Starting phenix.real_space_refine on Tue Mar 19 11:44:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fec_31552/03_2024/7fec_31552.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fec_31552/03_2024/7fec_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fec_31552/03_2024/7fec_31552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fec_31552/03_2024/7fec_31552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fec_31552/03_2024/7fec_31552.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fec_31552/03_2024/7fec_31552.pdb" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 15354 2.51 5 N 4140 2.21 5 O 4473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 379": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "G GLU 379": "OE1" <-> "OE2" Residue "H GLU 379": "OE1" <-> "OE2" Residue "I GLU 379": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24075 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "A" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "B" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "C" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "D" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "F" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "G" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "H" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "I" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2675 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Time building chain proxies: 12.56, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 9.67 Conformation dependent library (CDL) restraints added in 4.3 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: 2.81 Creating SS restraints... Processing helix chain 'E' and resid 365 through 382 Processing helix chain 'E' and resid 437 through 440 Processing helix chain 'E' and resid 447 through 457 Processing helix chain 'E' and resid 465 through 479 removed outlier: 3.847A pdb=" N CYS E 474 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 484 removed outlier: 4.054A pdb=" N ILE E 484 " --> pdb=" O GLY E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 497 Processing helix chain 'E' and resid 500 through 511 Processing helix chain 'E' and resid 512 through 525 Processing helix chain 'E' and resid 532 through 544 Processing helix chain 'E' and resid 549 through 561 Processing helix chain 'E' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN E 570 " --> pdb=" O LEU E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 590 removed outlier: 4.073A pdb=" N GLU E 586 " --> pdb=" O GLY E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 620 Processing helix chain 'E' and resid 634 through 641 Processing helix chain 'A' and resid 365 through 382 Processing helix chain 'A' and resid 437 through 440 Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.846A pdb=" N CYS A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 4.054A pdb=" N ILE A 484 " --> pdb=" O GLY A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 497 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 532 through 544 Processing helix chain 'A' and resid 549 through 561 Processing helix chain 'A' and resid 561 through 570 removed outlier: 3.675A pdb=" N ASN A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 590 removed outlier: 4.074A pdb=" N GLU A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 620 Processing helix chain 'A' and resid 634 through 641 Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 437 through 440 Processing helix chain 'B' and resid 447 through 457 Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.846A pdb=" N CYS B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 484 removed outlier: 4.055A pdb=" N ILE B 484 " --> pdb=" O GLY B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 497 Processing helix chain 'B' and resid 500 through 511 Processing helix chain 'B' and resid 512 through 525 Processing helix chain 'B' and resid 532 through 544 Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 590 removed outlier: 4.072A pdb=" N GLU B 586 " --> pdb=" O GLY B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 620 Processing helix chain 'B' and resid 634 through 641 Processing helix chain 'C' and resid 365 through 382 Processing helix chain 'C' and resid 437 through 440 Processing helix chain 'C' and resid 447 through 457 Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.847A pdb=" N CYS C 474 " --> pdb=" O ALA C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 484 removed outlier: 4.054A pdb=" N ILE C 484 " --> pdb=" O GLY C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 497 Processing helix chain 'C' and resid 500 through 511 Processing helix chain 'C' and resid 512 through 525 Processing helix chain 'C' and resid 532 through 544 Processing helix chain 'C' and resid 549 through 561 Processing helix chain 'C' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 590 removed outlier: 4.072A pdb=" N GLU C 586 " --> pdb=" O GLY C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 620 Processing helix chain 'C' and resid 634 through 641 Processing helix chain 'D' and resid 365 through 382 Processing helix chain 'D' and resid 437 through 440 Processing helix chain 'D' and resid 447 through 457 Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.847A pdb=" N CYS D 474 " --> pdb=" O ALA D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 484 removed outlier: 4.054A pdb=" N ILE D 484 " --> pdb=" O GLY D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 497 Processing helix chain 'D' and resid 500 through 511 Processing helix chain 'D' and resid 512 through 525 Processing helix chain 'D' and resid 532 through 544 Processing helix chain 'D' and resid 549 through 561 Processing helix chain 'D' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN D 570 " --> pdb=" O LEU D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 590 removed outlier: 4.073A pdb=" N GLU D 586 " --> pdb=" O GLY D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 620 Processing helix chain 'D' and resid 634 through 641 Processing helix chain 'F' and resid 365 through 382 Processing helix chain 'F' and resid 437 through 440 Processing helix chain 'F' and resid 447 through 457 Processing helix chain 'F' and resid 465 through 479 removed outlier: 3.846A pdb=" N CYS F 474 " --> pdb=" O ALA F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 484 removed outlier: 4.055A pdb=" N ILE F 484 " --> pdb=" O GLY F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 497 Processing helix chain 'F' and resid 500 through 511 Processing helix chain 'F' and resid 512 through 525 Processing helix chain 'F' and resid 532 through 544 Processing helix chain 'F' and resid 549 through 561 Processing helix chain 'F' and resid 561 through 570 removed outlier: 3.675A pdb=" N ASN F 570 " --> pdb=" O LEU F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 590 removed outlier: 4.073A pdb=" N GLU F 586 " --> pdb=" O GLY F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 620 Processing helix chain 'F' and resid 634 through 641 Processing helix chain 'G' and resid 365 through 382 Processing helix chain 'G' and resid 437 through 440 Processing helix chain 'G' and resid 447 through 457 Processing helix chain 'G' and resid 465 through 479 removed outlier: 3.847A pdb=" N CYS