Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 27 01:12:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fed_31553/08_2023/7fed_31553.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fed_31553/08_2023/7fed_31553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fed_31553/08_2023/7fed_31553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fed_31553/08_2023/7fed_31553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fed_31553/08_2023/7fed_31553.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fed_31553/08_2023/7fed_31553.pdb" } resolution = 3.55 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= 0.001 sd= 0.110 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 216 5.16 5 C 30708 2.51 5 N 8280 2.21 5 O 8946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 617": "OE1" <-> "OE2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "B PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 617": "OE1" <-> "OE2" Residue "C PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 617": "OE1" <-> "OE2" Residue "D PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 617": "OE1" <-> "OE2" Residue "F PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 617": "OE1" <-> "OE2" Residue "G PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 617": "OE1" <-> "OE2" Residue "H PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 617": "OE1" <-> "OE2" Residue "I PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 617": "OE1" <-> "OE2" Residue "J PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 617": "OE1" <-> "OE2" Residue "K PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 617": "OE1" <-> "OE2" Residue "L PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 617": "OE1" <-> "OE2" Residue "M PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 617": "OE1" <-> "OE2" Residue "N PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 617": "OE1" <-> "OE2" Residue "O PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 617": "OE1" <-> "OE2" Residue "P PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 617": "OE1" <-> "OE2" Residue "Q PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 617": "OE1" <-> "OE2" Residue "R PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 617": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 48150 Number of models: 1 Model: "" Number of chains: 18 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} Chain: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: 22.66, per 1000 atoms: 0.47 Number of scatterers: 48150 At special positions: 0 Unit cell: (181.31, 178.78, 139.145, 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 216 16.00 O 8946 8.00 N 8280 7.00 C 30708 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: 18.64 Conformation dependent library (CDL) restraints added in 7.2 seconds 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11484 Finding SS restraints... Secondary structure from input PDB file: 261 helices and 72 sheets defined 50.3% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.00 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 458 removed outlier: 3.524A pdb=" N GLY E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 479 removed outlier: 3.619A pdb=" N LEU E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS E 474 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 484 removed outlier: 4.063A 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: 4.041A pdb=" N ASN E 570 " --> pdb=" O LEU E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER E 592 " --> pdb=" O LEU E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 621 removed outlier: 3.582A pdb=" N LYS E 621 " --> pdb=" O GLU E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 643 Processing helix chain 'A' and resid 359 through 362 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 458 removed outlier: 3.524A pdb=" N GLY A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.619A pdb=" N LEU A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 4.063A 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: 4.041A pdb=" N ASN A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 621 removed outlier: 3.581A pdb=" N LYS A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'B' and resid 359 through 362 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 458 removed outlier: 3.524A pdb=" N GLY B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.619A pdb=" N LEU B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 484 removed outlier: 4.063A 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: 4.042A pdb=" N ASN B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 621 removed outlier: 3.581A pdb=" N LYS B 621 " --> pdb=" O GLU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'C' and resid 359 through 362 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 458 removed outlier: 3.524A pdb=" N GLY C 458 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.619A