHE 0.015 0.001 PHE G 457 TRP 0.005 0.001 TRP I 654 HIS 0.003 0.001 HIS I 608 Details of bonding type rmsd covalent geometry : bond 0.00284 (24471) covalent geometry : angle 0.57754 (33156) hydrogen bonds : bond 0.03340 ( 1134) hydrogen bonds : angle 4.34923 ( 3267) *********************** REFINEMENT MACRO_CYCLE 9 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 342 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 293 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 480 MET cc_start: 0.9042 (tpt) cc_final: 0.7822 (tpt) REVERT: E 518 GLU cc_start: 0.7871 (tt0) cc_final: 0.7611 (tm-30) REVERT: E 527 ARG cc_start: 0.7148 (mtt-85) cc_final: 0.6720 (mmt-90) REVERT: E 614 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7040 (pm20) REVERT: E 633 ASP cc_start: 0.7509 (t70) cc_final: 0.7296 (t0) REVERT: E 634 THR cc_start: 0.7707 (p) cc_final: 0.7447 (t) REVERT: E 669 ILE cc_start: 0.7704 (mm) cc_final: 0.7384 (mt) REVERT: A 527 ARG cc_start: 0.7051 (mtt-85) cc_final: 0.6684 (mmt-90) REVERT: A 669 ILE cc_start: 0.7741 (mm) cc_final: 0.7451 (mt) REVERT: B 440 MET cc_start: 0.7137 (mtp) cc_final: 0.6828 (mtm) REVERT: B 518 GLU cc_start: 0.7887 (tt0) cc_final: 0.7611 (tm-30) REVERT: B 527 ARG cc_start: 0.7094 (mtt-85) cc_final: 0.6754 (mmt-90) REVERT: B 614 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6911 (pm20) REVERT: B 669 ILE cc_start: 0.7842 (mm) cc_final: 0.7548 (mt) REVERT: C 420 TYR cc_start: 0.6801 (m-80) cc_final: 0.6074 (m-80) REVERT: C 480 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8264 (tpt) REVERT: C 518 GLU cc_start: 0.7811 (tt0) cc_final: 0.7565 (tm-30) REVERT: C 527 ARG cc_start: 0.7197 (mtt-85) cc_final: 0.6820 (mmt-90) REVERT: C 614 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7028 (pm20) REVERT: C 669 ILE cc_start: 0.7791 (mm) cc_final: 0.7576 (mt) REVERT: D 527 ARG cc_start: 0.7249 (mtt-85) cc_final: 0.6925 (mmt-90) REVERT: D 614 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6808 (pm20) REVERT: D 669 ILE cc_start: 0.7878 (mm) cc_final: 0.7628 (mt) REVERT: F 480 MET cc_start: 0.8824 (tpt) cc_final: 0.8506 (tpt) REVERT: F 527 ARG cc_start: 0.7175 (mtt-85) cc_final: 0.6863 (mmt-90) REVERT: F 552 MET cc_start: 0.7685 (tpp) cc_final: 0.7450 (tpp) REVERT: F 556 TYR cc_start: 0.8615 (m-10) cc_final: 0.8175 (m-10) REVERT: F 664 GLN cc_start: 0.5416 (pm20) cc_final: 0.5157 (pm20) REVERT: F 669 ILE cc_start: 0.7694 (mm) cc_final: 0.7398 (mt) REVERT: G 527 ARG cc_start: 0.7114 (mtt-85) cc_final: 0.6817 (mmt-90) REVERT: G 614 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7043 (pm20) REVERT: G 634 THR cc_start: 0.7750 (p) cc_final: 0.7438 (t) REVERT: G 669 ILE cc_start: 0.7677 (mm) cc_final: 0.7450 (mt) REVERT: H 518 GLU cc_start: 0.7921 (tt0) cc_final: 0.7462 (tm-30) REVERT: H 614 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: H 669 ILE cc_start: 0.7719 (mm) cc_final: 0.7462 (mt) REVERT: I 400 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6165 (pt) REVERT: I 527 ARG cc_start: 0.7040 (mtt-85) cc_final: 0.6706 (mmt-90) REVERT: I 669 ILE cc_start: 0.7778 (mm) cc_final: 0.7452 (mt) outliers start: 49 outliers final: 27 residues processed: 340 average time/residue: 0.1559 time to fit residues: 84.4320 Evaluate side-chains 315 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 614 GLN Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain A residue 400 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 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 C residue 657 LEU Chi-restraints excluded: chain D residue 381 THR 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 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 629 VAL 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 615 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 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 25 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 284 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 434 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.213883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.171902 restraints weight = 27195.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.168967 restraints weight = 41204.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.170206 restraints weight = 38511.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.169619 restraints weight = 22814.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.170794 restraints weight = 20346.371| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2487 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= 0.123 Angle : 0.592 14.024 33156 Z= 0.286 Chirality : 0.043 0.186 3924 Planarity : 0.004 0.090 4239 Dihedral : 3.618 17.010 3285 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.60 % Allowed : 14.39 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3006 helix: 1.31 (0.14), residues: 1395 sheet: -0.93 (0.21), residues: 576 loop : -1.33 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG H 590 TYR 0.010 0.001 TYR G 556 PHE 0.015 0.001 PHE G 457 TRP 0.005 0.001 TRP I 654 HIS 0.004 0.001 HIS I 608 Details of bonding type rmsd covalent geometry : bond 0.00297 (24471) covalent geometry : angle 0.59233 (33156) hydrogen bonds : bond 0.03405 ( 1134) hydrogen bonds : angle 4.38782 ( 3267) ********************** REFINEMENT MACRO_CYCLE 10 