G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 484 removed outlier: 4.055A pdb=" N ILE G 484 " --> pdb=" O GLY G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 497 Processing helix chain 'G' and resid 500 through 511 Processing helix chain 'G' and resid 512 through 525 Processing helix chain 'G' and resid 532 through 544 Processing helix chain 'G' and resid 549 through 561 Processing helix chain 'G' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN G 570 " --> pdb=" O LEU G 566 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 590 removed outlier: 4.073A pdb=" N GLU G 586 " --> pdb=" O GLY G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 620 Processing helix chain 'G' and resid 634 through 641 Processing helix chain 'H' and resid 365 through 382 Processing helix chain 'H' and resid 437 through 440 Processing helix chain 'H' and resid 447 through 457 Processing helix chain 'H' and resid 465 through 479 removed outlier: 3.846A pdb=" N CYS H 474 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 484 removed outlier: 4.055A pdb=" N ILE H 484 " --> pdb=" O GLY H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 497 Processing helix chain 'H' and resid 500 through 511 Processing helix chain 'H' and resid 512 through 525 Processing helix chain 'H' and resid 532 through 544 Processing helix chain 'H' and resid 549 through 561 Processing helix chain 'H' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN H 570 " --> pdb=" O LEU H 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 590 removed outlier: 4.073A pdb=" N GLU H 586 " --> pdb=" O GLY H 582 " (cutoff:3.500A) Processing helix chain 'H' and resid 605 through 620 Processing helix chain 'H' and resid 634 through 641 Processing helix chain 'I' and resid 365 through 382 Processing helix chain 'I' and resid 437 through 440 Processing helix chain 'I' and resid 447 through 457 Processing helix chain 'I' and resid 465 through 479 removed outlier: 3.847A pdb=" N CYS I 474 " --> pdb=" O ALA I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 480 through 484 removed outlier: 4.054A pdb=" N ILE I 484 " --> pdb=" O GLY I 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 485 through 497 Processing helix chain 'I' and resid 500 through 511 Processing helix chain 'I' and resid 512 through 525 Processing helix chain 'I' and resid 532 through 544 Processing helix chain 'I' and resid 549 through 561 Processing helix chain 'I' and resid 561 through 570 removed outlier: 3.676A pdb=" N ASN I 570 " --> pdb=" O LEU I 566 " (cutoff:3.500A) Processing helix chain 'I' and resid 582 through 590 removed outlier: 4.073A pdb=" N GLU I 586 " --> pdb=" O GLY I 582 " (cutoff:3.500A) Processing helix chain 'I' and resid 605 through 620 Processing helix chain 'I' and resid 634 through 641 Processing sheet with id=AA1, first strand: chain 'E' and resid 389 through 392 removed outlier: 6.871A pdb=" N LEU E 353 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU E 391 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU E 355 " --> pdb=" O GLU E 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU E 404 " --> pdb=" O PRO E 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY E 441 " --> pdb=" O LEU E 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR E 420 " --> pdb=" O LEU E 446 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 651 through 653 removed outlier: 6.645A pdb=" N ILE E 628 " --> pdb=" O LEU E 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE E 578 " --> pdb=" O VAL E 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER E 668 " --> pdb=" O ILE E 578 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG E 580 " --> pdb=" O SER E 668 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 593 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 392 removed outlier: 6.870A pdb=" N LEU A 353 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU A 391 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 355 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 404 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY A 441 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 420 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.645A pdb=" N ILE A 628 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE A 578 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 668 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG A 580 " --> pdb=" O SER A 668 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA9, first strand: chain 'B' and resid 389 through 392 removed outlier: 6.871A pdb=" N LEU B 353 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU B 391 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 355 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 404 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY B 441 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 420 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 651 through 653 removed outlier: 6.645A pdb=" N ILE B 628 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE B 578 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER B 668 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG B 580 " --> pdb=" O SER B 668 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 593 through 596 Processing sheet with id=AB4, first strand: chain 'C' and resid 389 through 392 removed outlier: 6.871A pdb=" N LEU C 353 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU C 391 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU C 355 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 404 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY C 441 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 420 " --> pdb=" O LEU C 446 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 651 through 653 removed outlier: 6.646A pdb=" N ILE C 628 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE C 578 " --> pdb=" O VAL C 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER C 668 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG C 580 " --> pdb=" O SER C 668 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 593 through 596 Processing sheet with id=AB8, first strand: chain 'D' and resid 389 through 392 removed outlier: 6.870A pdb=" N LEU D 353 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU D 391 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU D 355 " --> pdb=" O GLU D 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU D 404 " --> pdb=" O PRO D 408 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY D 441 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR D 420 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 651 through 653 removed outlier: 6.646A pdb=" N ILE D 628 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE D 578 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER D 668 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG D 580 " --> pdb=" O SER D 668 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 593 through 596 Processing sheet with id=AC3, first strand: chain 'F' and resid 389 through 392 removed outlier: 6.870A pdb=" N LEU F 353 " --> pdb=" O ASN F 389 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU F 391 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU F 355 " --> pdb=" O GLU F 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU F 404 " --> pdb=" O PRO F 408 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY F 441 " --> pdb=" O LEU F 436 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR F 420 " --> pdb=" O LEU F 446 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 651 through 653 removed outlier: 6.644A pdb=" N ILE F 628 " --> pdb=" O LEU F 652 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE F 578 " --> pdb=" O VAL F 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER F 668 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG F 580 " --> pdb=" O SER F 668 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 593 through 596 Processing sheet with id=AC7, first strand: chain 'G' and resid 389 through 392 removed outlier: 6.870A pdb=" N LEU G 353 " --> pdb=" O ASN G 389 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU G 391 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU G 355 " --> pdb=" O GLU G 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU G 404 " --> pdb=" O PRO G 408 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY G 441 " --> pdb=" O LEU G 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR G 420 " --> pdb=" O LEU G 446 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 651 through 653 removed outlier: 6.646A pdb=" N ILE G 628 " --> pdb=" O LEU G 652 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE G 578 " --> pdb=" O VAL G 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER G 668 " --> pdb=" O ILE G 578 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG G 580 " --> pdb=" O SER G 668 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 593 through 596 Processing sheet with id=AD2, first strand: chain 'H' and resid 389 through 392 removed outlier: 6.870A pdb=" N LEU H 353 " --> pdb=" O ASN H 389 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU H 391 " --> pdb=" O LEU H 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU H 355 " --> pdb=" O GLU H 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU H 404 " --> pdb=" O PRO H 408 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY H 441 " --> pdb=" O LEU H 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR H 420 " --> pdb=" O LEU H 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 651 through 653 removed outlier: 6.644A pdb=" N ILE H 628 " --> pdb=" O LEU H 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE H 578 " --> pdb=" O VAL H 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER H 668 " --> pdb=" O ILE H 578 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG H 580 " --> pdb=" O SER H 668 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 593 through 596 Processing sheet with id=AD6, first strand: chain 'I' and resid 389 through 392 removed outlier: 6.870A pdb=" N LEU I 353 " --> pdb=" O ASN I 389 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU I 391 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU I 355 " --> pdb=" O GLU I 391 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU I 404 " --> pdb=" O PRO I 408 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 433 through 436 removed outlier: 4.309A pdb=" N GLY I 441 " --> pdb=" O LEU I 436 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR I 420 " --> pdb=" O LEU I 446 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 651 through 653 removed outlier: 6.645A pdb=" N ILE I 628 " --> pdb=" O LEU I 652 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE I 578 " --> pdb=" O VAL I 666 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER I 668 " --> pdb=" O ILE I 578 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG I 580 " --> pdb=" O SER I 668 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 593 through 596 1134 hydrogen bonds defined for protein. 3267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.51 Time building geometry restraints manager: 10.39 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: 98.79 - 105.84: 610 105.84 - 112.89: 13377 112.89 - 119.94: 8443 119.94 - 126.99: 10483 126.99 - 134.04: 243 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 2.520 nonbonded pdb=" NE2 GLN B 417 " pdb=" OD2 ASP B 432 " model vdw 2.217 2.520 nonbonded pdb=" NE2 GLN G 417 " pdb=" OD2 ASP G 432 " model vdw 2.217 2.520 nonbonded pdb=" NE2 GLN H 417 " pdb=" OD2 ASP H 432 " model vdw 2.217 2.520 nonbonded pdb=" NE2 GLN E 417 " pdb=" OD2 ASP E 432 " model vdw 2.217 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 14.550 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 62.200 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.770 ------------------------------------------------------------------------------- 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= 0.293 Angle : 0.831 7.780 33156 Z= 0.481 Chirality : 0.056 0.307 3924 Planarity : 0.004 0.028 4239 Dihedral : 14.618 83.946 9396 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.14), residues: 3006 helix: -0.81 (0.13), residues: 1314 sheet: -0.94 (0.22), residues: 558 loop : -1.99 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 445 HIS 0.006 0.001 HIS A 564 PHE 0.007 0.001 PHE F 410 TYR 0.008 0.001 TYR I 420 ARG 0.020 0.001 ARG B 580 *********************** 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 fitting. rotamer outliers: 9 poor density : 392 time to evaluate : 2.865 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: 0.4051 time to fit residues: 237.8130 Evaluate side-chains 302 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.5980 chunk 225 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 151 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 173 optimal weight: 0.0670 chunk 269 optimal weight: 3.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 570 ASN ** A 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24471 Z= 0.214 Angle : 0.583 5.719 33156 Z= 0.288 Chirality : 0.045 0.264 3924 Planarity : 0.004 0.034 4239 Dihedral : 4.240 19.912 3285 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.08 % Allowed : 6.90 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.15), residues: 3006 helix: 0.40 (0.14), residues: 1386 sheet: -0.87 (0.22), residues: 558 loop : -2.17 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 543 HIS 0.008 0.002 HIS A 608 PHE 0.029 0.001 PHE H 457 TYR 0.008 0.001 TYR D 556 ARG 0.005 0.001 ARG H 580 *********************** 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 368 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 339 time to evaluate : 2.632 Fit side-chains REVERT: E 578 ILE cc_start: 0.8041 (mt) cc_final: 0.7730 (mt) REVERT: A 480 MET cc_start: 0.9135 (tpp) cc_final: 0.8864 (mmt) REVERT: A 552 MET cc_start: 0.7808 (tpp) cc_final: 0.7386 (tpt) REVERT: A 556 TYR cc_start: 0.8269 (m-10) cc_final: 0.8067 (m-10) REVERT: A 578 ILE cc_start: 0.8075 (mt) cc_final: 0.7813 (mt) REVERT: B 440 MET cc_start: 0.6969 (mtp) cc_final: 0.6598 (mtm) REVERT: B 527 ARG cc_start: 0.7194 (mtt-85) cc_final: 0.6860 (mmt-90) REVERT: B 552 MET cc_start: 0.7828 (tpp) cc_final: 0.7388 (tpt) REVERT: B 556 TYR cc_start: 0.8448 (m-10) cc_final: 0.8200 (m-10) REVERT: B 578 ILE cc_start: 0.7998 (mt) cc_final: 0.7708 (mt) REVERT: B 601 TYR cc_start: 0.7459 (p90) cc_final: 0.7128 (p90) REVERT: C 422 LEU cc_start: 0.7667 (tp) cc_final: 0.7395 (tp) REVERT: C 578 ILE cc_start: 0.7984 (mt) cc_final: 0.7662 (mt) REVERT: C 601 TYR cc_start: 0.7557 (p90) cc_final: 0.7231 (p90) REVERT: C 608 HIS cc_start: 0.7805 (m90) cc_final: 0.7586 (m90) REVERT: D 578 ILE cc_start: 0.7955 (mt) cc_final: 0.7670 (mt) REVERT: F 556 TYR cc_start: 0.8454 (m-10) cc_final: 0.8168 (m-10) REVERT: F 570 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7864 (p0) REVERT: F 578 ILE cc_start: 0.8093 (mt) cc_final: 0.7768 (mt) REVERT: F 608 HIS cc_start: 0.7760 (m90) cc_final: 0.7506 (m-70) REVERT: G 440 MET cc_start: 0.7046 (mtm) cc_final: 0.6705 (mtm) REVERT: G 578 ILE cc_start: 0.7995 (mt) cc_final: 0.7688 (mt) REVERT: H 527 ARG cc_start: 0.7121 (mtt-85) cc_final: 0.6841 (mmt-90) REVERT: H 578 ILE cc_start: 0.8152 (mt) cc_final: 0.7844 (mt) REVERT: I 578 ILE cc_start: 0.8030 (mt) cc_final: 0.7689 (mt) outliers start: 29 outliers final: 6 residues processed: 365 average time/residue: 0.3648 time to fit residues: 205.1271 Evaluate side-chains 310 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 303 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 634 THR Chi-restraints excluded: chain I residue 634 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 270 optimal weight: 0.6980 chunk 291 optimal weight: 1.9990 chunk 240 optimal weight: 0.1980 chunk 267 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 216 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 ASN ** A 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 ASN ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 570 ASN ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 570 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1482 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= 0.214 Angle : 0.550 5.633 33156 Z= 0.273 Chirality : 0.043 0.218 3924 Planarity : 0.003 0.033 4239 Dihedral : 4.032 16.988 3285 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.45 % Allowed : 10.66 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3006 helix: 0.69 (0.14), residues: 1386 sheet: -1.00 (0.21), residues: 576 loop : -2.14 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 543 HIS 0.004 0.001 HIS I 564 PHE 0.023 0.001 PHE D 457 TYR 0.008 0.001 TYR D 556 ARG 0.007 0.001 ARG A 580 *********************** 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 369 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 330 time to evaluate : 2.929 Fit side-chains REVERT: E 518 GLU cc_start: 0.7891 (tt0) cc_final: 0.7658 (tm-30) REVERT: E 527 ARG cc_start: 0.7069 (mtt-85) cc_final: 0.6571 (mmt-90) REVERT: E 578 ILE cc_start: 0.8042 (mt) cc_final: 0.7752 (mt) REVERT: E 590 ARG cc_start: 0.8014 (mtt-85) cc_final: 0.7769 (mtt90) REVERT: A 552 MET cc_start: 0.7767 (tpp) cc_final: 0.7473 (tpt) REVERT: A 578 ILE cc_start: 0.8023 (mt) cc_final: 0.7755 (mt) REVERT: A 613 LEU cc_start: 0.8152 (mp) cc_final: 0.7833 (mp) REVERT: B 440 MET cc_start: 0.6926 (mtp) cc_final: 0.6657 (mtm) REVERT: B 518 GLU cc_start: 0.7866 (tt0) cc_final: 0.7665 (tm-30) REVERT: B 527 ARG cc_start: 0.7139 (mtt-85) cc_final: 0.6822 (mtt-85) REVERT: B 552 MET cc_start: 0.7744 (tpp) cc_final: 0.7287 (tpt) REVERT: B 556 TYR cc_start: 0.8483 (m-10) cc_final: 0.8201 (m-10) REVERT: B 578 ILE cc_start: 0.8037 (mt) cc_final: 0.7713 (mt) REVERT: B 613 LEU cc_start: 0.8354 (mp) cc_final: 0.8116 (mp) REVERT: B 648 ASP cc_start: 0.7295 (t0) cc_final: 0.7037 (t0) REVERT: C 578 ILE cc_start: 0.7953 (mt) cc_final: 0.7626 (mt) REVERT: C 601 TYR cc_start: 0.7559 (p90) cc_final: 0.7197 (p90) REVERT: D 527 ARG cc_start: 0.7191 (mtt-85) cc_final: 0.6791 (mmt-90) REVERT: D 570 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7886 (p0) REVERT: D 578 ILE cc_start: 0.7941 (mt) cc_final: 0.7640 (mt) REVERT: D 613 LEU cc_start: 0.8358 (mp) cc_final: 0.8065 (mp) REVERT: D 648 ASP cc_start: 0.7370 (t0) cc_final: 0.7090 (t0) REVERT: F 527 ARG cc_start: 0.7090 (mtt-85) cc_final: 0.6694 (mmt-90) REVERT: F 556 TYR cc_start: 0.8493 (m-10) cc_final: 0.8120 (m-10) REVERT: F 570 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.8016 (p0) REVERT: F 578 ILE cc_start: 0.8114 (mt) cc_final: 0.7787 (mt) REVERT: F 613 LEU cc_start: 0.8389 (mp) cc_final: 0.8026 (mp) REVERT: F 648 ASP cc_start: 0.7341 (t0) cc_final: 0.7093 (t0) REVERT: G 440 MET cc_start: 0.7056 (mtm) cc_final: 0.6720 (mtm) REVERT: G 552 MET cc_start: 0.7850 (tpp) cc_final: 0.7304 (tpt) REVERT: G 556 TYR cc_start: 0.8329 (m-10) cc_final: 0.8078 (m-10) REVERT: G 578 ILE cc_start: 0.7987 (mt) cc_final: 0.7691 (mt) REVERT: G 613 LEU cc_start: 0.8360 (mp) cc_final: 0.7998 (mp) REVERT: H 480 MET cc_start: 0.9127 (tpp) cc_final: 0.8735 (tpt) REVERT: H 518 GLU cc_start: 0.7841 (tt0) cc_final: 0.7580 (tm-30) REVERT: H 578 ILE cc_start: 0.8137 (mt) cc_final: 0.7796 (mt) REVERT: I 527 ARG cc_start: 0.7049 (mtt-85) cc_final: 0.6702 (mmt-90) REVERT: I 578 ILE cc_start: 0.8004 (mt) cc_final: 0.7662 (mt) REVERT: I 648 ASP cc_start: 0.7340 (t0) cc_final: 0.7018 (t0) outliers start: 39 outliers final: 8 residues processed: 368 average time/residue: 0.3355 time to fit residues: 195.9776 Evaluate side-chains 325 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 315 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 570 ASN Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain G residue 387 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 271 optimal weight: 8.9990 chunk 287 optimal weight: 0.0010 chunk 141 optimal weight: 0.0470 chunk 256 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.2090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B 570 ASN ** C 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 ASN ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 570 ASN ** I 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 570 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24471 Z= 0.246 Angle : 0.564 7.337 33156 Z= 0.275 Chirality : 0.044 0.263 3924 Planarity : 0.004 0.039 4239 Dihedral : 3.956 15.444 3285 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.01 % Allowed : 12.04 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 3006 helix: 0.77 (0.14), residues: 1386 sheet: -0.97 (0.21), residues: 576 loop : -2.09 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 543 HIS 0.004 0.001 HIS I 564 PHE 0.031 0.001 PHE G 457 TYR 0.008 0.001 TYR D 556 ARG 0.008 0.001 ARG D 580 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 318 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 518 GLU cc_start: 0.7910 (tt0) cc_final: 0.7675 (tm-30) REVERT: E 549 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7657 (p0) REVERT: E 578 ILE cc_start: 0.8019 (mt) cc_final: 0.7746 (mt) REVERT: E 614 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8338 (pp30) REVERT: A 552 MET cc_start: 0.7790 (tpp) cc_final: 0.7555 (tpt) REVERT: A 578 ILE cc_start: 0.8050 (mt) cc_final: 0.7816 (mt) REVERT: A 613 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8042 (mp) REVERT: A 614 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: A 630 THR cc_start: 0.8387 (t) cc_final: 0.8179 (t) REVERT: B 440 MET cc_start: 0.6947 (mtp) cc_final: 0.6602 (mtm) REVERT: B 518 GLU cc_start: 0.7883 (tt0) cc_final: 0.7675 (tm-30) REVERT: B 527 ARG cc_start: 0.7182 (mtt-85) cc_final: 0.6746 (mmt-90) REVERT: B 578 ILE cc_start: 0.8002 (mt) cc_final: 0.7739 (mt) REVERT: B 613 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8171 (mp) REVERT: B 614 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7984 (pm20) REVERT: B 664 GLN cc_start: 0.5550 (pm20) cc_final: 0.5307 (pm20) REVERT: C 420 TYR cc_start: 0.6833 (m-80) cc_final: 0.6129 (m-80) REVERT: C 578 ILE cc_start: 0.7959 (mt) cc_final: 0.7703 (mt) REVERT: C 669 ILE cc_start: 0.6637 (mm) cc_final: 0.6248 (mt) REVERT: D 578 ILE cc_start: 0.7931 (mt) cc_final: 0.7645 (mt) REVERT: D 614 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7801 (pm20) REVERT: D 664 GLN cc_start: 0.5710 (pm20) cc_final: 0.5488 (pm20) REVERT: F 556 TYR cc_start: 0.8510 (m-10) cc_final: 0.8148 (m-10) REVERT: F 578 ILE cc_start: 0.8087 (mt) cc_final: 0.7809 (mt) REVERT: F 664 GLN cc_start: 0.5609 (pm20) cc_final: 0.5350 (pm20) REVERT: G 440 MET cc_start: 0.7088 (mtm) cc_final: 0.6674 (mtm) REVERT: G 527 ARG cc_start: 0.6926 (mtt-85) cc_final: 0.6649 (mmt-90) REVERT: G 552 MET cc_start: 0.7841 (tpp) cc_final: 0.7363 (tpt) REVERT: G 556 TYR cc_start: 0.8387 (m-10) cc_final: 0.8137 (m-10) REVERT: G 570 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7879 (p0) REVERT: G 578 ILE cc_start: 0.8007 (mt) cc_final: 0.7731 (mt) REVERT: G 613 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8150 (mp) REVERT: G 614 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7915 (pm20) REVERT: H 518 GLU cc_start: 0.7857 (tt0) cc_final: 0.7586 (tm-30) REVERT: H 578 ILE cc_start: 0.8105 (mt) cc_final: 0.7811 (mt) REVERT: H 614 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: H 664 GLN cc_start: 0.5811 (pm20) cc_final: 0.5497 (pm20) REVERT: I 578 ILE cc_start: 0.7972 (mt) cc_final: 0.7668 (mt) REVERT: I 648 ASP cc_start: 0.7365 (t0) cc_final: 0.7134 (t0) REVERT: I 664 GLN cc_start: 0.5681 (pm20) cc_final: 0.5393 (pm20) outliers start: 54 outliers final: 22 residues processed: 364 average time/residue: 0.3207 time to fit residues: 186.6685 Evaluate side-chains 339 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 306 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 570 ASN Chi-restraints excluded: chain E residue 614 GLN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 613 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 613 LEU Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 634 THR 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 615 LEU Chi-restraints excluded: chain F residue 634 THR Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 401 THR Chi-restraints excluded: chain G residue 570 ASN Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain I residue 614 GLN Chi-restraints excluded: chain I residue 634 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 213 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 244 optimal weight: 0.6980 chunk 198 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 72 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 ASN ** A 389 ASN ** 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** ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 ASN ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 570 ASN ** I 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1931 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= 0.154 Angle : 0.519 7.306 33156 Z= 0.254 Chirality : 0.042 0.215 3924 Planarity : 0.003 0.031 4239 Dihedral : 3.670 14.548 3285 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.13 % Allowed : 12.68 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3006 helix: 1.15 (0.14), residues: 1386 sheet: -0.91 (0.21), residues: 576 loop : -1.96 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 543 HIS 0.003 0.000 HIS C 608 PHE 0.024 0.001 PHE G 457 TYR 0.006 0.001 TYR D 556 ARG 0.004 0.000 ARG H 580 *********************** 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 384 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 327 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 518 GLU cc_start: 0.7883 (tt0) cc_final: 0.7641 (tm-30) REVERT: E 549 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7474 (p0) REVERT: E 578 ILE cc_start: 0.8009 (mt) cc_final: 0.7749 (mt) REVERT: A 527 ARG cc_start: 0.6850 (mtt-85) cc_final: 0.6506 (mmt-90) REVERT: A 578 ILE cc_start: 0.8031 (mt) cc_final: 0.7795 (mt) REVERT: A 669 ILE cc_start: 0.6502 (mm) cc_final: 0.6084 (mt) REVERT: B 440 MET cc_start: 0.6901 (mtp) cc_final: 0.6537 (mtm) REVERT: B 578 ILE cc_start: 0.8016 (mt) cc_final: 0.7725 (mt) REVERT: B 664 GLN cc_start: 0.5534 (pm20) cc_final: 0.5268 (pm20) REVERT: C 420 TYR cc_start: 0.6782 (m-80) cc_final: 0.6076 (m-80) REVERT: C 527 ARG cc_start: 0.7005 (mtt-85) cc_final: 0.6610 (mmt-90) REVERT: C 578 ILE cc_start: 0.7955 (mt) cc_final: 0.7663 (mt) REVERT: D 496 MET cc_start: 0.8055 (tpp) cc_final: 0.7644 (tpp) REVERT: D 578 ILE cc_start: 0.7900 (mt) cc_final: 0.7675 (mt) REVERT: D 664 GLN cc_start: 0.5552 (pm20) cc_final: 0.5344 (pm20) REVERT: F 556 TYR cc_start: 0.8495 (m-10) cc_final: 0.8058 (m-10) REVERT: F 578 ILE cc_start: 0.8062 (mt) cc_final: 0.7802 (mt) REVERT: F 664 GLN cc_start: 0.5654 (pm20) cc_final: 0.5281 (pm20) REVERT: G 440 MET cc_start: 0.7008 (mtm) cc_final: 0.6729 (mtm) REVERT: G 549 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7714 (p0) REVERT: G 578 ILE cc_start: 0.7985 (mt) cc_final: 0.7700 (mt) REVERT: H 578 ILE cc_start: 0.8142 (mt) cc_final: 0.7851 (mt) REVERT: H 664 GLN cc_start: 0.5907 (pm20) cc_final: 0.5625 (pm20) REVERT: I 400 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6234 (pt) REVERT: I 417 GLN cc_start: 0.8448 (pp30) cc_final: 0.7982 (pp30) REVERT: I 527 ARG cc_start: 0.6942 (mtt-85) cc_final: 0.6600 (mmt-90) REVERT: I 549 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7543 (p0) REVERT: I 578 ILE cc_start: 0.7962 (mt) cc_final: 0.7695 (mt) REVERT: I 648 ASP cc_start: 0.7201 (t0) cc_final: 0.6897 (t0) REVERT: I 664 GLN cc_start: 0.5754 (pm20) cc_final: 0.5458 (pm20) outliers start: 57 outliers final: 18 residues processed: 372 average time/residue: 0.3284 time to fit residues: 195.3479 Evaluate side-chains 321 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 299 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 570 ASN Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 634 THR 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 F residue 634 THR Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 549 ASP Chi-restraints excluded: chain H residue 634 THR Chi-restraints excluded: chain I residue 400 LEU Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 634 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 3.9990 chunk 258 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 168 optimal weight: 0.0470 chunk 70 optimal weight: 0.5980 chunk 287 optimal weight: 0.2980 chunk 238 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 ASN ** E 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** 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 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 570 ASN ** I 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24471 Z= 0.133 Angle : 0.503 7.572 33156 Z= 0.247 Chirality : 0.042 0.284 3924 Planarity : 0.003 0.031 4239 Dihedral : 3.459 15.352 3285 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.75 % Allowed : 13.05 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3006 helix: 1.47 (0.14), residues: 1386 sheet: -0.83 (0.21), residues: 576 loop : -1.83 