pdb=" N LEU C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS C 474 " --> pdb=" O ALA C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 484 removed outlier: 4.063A 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: 4.041A pdb=" N ASN C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 621 removed outlier: 3.582A pdb=" N LYS C 621 " --> pdb=" O GLU C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 Processing helix chain 'D' and resid 359 through 362 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 458 removed outlier: 3.524A pdb=" N GLY D 458 " --> pdb=" O ALA D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.618A pdb=" N LEU D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS D 474 " --> pdb=" O ALA D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 484 removed outlier: 4.063A 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: 4.042A pdb=" N ASN D 570 " --> pdb=" O LEU D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.680A pdb=" N SER D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 621 removed outlier: 3.581A pdb=" N LYS D 621 " --> pdb=" O GLU D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 Processing helix chain 'F' and resid 359 through 362 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 458 removed outlier: 3.523A pdb=" N GLY F 458 " --> pdb=" O ALA F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 479 removed outlier: 3.618A pdb=" N LEU F 471 " --> pdb=" O ARG F 467 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS F 474 " --> pdb=" O ALA F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 484 removed outlier: 4.063A 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: 4.040A pdb=" N ASN F 570 " --> pdb=" O LEU F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER F 592 " --> pdb=" O LEU F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 621 removed outlier: 3.582A pdb=" N LYS F 621 " --> pdb=" O GLU F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 643 Processing helix chain 'G' and resid 359 through 362 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 458 removed outlier: 3.524A pdb=" N GLY G 458 " --> pdb=" O ALA G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 465 through 479 removed outlier: 3.618A pdb=" N LEU G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 484 removed outlier: 4.063A 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: 4.041A pdb=" N ASN G 570 " --> pdb=" O LEU G 566 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 592 removed outlier: 3.682A pdb=" N SER G 592 " --> pdb=" O LEU G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 621 removed outlier: 3.582A pdb=" N LYS G 621 " --> pdb=" O GLU G 617 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 643 Processing helix chain 'H' and resid 359 through 362 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 458 removed outlier: 3.525A pdb=" N GLY H 458 " --> pdb=" O ALA H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 465 through 479 removed outlier: 3.619A pdb=" N LEU H 471 " --> pdb=" O ARG H 467 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS H 474 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 484 removed outlier: 4.064A 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: 4.041A pdb=" N ASN H 570 " --> pdb=" O LEU H 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER H 592 " --> pdb=" O LEU H 588 " (cutoff:3.500A) Processing helix chain 'H' and resid 605 through 621 removed outlier: 3.581A pdb=" N LYS H 621 " --> pdb=" O GLU H 617 " (cutoff:3.500A) Processing helix chain 'H' and resid 634 through 643 Processing helix chain 'I' and resid 359 through 362 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 458 removed outlier: 3.524A pdb=" N GLY I 458 " --> pdb=" O ALA I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 465 through 479 removed outlier: 3.618A pdb=" N LEU I 471 " --> pdb=" O ARG I 467 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS I 474 " --> pdb=" O ALA I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 480 through 484 removed outlier: 4.063A 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: 4.041A pdb=" N ASN I 570 " --> pdb=" O LEU I 566 " (cutoff:3.500A) Processing helix chain 'I' and resid 582 through 592 removed outlier: 3.680A pdb=" N SER I 592 " --> pdb=" O LEU I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 605 through 621 removed outlier: 3.582A pdb=" N LYS I 621 " --> pdb=" O GLU I 617 " (cutoff:3.500A) Processing helix chain 'I' and resid 634 through 643 Processing helix chain 'J' and resid 359 through 362 Processing helix chain 'J' and resid 365 through 382 Processing helix chain 'J' and resid 437 through 440 Processing helix chain 'J' and resid 447 through 458 removed outlier: 3.524A pdb=" N GLY J 458 " --> pdb=" O ALA J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 465 through 479 removed outlier: 3.619A pdb=" N LEU J 471 " --> pdb=" O ARG J 467 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS J 474 " --> pdb=" O ALA J 470 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 484 removed outlier: 4.063A pdb=" N ILE J 484 " --> pdb=" O GLY J 481 " (cutoff:3.500A) Processing helix chain 'J' and resid 485 through 497 Processing helix chain 'J' and resid 500 through 511 Processing helix chain 'J' and resid 512 through 525 Processing helix chain 'J' and resid 532 through 544 Processing helix chain 'J' and resid 549 through 561 Processing helix chain 'J' and resid 561 through 570 removed outlier: 4.041A pdb=" N ASN J 570 " --> pdb=" O LEU J 566 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER J 592 " --> pdb=" O LEU J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 605 through 621 removed outlier: 3.582A pdb=" N LYS J 621 " --> pdb=" O GLU J 617 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 643 Processing helix chain 'K' and resid 365 through 382 Processing helix chain 'K' and resid 437 through 440 Processing helix chain 'K' and resid 447 through 458 removed outlier: 3.524A pdb=" N GLY K 458 " --> pdb=" O ALA K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 465 through 479 removed outlier: 3.619A pdb=" N LEU K 471 " --> pdb=" O ARG K 467 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS K 474 " --> pdb=" O ALA K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 480 through 484 removed outlier: 4.063A pdb=" N ILE K 484 " --> pdb=" O GLY K 481 " (cutoff:3.500A) Processing helix chain 'K' and resid 485 through 497 Processing helix chain 'K' and resid 500 through 511 Processing helix chain 'K' and resid 512 through 525 Processing helix chain 'K' and resid 532 through 544 Processing helix chain 'K' and resid 549 through 561 Processing helix chain 'K' and resid 561 through 570 removed outlier: 4.041A pdb=" N ASN K 570 " --> pdb=" O LEU K 566 " (cutoff:3.500A) Processing helix chain 'K' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER K 592 " --> pdb=" O LEU K 588 " (cutoff:3.500A) Processing helix chain 'K' and resid 605 through 621 removed outlier: 3.581A pdb=" N LYS K 621 " --> pdb=" O GLU K 617 " (cutoff:3.500A) Processing helix chain 'K' and resid 634 through 643 Processing helix chain 'L' and resid 365 through 382 Processing helix chain 'L' and resid 437 through 440 Processing helix chain 'L' and resid 447 through 458 removed outlier: 3.523A pdb=" N GLY L 458 " --> pdb=" O ALA L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 465 through 479 removed outlier: 3.618A pdb=" N LEU L 471 " --> pdb=" O ARG L 467 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS L 474 " --> pdb=" O ALA L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 480 through 484 removed outlier: 4.063A pdb=" N ILE L 484 " --> pdb=" O GLY L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 485 through 497 Processing helix chain 'L' and resid 500 through 511 Processing helix chain 'L' and resid 512 through 525 Processing helix chain 'L' and resid 532 through 544 Processing helix chain 'L' and resid 549 through 561 Processing helix chain 'L' and resid 561 through 570 removed outlier: 4.041A pdb=" N ASN L 570 " --> pdb=" O LEU L 566 " (cutoff:3.500A) Processing helix chain 'L' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER L 592 " --> pdb=" O LEU L 588 " (cutoff:3.500A) Processing helix chain 'L' and resid 605 through 621 removed outlier: 3.582A pdb=" N LYS L 621 " --> pdb=" O GLU L 617 " (cutoff:3.500A) Processing helix chain 'L' and resid 634 through 643 Processing helix chain 'M' and resid 365 through 382 Processing helix chain 'M' and resid 437 through 440 Processing helix chain 'M' and resid 447 through 458 removed outlier: 3.524A pdb=" N GLY M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 465 through 479 removed outlier: 3.619A pdb=" N LEU M 471 " --> pdb=" O ARG M 467 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS M 474 " --> pdb=" O ALA M 470 " (cutoff:3.500A) Processing helix chain 'M' and resid 480 through 484 removed outlier: 4.063A pdb=" N ILE M 484 " --> pdb=" O GLY M 481 " (cutoff:3.500A) Processing helix chain 'M' and resid 485 through 497 Processing helix chain 'M' and resid 500 through 511 Processing helix chain 'M' and resid 512 through 525 Processing helix chain 'M' and resid 532 through 544 Processing helix chain 'M' and resid 549 through 561 Processing helix chain 'M' and resid 561 through 570 removed outlier: 4.041A pdb=" N ASN M 570 " --> pdb=" O LEU M 566 " (cutoff:3.500A) Processing helix chain 'M' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER M 592 " --> pdb=" O LEU M 588 " (cutoff:3.500A) Processing helix chain 'M' and resid 605 through 621 removed outlier: 3.582A pdb=" N LYS M 621 " --> pdb=" O GLU M 617 " (cutoff:3.500A) Processing helix chain 'M' and resid 634 through 643 Processing helix chain 'N' and resid 365 through 382 Processing helix chain 'N' and resid 437 through 440 Processing