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 336 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 293 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 480 MET cc_start: 0.9028 (tpt) cc_final: 0.7773 (tpt) REVERT: E 518 GLU cc_start: 0.7911 (tt0) cc_final: 0.7620 (tm-30) REVERT: E 527 ARG cc_start: 0.7134 (mtt-85) cc_final: 0.6708 (mmt-90) REVERT: E 633 ASP cc_start: 0.7523 (t70) cc_final: 0.7294 (t0) REVERT: E 634 THR cc_start: 0.7758 (p) cc_final: 0.7499 (t) REVERT: E 669 ILE cc_start: 0.7733 (mm) cc_final: 0.7406 (mt) REVERT: A 527 ARG cc_start: 0.7053 (mtt-85) cc_final: 0.6679 (mmt-90) REVERT: A 614 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7032 (pm20) REVERT: A 669 ILE cc_start: 0.7741 (mm) cc_final: 0.7478 (mt) REVERT: B 440 MET cc_start: 0.7154 (mtp) cc_final: 0.6794 (mtm) REVERT: B 518 GLU cc_start: 0.7872 (tt0) cc_final: 0.7610 (tm-30) REVERT: B 527 ARG cc_start: 0.7089 (mtt-85) cc_final: 0.6759 (mmt-90) REVERT: B 552 MET cc_start: 0.7846 (tpp) cc_final: 0.7397 (tpt) REVERT: B 614 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6899 (pm20) REVERT: B 669 ILE cc_start: 0.7840 (mm) cc_final: 0.7573 (mt) REVERT: C 420 TYR cc_start: 0.6794 (m-80) cc_final: 0.6116 (m-80) REVERT: C 480 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8258 (tpt) REVERT: C 518 GLU cc_start: 0.7823 (tt0) cc_final: 0.7572 (tm-30) REVERT: C 527 ARG cc_start: 0.7193 (mtt-85) cc_final: 0.6815 (mmt-90) REVERT: C 614 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.6961 (pm20) REVERT: C 669 ILE cc_start: 0.7892 (mm) cc_final: 0.7659 (mt) REVERT: D 527 ARG cc_start: 0.7242 (mtt-85) cc_final: 0.6908 (mmt-90) REVERT: D 614 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6805 (pm20) REVERT: D 669 ILE cc_start: 0.7881 (mm) cc_final: 0.7642 (mt) REVERT: F 527 ARG cc_start: 0.7195 (mtt-85) cc_final: 0.6872 (mmt-90) REVERT: F 552 MET cc_start: 0.7737 (tpp) cc_final: 0.7463 (tpp) REVERT: F 556 TYR cc_start: 0.8599 (m-10) cc_final: 0.8150 (m-10) REVERT: F 664 GLN cc_start: 0.5522 (pm20) cc_final: 0.5297 (pm20) REVERT: F 669 ILE cc_start: 0.7695 (mm) cc_final: 0.7420 (mt) REVERT: G 527 ARG cc_start: 0.7111 (mtt-85) cc_final: 0.6815 (mmt-90) REVERT: G 614 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7045 (pm20) REVERT: G 634 THR cc_start: 0.7763 (p) cc_final: 0.7468 (t) REVERT: G 669 ILE cc_start: 0.7698 (mm) cc_final: 0.7473 (mt) REVERT: H 518 GLU cc_start: 0.7930 (tt0) cc_final: 0.7519 (tm-30) REVERT: H 614 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: H 669 ILE cc_start: 0.7725 (mm) cc_final: 0.7477 (mt) REVERT: I 400 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6181 (pt) REVERT: I 527 ARG cc_start: 0.7037 (mtt-85) cc_final: 0.6691 (mmt-90) REVERT: I 634 THR cc_start: 0.7597 (p) cc_final: 0.7256 (t) REVERT: I 669 ILE cc_start: 0.7772 (mm) cc_final: 0.7481 (mt) outliers start: 43 outliers final: 26 residues processed: 334 average time/residue: 0.1520 time to fit residues: 82.0163 Evaluate side-chains 321 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 570 ASN 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 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 C residue 657 LEU Chi-restraints excluded: chain D residue 381 THR 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 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 629 VAL 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 615 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 9 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 245 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 193 optimal weight: 0.4980 chunk 191 optimal weight: 2.9990 chunk 273 optimal weight: 0.0030 chunk 222 optimal weight: 0.7980 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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** ** 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 434 GLN ** 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 = 0.4478 r_free = 0.4478 target = 0.213837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.175843 restraints weight = 27079.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.172899 restraints weight = 44304.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.174057 restraints weight = 42415.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.173383 restraints weight = 27241.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.174108 restraints weight = 25684.627| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 24471 Z= 0.136 Angle : 0.727 59.181 33156 Z= 0.386 Chirality : 0.046 1.097 3924 Planarity : 0.004 0.080 4239 Dihedral : 3.668 38.581 3285 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.45 % Allowed : 14.73 % Favored : 83.82 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3006 helix: 1.32 (0.14), residues: 1395 sheet: -0.93 (0.21), residues: 576 loop : -1.33 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 636 TYR 0.006 0.001 TYR G 556 PHE 0.014 0.001 PHE G 457 TRP 0.010 0.001 TRP G 543 HIS 0.004 0.001 HIS I 608 Details of bonding type rmsd covalent geometry : bond 0.00311 (24471) covalent geometry : angle 0.72699 (33156) hydrogen bonds : bond 0.03394 ( 1134) hydrogen bonds : angle 4.38458 ( 3267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3425.98 seconds wall clock time: 60 minutes 7.58 seconds (3607.58 seconds total)