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 654 HIS 0.003 0.000 HIS G 608 PHE 0.020 0.001 PHE G 457 TYR 0.006 0.001 TYR E 556 ARG 0.004 0.000 ARG H 580 *********************** 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 365 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 318 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 480 MET cc_start: 0.9039 (tpt) cc_final: 0.7890 (tpt) REVERT: E 549 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7393 (p0) REVERT: E 578 ILE cc_start: 0.8005 (mt) cc_final: 0.7737 (mt) REVERT: A 527 ARG cc_start: 0.6838 (mtt-85) cc_final: 0.6544 (mmt-90) REVERT: A 578 ILE cc_start: 0.8011 (mt) cc_final: 0.7780 (mt) REVERT: A 635 ARG cc_start: 0.7333 (tmm160) cc_final: 0.7117 (tmm160) REVERT: A 669 ILE cc_start: 0.6543 (mm) cc_final: 0.6122 (mt) REVERT: B 440 MET cc_start: 0.6828 (mtp) cc_final: 0.6429 (mtm) REVERT: B 527 ARG cc_start: 0.6951 (mtt-85) cc_final: 0.6593 (mmt-90) REVERT: B 578 ILE cc_start: 0.7997 (mt) cc_final: 0.7716 (mt) REVERT: B 664 GLN cc_start: 0.5542 (pm20) cc_final: 0.5291 (pm20) REVERT: C 420 TYR cc_start: 0.6862 (m-80) cc_final: 0.6156 (m-80) REVERT: C 578 ILE cc_start: 0.7919 (mt) cc_final: 0.7645 (mt) REVERT: D 496 MET cc_start: 0.8019 (tpp) cc_final: 0.7604 (tpp) REVERT: D 578 ILE cc_start: 0.7971 (mt) cc_final: 0.7722 (mt) REVERT: D 614 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: D 664 GLN cc_start: 0.5518 (pm20) cc_final: 0.5299 (pm20) REVERT: F 527 ARG cc_start: 0.7084 (mtt-85) cc_final: 0.6729 (mmt-90) REVERT: F 578 ILE cc_start: 0.8008 (mt) cc_final: 0.7761 (mt) REVERT: F 664 GLN cc_start: 0.5711 (pm20) cc_final: 0.5320 (pm20) REVERT: G 527 ARG cc_start: 0.7032 (mtt-85) cc_final: 0.6677 (mmt-90) REVERT: G 549 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7569 (p0) REVERT: G 578 ILE cc_start: 0.7937 (mt) cc_final: 0.7665 (mt) REVERT: H 518 GLU cc_start: 0.7819 (tt0) cc_final: 0.7567 (tm-30) REVERT: H 578 ILE cc_start: 0.8129 (mt) cc_final: 0.7896 (mt) REVERT: H 614 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: H 664 GLN cc_start: 0.5727 (pm20) cc_final: 0.5423 (pm20) REVERT: I 400 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6320 (pt) REVERT: I 549 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7450 (p0) REVERT: I 578 ILE cc_start: 0.7967 (mt) cc_final: 0.7678 (mt) REVERT: I 664 GLN cc_start: 0.5707 (pm20) cc_final: 0.5350 (pm20) outliers start: 47 outliers final: 24 residues processed: 354 average time/residue: 0.3259 time to fit residues: 184.1904 Evaluate side-chains 326 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 296 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 634 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 634 THR 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 634 THR Chi-restraints excluded: chain F residue 387 GLU Chi-restraints excluded: chain F residue 400 LEU 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 549 ASP Chi-restraints excluded: chain G residue 634 THR Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain H residue 634 THR Chi-restraints excluded: chain I residue 400 LEU Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 614 GLN Chi-restraints excluded: chain I residue 634 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 ASN ** E 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** 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 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 ASN ** 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 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 570 ASN ** I 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 570 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24471 Z= 0.274 Angle : 0.607 13.935 33156 Z= 0.287 Chirality : 0.044 0.230 3924 Planarity : 0.004 0.039 4239 Dihedral : 3.713 15.593 3285 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.09 % Allowed : 13.42 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3006 helix: 1.12 (0.14), residues: 1395 sheet: -0.93 (0.21), residues: 576 loop : -1.82 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 543 HIS 0.005 0.001 HIS B 564 PHE 0.019 0.001 PHE C 457 TYR 0.010 0.001 TYR H 420 ARG 0.006 0.000 ARG C 580 *********************** 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 359 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 303 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 527 ARG cc_start: 0.6892 (mtt-85) cc_final: 0.6534 (mmt-90) REVERT: A 613 LEU cc_start: 0.8092 (mp) cc_final: 0.7884 (mp) REVERT: A 669 ILE cc_start: 0.6848 (mm) cc_final: 0.6507 (mt) REVERT: B 440 MET cc_start: 0.6989 (mtp) cc_final: 0.6695 (mtm) REVERT: B 578 ILE cc_start: 0.7992 (mt) cc_final: 0.7725 (mt) REVERT: B 614 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: B 664 GLN cc_start: 0.5701 (pm20) cc_final: 0.5423 (pm20) REVERT: C 420 TYR cc_start: 0.6990 (m-80) cc_final: 0.6196 (m-80) REVERT: C 527 ARG cc_start: 0.7028 (mtt-85) cc_final: 0.6618 (mmt-90) REVERT: C 578 ILE cc_start: 0.7862 (mt) cc_final: 0.7599 (mt) REVERT: D 496 MET cc_start: 0.8129 (tpp) cc_final: 0.7814 (tpp) REVERT: D 527 ARG cc_start: 0.7081 (mtt-85) cc_final: 0.6748 (mmt-90) REVERT: D 578 ILE cc_start: 0.7944 (mt) cc_final: 0.7698 (mt) REVERT: D 613 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7987 (mp) REVERT: D 614 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: D 664 GLN cc_start: 0.5728 (pm20) cc_final: 0.5486 (pm20) REVERT: F 556 TYR cc_start: 0.8501 (m-10) cc_final: 0.8216 (m-10) REVERT: F 578 ILE cc_start: 0.8071 (mt) cc_final: 0.7827 (mt) REVERT: F 664 GLN cc_start: 0.5765 (pm20) cc_final: 0.5344 (pm20) REVERT: G 549 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7863 (p0) REVERT: G 578 ILE cc_start: 0.7920 (mt) cc_final: 0.7631 (mt) REVERT: G 613 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8012 (mp) REVERT: G 614 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7991 (pm20) REVERT: H 518 GLU cc_start: 0.7840 (tt0) cc_final: 0.7561 (tm-30) REVERT: H 527 ARG cc_start: 0.7006 (mtt-85) cc_final: 0.6640 (mmt-90) REVERT: H 578 ILE cc_start: 0.8135 (mt) cc_final: 0.7854 (mt) REVERT: H 648 ASP cc_start: 0.7335 (t0) cc_final: 0.7073 (t0) REVERT: H 664 GLN cc_start: 0.5906 (pm20) cc_final: 0.5628 (pm20) REVERT: I 400 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6203 (pt) REVERT: I 527 ARG cc_start: 0.6904 (mtt-85) cc_final: 0.6547 (mmt-90) REVERT: I 578 ILE cc_start: 0.7968 (mt) cc_final: 0.7659 (mt) REVERT: I 648 ASP cc_start: 0.7299 (t0) cc_final: 0.6925 (t0) outliers start: 56 outliers final: 37 residues processed: 346 average time/residue: 0.3445 time to fit residues: 187.7587 Evaluate side-chains 341 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 297 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 570 ASN Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 634 THR Chi-restraints excluded: chain E residue 657 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 634 THR 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 634 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 634 THR 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 613 LEU Chi-restraints excluded: chain D residue 614 GLN Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 634 THR 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 615 