Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 18 03:35:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fec_31552/08_2023/7fec_31552.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fec_31552/08_2023/7fec_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_31552/08_2023/7fec_31552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fec_31552/08_2023/7fec_31552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fec_31552/08_2023/7fec_31552.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fec_31552/08_2023/7fec_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 8.58, per 1000 atoms: 0.36 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: 10.80 Conformation dependent library (CDL) restraints added in 3.9 seconds 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5742 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 36 sheets defined 47.9% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 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: 9.51 Time building geometry restraints manager: 11.48 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 27.680 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 58.490 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.150 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.340 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.583 Fit side-chains outliers start: 9 outliers final: 0 residues processed: 397 average time/residue: 0.4166 time to fit residues: 244.6039 Evaluate side-chains 300 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 2.874 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1861 ------------------------------------------------------------------------------- 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: 10.0000 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: 0.0670 chunk 173 optimal weight: 0.0670 chunk 269 optimal weight: 3.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 570 ASN A 608 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 24471 Z= 0.175 Angle : 0.569 5.624 33156 Z= 0.282 Chirality : 0.044 0.249 3924 Planarity : 0.004 0.035 4239 Dihedral : 4.145 19.429 3285 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.75 % 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: -0.98 (0.15), residues: 3006 helix: 0.58 (0.14), residues: 1377 sheet: -0.87 (0.22), residues: 558 loop : -2.13 (0.16), residues: 1071 *********************** 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 367 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 347 time to evaluate : 2.706 Fit side-chains outliers start: 20 outliers final: 6 residues processed: 364 average time/residue: 0.3611 time to fit residues: 203.2260 Evaluate side-chains 304 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 298 time to evaluate : 2.603 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2104 time to fit residues: 6.0601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 224 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 270 optimal weight: 0.3980 chunk 291 optimal weight: 0.9990 chunk 240 optimal weight: 0.0060 chunk 267 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 570 ASN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 ASN H 570 ASN ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 570 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 24471 Z= 0.159 Angle : 0.527 5.692 33156 Z= 0.262 Chirality : 0.042 0.189 3924 Planarity : 0.003 0.034 4239 Dihedral : 3.861 16.718 3285 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.86 % 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: -0.62 (0.15), residues: 3006 helix: 0.99 (0.14), residues: 1377 sheet: -0.90 (0.22), residues: 576 loop : -2.00 (0.17), residues: 1053 *********************** 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 378 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 328 time to evaluate : 2.878 Fit side-chains outliers start: 50 outliers final: 5 residues processed: 378 average time/residue: 0.3390 time to fit residues: 204.4935 Evaluate side-chains 305 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 300 time to evaluate : 2.718 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2412 time to fit residues: 6.0662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 128 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 10.0000 chunk 287 optimal weight: 0.4980 chunk 141 optimal weight: 0.0170 chunk 256 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 overall best weight: 2.1024 ------------------------------------------------------------------------------- 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** B 570 ASN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 24471 Z= 0.390 Angle : 0.666 7.885 33156 Z= 0.328 Chirality : 0.048 0.287 3924 Planarity : 0.004 0.043 4239 Dihedral : 4.269 16.197 3285 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 1.94 % 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: -0.99 (0.15), residues: 3006 helix: 0.59 (0.14), residues: 1377 sheet: -0.77 (0.22), residues: 558 loop : -2.22 (0.16), residues: 1071 *********************** 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 356 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 304 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 13 residues processed: 351 average time/residue: 0.3399 time to fit residues: 194.3733 Evaluate side-chains 295 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 282 time to evaluate : 2.572 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2120 time to fit residues: 8.7877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 4 optimal weight: 0.0060 chunk 213 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 244 optimal weight: 0.5980 chunk 198 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 257 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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: 0.7933 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 24471 Z= 0.173 Angle : 0.556 9.257 33156 Z= 0.273 Chirality : 0.043 0.242 3924 Planarity : 0.003 0.033 4239 Dihedral : 3.840 14.255 3285 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 1.57 % 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: -0.61 (0.15), residues: 3006 helix: 0.93 (0.14), residues: 1386 sheet: -0.93 (0.21), residues: 576 loop : -1.87 (0.17), residues: 1044 *********************** 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 343 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 301 time to evaluate : 2.910 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 9 residues processed: 336 average time/residue: 0.3222 time to fit residues: 175.4471 Evaluate side-chains 289 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 280 time to evaluate : 2.974 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2115 time to fit residues: 7.7516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 0.9990 chunk 258 optimal weight: 0.9980 chunk 56 optimal weight: 0.0370 chunk 168 optimal weight: 0.0470 chunk 70 optimal weight: 0.5980 chunk 287 optimal weight: 0.0270 chunk 238 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 