LEU Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 401 THR Chi-restraints excluded: chain G residue 549 ASP Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain G residue 634 THR Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 570 ASN Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain H residue 634 THR Chi-restraints excluded: chain H residue 657 LEU Chi-restraints excluded: chain I residue 400 LEU Chi-restraints excluded: chain I residue 614 GLN Chi-restraints excluded: chain I residue 634 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 195 optimal weight: 0.0770 chunk 141 optimal weight: 0.3980 chunk 26 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 ASN ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN ** B 389 ASN ** 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 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 ASN ** 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 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 570 ASN ** I 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24471 Z= 0.161 Angle : 0.556 13.972 33156 Z= 0.265 Chirality : 0.042 0.195 3924 Planarity : 0.004 0.048 4239 Dihedral : 3.532 14.060 3285 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.64 % Allowed : 14.43 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3006 helix: 1.38 (0.14), residues: 1395 sheet: -0.93 (0.21), residues: 576 loop : -1.67 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 654 HIS 0.002 0.000 HIS E 608 PHE 0.016 0.001 PHE G 457 TYR 0.008 0.001 TYR E 556 ARG 0.010 0.000 ARG E 590 *********************** 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 349 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 305 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 GLN cc_start: 0.8470 (pp30) cc_final: 0.8025 (pp30) REVERT: B 440 MET cc_start: 0.6882 (mtp) cc_final: 0.6525 (mtm) REVERT: B 527 ARG cc_start: 0.6951 (mtt-85) cc_final: 0.6596 (mmt-90) REVERT: B 578 ILE cc_start: 0.8005 (mt) cc_final: 0.7735 (mt) REVERT: B 614 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7941 (pm20) REVERT: B 664 GLN cc_start: 0.5764 (pm20) cc_final: 0.5415 (pm20) REVERT: C 420 TYR cc_start: 0.6922 (m-80) cc_final: 0.6147 (m-80) REVERT: C 527 ARG cc_start: 0.6969 (mtt-85) cc_final: 0.6593 (mmt-90) REVERT: C 578 ILE cc_start: 0.7874 (mt) cc_final: 0.7601 (mt) REVERT: D 496 MET cc_start: 0.8122 (tpp) cc_final: 0.7742 (tpp) REVERT: D 578 ILE cc_start: 0.7975 (mt) cc_final: 0.7708 (mt) REVERT: D 613 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7948 (mp) REVERT: D 614 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: D 664 GLN cc_start: 0.5614 (pm20) cc_final: 0.5405 (pm20) REVERT: F 527 ARG cc_start: 0.7047 (mtt-85) cc_final: 0.6697 (mmt-90) REVERT: F 556 TYR cc_start: 0.8480 (m-10) cc_final: 0.8218 (m-10) REVERT: F 578 ILE cc_start: 0.8063 (mt) cc_final: 0.7809 (mt) REVERT: F 664 GLN cc_start: 0.5689 (pm20) cc_final: 0.5304 (pm20) REVERT: G 527 ARG cc_start: 0.7018 (mtt-85) cc_final: 0.6637 (mmt-90) REVERT: G 549 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7600 (p0) REVERT: G 578 ILE cc_start: 0.7912 (mt) cc_final: 0.7640 (mt) REVERT: G 613 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7992 (mp) REVERT: G 614 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: H 518 GLU cc_start: 0.7820 (tt0) cc_final: 0.7526 (tm-30) REVERT: H 578 ILE cc_start: 0.8150 (mt) cc_final: 0.7908 (mt) REVERT: H 664 GLN cc_start: 0.5740 (pm20) cc_final: 0.5445 (pm20) REVERT: I 400 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6245 (pt) REVERT: I 527 ARG cc_start: 0.6867 (mtt-85) cc_final: 0.6525 (mmt-90) REVERT: I 578 ILE cc_start: 0.7972 (mt) cc_final: 0.7676 (mt) REVERT: I 648 ASP cc_start: 0.7229 (t0) cc_final: 0.6875 (t0) outliers start: 44 outliers final: 25 residues processed: 339 average time/residue: 0.3333 time to fit residues: 181.5961 Evaluate side-chains 326 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 294 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 614 GLN Chi-restraints excluded: chain D residue 634 THR 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 615 LEU Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 401 THR Chi-restraints excluded: chain G residue 549 ASP Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 614 GLN Chi-restraints excluded: chain H residue 400 LEU Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain I residue 400 LEU Chi-restraints excluded: chain I residue 614 GLN Chi-restraints excluded: chain I residue 634 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.1980 chunk 274 optimal weight: 9.9990 chunk 250 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 chunk 252 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN ** B 389 ASN ** 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 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 ASN ** 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 389 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24471 Z= 0.252 Angle : 0.590 13.646 33156 Z= 0.284 Chirality : 0.044 0.181 3924 Planarity : 0.004 0.041 4239 Dihedral : 3.668 15.946 3285 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.68 % Allowed : 14.91 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3006 helix: 1.21 (0.14), residues: 1395 sheet: -0.99 (0.21), residues: 576 loop : -1.65 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 543 HIS 0.004 0.001 HIS H 564 PHE 0.016 0.001 PHE C 457 TYR 0.009 0.001 TYR E 556 ARG 0.006 0.000 ARG G 580 *********************** 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 348 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 303 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 527 ARG cc_start: 0.6894 (mtt-85) cc_final: 0.6520 (mmt-90) REVERT: E 648 ASP cc_start: 0.7094 (t0) cc_final: 0.6829 (t0) REVERT: B 440 MET cc_start: 0.7014 (mtp) cc_final: 0.6698 (mtm) REVERT: B 527 ARG cc_start: 0.6940 (mtt-85) cc_final: 0.6580 (mmt-90) REVERT: B 578 ILE cc_start: 0.8013 (mt) cc_final: 0.7756 (mt) REVERT: B 614 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: B 664 GLN cc_start: 0.5811 (pm20) cc_final: 0.5432 (pm20) REVERT: C 420 TYR cc_start: 0.6969 (m-80) cc_final: 0.6174 (m-80) REVERT: C 527 ARG cc_start: 0.6993 (mtt-85) cc_final: 0.6616 (mmt-90) REVERT: C 578 ILE cc_start: 0.7871 (mt) cc_final: 0.7593 (mt) REVERT: D 527 ARG cc_start: 0.7060 (mtt-85) cc_final: 0.6734 (mmt-90) REVERT: D 578 ILE cc_start: 0.7938 (mt) cc_final: 0.7689 (mt) REVERT: D 613 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7981 (mp) REVERT: D 614 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7970 (pm20) REVERT: D 664 GLN cc_start: 0.5720 (pm20) cc_final: 0.5481 (pm20) REVERT: F 527 ARG cc_start: 0.7026 (mtt-85) cc_final: 0.6719 (mmt-90) REVERT: F 556 TYR cc_start: 0.8525 (m-10) cc_final: 0.8297 (m-10) REVERT: F 578 ILE cc_start: 0.8095 (mt) cc_final: 0.7859 (mt) REVERT: F 664 GLN cc_start: 0.5725 (pm20) cc_final: 0.5355 (pm20) REVERT: G 527 ARG cc_start: 0.6930 (mtt-85) cc_final: 0.6585 (mmt-90) REVERT: G 549 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7810 (p0) REVERT: G 578 ILE cc_start: 0.7931 (mt) cc_final: 0.7656 (mt) REVERT: G 613 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7919 (mp) REVERT: G 614 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7936 (pm20) REVERT: H 518 GLU cc_start: 0.7880 (tt0) cc_final: 0.7570 (tm-30) REVERT: H 527 ARG cc_start: 0.6976 (mtt-85) cc_final: 0.6608 (mmt-90) REVERT: H 578 ILE cc_start: 0.8103 (mt) cc_final: 0.7862 (mt) REVERT: H 648 ASP cc_start: 0.7354 (t0) cc_final: 0.7094 (t0) REVERT: H 664 GLN cc_start: 0.5873 (pm20) cc_final: 0.5576 (pm20) REVERT: I 400 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6201 (pt) REVERT: I 527 ARG cc_start: 0.6851 (mtt-85) cc_final: 0.6531 (mmt-90) REVERT: I 648 ASP cc_start: 0.7276 (t0) cc_final: 0.6917 (t0) REVERT: I 664 GLN cc_start: 0.5119 (pm20) cc_final: 0.4840 (mp10) outliers start: 45 outliers final: 33 residues processed: 337 average time/residue: 0.3340 time to fit residues: 177.3031 Evaluate side-chains 337 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 297 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 578 ILE 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 578 ILE Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 614 GLN Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 634 THR 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 569 LEU 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 499 ASN Chi-restraints excluded: chain G residue 513 ILE Chi-restraints excluded: chain G residue 549 ASP Chi-restraints excluded: chain G residue 613 LEU 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 570 ASN Chi-restraints excluded: chain H residue 614 GLN Chi-restraints excluded: chain H residue 657 LEU Chi-restraints excluded: chain I residue 400 LEU Chi-restraints excluded: chain I residue 614 GLN Chi-restraints excluded: chain I residue 634 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 10.0000 chunk 282 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 196 optimal weight: 0.9980 chunk 295 optimal weight: 0.9990 chunk 272 optimal weight: 20.0000 chunk 235 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 181 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** 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 389 ASN ** 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 389 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.278 24471 Z= 0.319 Angle : 0.834 59.199 33156 Z= 0.461 Chirality : 0.046 0.490 3924 Planarity : 0.004 0.075 4239 Dihedral : 3.769 34.563 3285 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.64 % Allowed : 15.18 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3006 helix: 1.18 (0.14), residues: 1395 sheet: -1.00 (0.20), residues: 576 loop : -1.64 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 543 HIS 0.004 0.001 HIS H 564 PHE 0.015 0.001 PHE C 457 TYR 0.009 0.001 TYR A 556 ARG 0.066 0.001 ARG D 590 ********************** 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 341 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 297 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 527 ARG cc_start: 0.6892 (mtt-85) cc_final: 0.6519 (mmt-90) REVERT: E 648 ASP cc_start: 0.7085 (t0) cc_final: 0.6826 (t0) REVERT: B 440 MET cc_start: 0.7012 (mtp) cc_final: 0.6696 (mtm) REVERT: B 527 ARG cc_start: 0.6939 (mtt-85) cc_final: 0.6581 (mmt-90) REVERT: B 578 ILE cc_start: 0.8016 (mt) cc_final: 0.7756 (mt) REVERT: B 614 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: B 664 GLN cc_start: 0.5811 (pm20) cc_final: 0.5426 (pm20) REVERT: C 420 TYR cc_start: 0.6956 (m-80) cc_final: 0.6179 (m-80) REVERT: C 527 ARG cc_start: 0.6993 (mtt-85) cc_final: 0.6609 (mmt-90) REVERT: C 578 ILE cc_start: 0.7868 (mt) cc_final: 0.7593 (mt) REVERT: D 496 MET cc_start: 0.8167 (tpp) cc_final: 0.7827 (tpp) REVERT: D 527 ARG cc_start: 0.7055 (mtt-85) cc_final: 0.6733 (mmt-90) REVERT: D 578 ILE cc_start: 0.7933 (mt) cc_final: 0.7686 (mt) REVERT: D 613 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7977 (mp) REVERT: D 614 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7974 (pm20) REVERT: D 664 GLN cc_start: 0.5717 (pm20) cc_final: 0.5475 (pm20) REVERT: F 527 ARG cc_start: 0.7022 (mtt-85) cc_final: 0.6717 (mmt-90) REVERT: F 556 TYR cc_start: 0.8508 (m-10) cc_final: 0.8290 (m-10) REVERT: F 578 ILE cc_start: 0.8094 (mt) cc_final: 0.7860 (mt) REVERT: F 664 GLN cc_start: 0.5706 (pm20) cc_final: 0.5320 (pm20) REVERT: G 527 ARG cc_start: 0.6928 (mtt-85) cc_final: 0.6585 (mmt-90) REVERT: G 549 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7824 (p0) REVERT: G 578 ILE cc_start: 0.7928 (mt) cc_final: 0.7657 (mt) REVERT: G 613 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7918 (mp) REVERT: G 614 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: H 518 GLU cc_start: 0.7876 (tt0) cc_final: 0.7563 (tm-30) REVERT: H 527 ARG cc_start: 0.6983 (mtt-85) cc_final: 0.6611 (mmt-90) REVERT: H 578 ILE cc_start: 0.8079 (mt) cc_final: 0.7845 (mt) REVERT: H 613 LEU cc_start: 0.8080 (mp) cc_final: 0.7799 (mp) REVERT: H 648 ASP cc_start: 0.7353 (t0) cc_final: 0.7090 (t0) REVERT: H 664 GLN cc_start: 0.5863 (pm20) cc_final: 0.5544 (pm20) REVERT: I 400 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6198 (pt) REVERT: I 527 ARG cc_start: 0.6843 (mtt-85) cc_final: 0.6528 (mmt-90) REVERT: I 648 ASP cc_start: 0.7274 (t0) cc_final: 0.6914 (t0) outliers start: 44 outliers final: 34 residues processed: 331 average time/residue: 0.3362 time to fit residues: 178.5629 Evaluate side-chains 338 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 297 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 614 GLN Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 634 THR 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 569 LEU Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 401 THR Chi-restraints excluded: chain G residue 499 ASN Chi-restraints excluded: chain G residue 513 ILE Chi-restraints excluded: chain G residue 549 ASP Chi-restraints excluded: chain G residue 613 LEU 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 657 LEU Chi-restraints excluded: chain I residue 400 LEU Chi-restraints excluded: chain I residue 578 ILE Chi-restraints excluded: chain I residue 614 GLN Chi-restraints excluded: chain I residue 634 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 242 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** 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 389 ASN ** 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 389 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.211005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.168110 restraints weight = 27325.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.165641 restraints weight = 40299.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.166832 restraints weight = 39691.050| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.278 24471 Z= 0.319 Angle : 0.834 59.199 33156 Z= 0.461 Chirality : 0.046 0.490 3924 Planarity : 0.004 0.075 4239 Dihedral : 3.769 34.563 3285 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.53 % Allowed : 15.14 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3006 helix: 1.18 (0.14), residues: 1395 sheet: -1.00 (0.20), residues: 576 loop : -1.64 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 543 HIS 0.004 0.001 HIS H 564 PHE 0.015 0.001 PHE C 457 TYR 0.009 0.001 TYR A 556 ARG 0.066 0.001 ARG D 590 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4514.60 seconds wall clock time: 82 minutes 10.76 seconds (4930.76 seconds total)