overall best weight: 0.3414 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 24471 Z= 0.139 Angle : 0.520 12.078 33156 Z= 0.256 Chirality : 0.041 0.203 3924 Planarity : 0.003 0.041 4239 Dihedral : 3.563 13.550 3285 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 1.30 % 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: 1.24 (0.14), residues: 1386 sheet: -0.87 (0.21), residues: 576 loop : -1.76 (0.17), residues: 1044 *********************** 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 344 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 309 time to evaluate : 2.719 Fit side-chains outliers start: 35 outliers final: 5 residues processed: 341 average time/residue: 0.3418 time to fit residues: 185.6397 Evaluate side-chains 284 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 279 time to evaluate : 2.941 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2123 time to fit residues: 6.0877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 163 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 286 optimal weight: 0.0270 chunk 179 optimal weight: 0.8980 chunk 174 optimal weight: 0.0470 chunk 132 optimal weight: 5.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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 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** G 570 ASN ** 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: 0.7945 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 24471 Z= 0.217 Angle : 0.609 14.028 33156 Z= 0.289 Chirality : 0.043 0.202 3924 Planarity : 0.004 0.039 4239 Dihedral : 3.618 13.267 3285 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.78 % 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: -0.41 (0.15), residues: 3006 helix: 1.07 (0.14), residues: 1386 sheet: -0.88 (0.21), residues: 576 loop : -1.71 (0.17), residues: 1044 *********************** 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 317 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 296 time to evaluate : 2.585 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 315 average time/residue: 0.3569 time to fit residues: 177.3662 Evaluate side-chains 293 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 283 time to evaluate : 2.595 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2344 time to fit residues: 7.8563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 170 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 225 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 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** ** I 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 608 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 24471 Z= 0.197 Angle : 0.590 15.878 33156 Z= 0.279 Chirality : 0.043 0.220 3924 Planarity : 0.004 0.051 4239 Dihedral : 3.569 13.560 3285 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.30 % 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: -0.33 (0.15), residues: 3006 helix: 1.14 (0.14), residues: 1395 sheet: -0.88 (0.21), residues: 576 loop : -1.66 (0.18), residues: 1035 *********************** 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 308 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 300 time to evaluate : 2.776 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 306 average time/residue: 0.3784 time to fit residues: 182.5318 Evaluate side-chains 297 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 292 time to evaluate : 2.859 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2420 time to fit residues: 5.9861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 2.9990 chunk 274 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 241 optimal weight: 7.9990 chunk 252 optimal weight: 0.8980 chunk 265 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 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 389 ASN ** 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 24471 Z= 0.265 Angle : 0.613 16.359 33156 Z= 0.293 Chirality : 0.044 0.188 3924 Planarity : 0.004 0.048 4239 Dihedral : 3.715 14.490 3285 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.19 % 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: -0.43 (0.15), residues: 3006 helix: 1.02 (0.14), residues: 1395 sheet: -0.91 (0.21), residues: 576 loop : -1.64 (0.18), residues: 1035 *********************** 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 315 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 310 time to evaluate : 2.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 315 average time/residue: 0.3615 time to fit residues: 177.7872 Evaluate side-chains 294 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 2.566 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2582 time to fit residues: 4.2011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 chunk 272 optimal weight: 20.0000 chunk 235 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 HIS ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 24471 Z= 0.209 Angle : 0.609 16.886 33156 Z= 0.287 Chirality : 0.043 0.268 3924 Planarity : 0.004 0.048 4239 Dihedral : 3.625 14.041 3285 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.07 % 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: -0.29 (0.15), residues: 3006 helix: 1.15 (0.14), residues: 1395 sheet: -0.91 (0.21), residues: 576 loop : -1.58 (0.18), residues: 1035 ********************** 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 309 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 307 time to evaluate : 2.900 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 309 average time/residue: 0.3518 time to fit residues: 172.8762 Evaluate side-chains 296 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 295 time to evaluate : 2.549 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2104 time to fit residues: 4.2061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.7980 chunk 250 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 217 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 242 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 HIS ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** 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** ** I 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 608 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.212949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.175533 restraints weight = 27283.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.173588 restraints weight = 44671.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.173458 restraints weight = 42479.948| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 24471 Z= 0.212 Angle : 0.596 15.980 33156 Z= 0.282 Chirality : 0.043 0.232 3924 Planarity : 0.004 0.059 4239 Dihedral : 3.616 13.996 3285 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.22 % 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: -0.28 (0.15), residues: 3006 helix: 1.16 (0.14), residues: 1395 sheet: -0.92 (0.21), residues: 576 loop : -1.55 (0.18), residues: 1035 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4337.85 seconds wall clock time: 80 minutes 26.67 seconds (4826.67 seconds total)