helix chain 'N' and resid 447 through 458 removed outlier: 3.524A pdb=" N GLY N 458 " --> pdb=" O ALA N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 465 through 479 removed outlier: 3.618A pdb=" N LEU N 471 " --> pdb=" O ARG N 467 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS N 474 " --> pdb=" O ALA N 470 " (cutoff:3.500A) Processing helix chain 'N' and resid 480 through 484 removed outlier: 4.063A pdb=" N ILE N 484 " --> pdb=" O GLY N 481 " (cutoff:3.500A) Processing helix chain 'N' and resid 485 through 497 Processing helix chain 'N' and resid 500 through 511 Processing helix chain 'N' and resid 512 through 525 Processing helix chain 'N' and resid 532 through 544 Processing helix chain 'N' and resid 549 through 561 Processing helix chain 'N' and resid 561 through 570 removed outlier: 4.042A pdb=" N ASN N 570 " --> pdb=" O LEU N 566 " (cutoff:3.500A) Processing helix chain 'N' and resid 582 through 592 removed outlier: 3.680A pdb=" N SER N 592 " --> pdb=" O LEU N 588 " (cutoff:3.500A) Processing helix chain 'N' and resid 605 through 621 removed outlier: 3.581A pdb=" N LYS N 621 " --> pdb=" O GLU N 617 " (cutoff:3.500A) Processing helix chain 'N' and resid 634 through 643 Processing helix chain 'O' and resid 365 through 382 Processing helix chain 'O' and resid 437 through 440 Processing helix chain 'O' and resid 447 through 458 removed outlier: 3.524A pdb=" N GLY O 458 " --> pdb=" O ALA O 454 " (cutoff:3.500A) Processing helix chain 'O' and resid 465 through 479 removed outlier: 3.619A pdb=" N LEU O 471 " --> pdb=" O ARG O 467 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS O 474 " --> pdb=" O ALA O 470 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 484 removed outlier: 4.063A pdb=" N ILE O 484 " --> pdb=" O GLY O 481 " (cutoff:3.500A) Processing helix chain 'O' and resid 485 through 497 Processing helix chain 'O' and resid 500 through 511 Processing helix chain 'O' and resid 512 through 525 Processing helix chain 'O' and resid 532 through 544 Processing helix chain 'O' and resid 549 through 561 Processing helix chain 'O' and resid 561 through 570 removed outlier: 4.041A pdb=" N ASN O 570 " --> pdb=" O LEU O 566 " (cutoff:3.500A) Processing helix chain 'O' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER O 592 " --> pdb=" O LEU O 588 " (cutoff:3.500A) Processing helix chain 'O' and resid 605 through 621 removed outlier: 3.582A pdb=" N LYS O 621 " --> pdb=" O GLU O 617 " (cutoff:3.500A) Processing helix chain 'O' and resid 634 through 643 Processing helix chain 'P' and resid 365 through 382 Processing helix chain 'P' and resid 437 through 440 Processing helix chain 'P' and resid 447 through 458 removed outlier: 3.524A pdb=" N GLY P 458 " --> pdb=" O ALA P 454 " (cutoff:3.500A) Processing helix chain 'P' and resid 465 through 479 removed outlier: 3.618A pdb=" N LEU P 471 " --> pdb=" O ARG P 467 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS P 474 " --> pdb=" O ALA P 470 " (cutoff:3.500A) Processing helix chain 'P' and resid 480 through 484 removed outlier: 4.063A pdb=" N ILE P 484 " --> pdb=" O GLY P 481 " (cutoff:3.500A) Processing helix chain 'P' and resid 485 through 497 Processing helix chain 'P' and resid 500 through 511 Processing helix chain 'P' and resid 512 through 525 Processing helix chain 'P' and resid 532 through 544 Processing helix chain 'P' and resid 549 through 561 Processing helix chain 'P' and resid 561 through 570 removed outlier: 4.041A pdb=" N ASN P 570 " --> pdb=" O LEU P 566 " (cutoff:3.500A) Processing helix chain 'P' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER P 592 " --> pdb=" O LEU P 588 " (cutoff:3.500A) Processing helix chain 'P' and resid 605 through 621 removed outlier: 3.582A pdb=" N LYS P 621 " --> pdb=" O GLU P 617 " (cutoff:3.500A) Processing helix chain 'P' and resid 634 through 643 Processing helix chain 'Q' and resid 365 through 382 Processing helix chain 'Q' and resid 437 through 440 Processing helix chain 'Q' and resid 447 through 458 removed outlier: 3.525A pdb=" N GLY Q 458 " --> pdb=" O ALA Q 454 " (cutoff:3.500A) Processing helix chain 'Q' and resid 465 through 479 removed outlier: 3.619A pdb=" N LEU Q 471 " --> pdb=" O ARG Q 467 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS Q 474 " --> pdb=" O ALA Q 470 " (cutoff:3.500A) Processing helix chain 'Q' and resid 480 through 484 removed outlier: 4.063A pdb=" N ILE Q 484 " --> pdb=" O GLY Q 481 " (cutoff:3.500A) Processing helix chain 'Q' and resid 485 through 497 Processing helix chain 'Q' and resid 500 through 511 Processing helix chain 'Q' and resid 512 through 525 Processing helix chain 'Q' and resid 532 through 544 Processing helix chain 'Q' and resid 549 through 561 Processing helix chain 'Q' and resid 561 through 570 removed outlier: 4.041A pdb=" N ASN Q 570 " --> pdb=" O LEU Q 566 " (cutoff:3.500A) Processing helix chain 'Q' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER Q 592 " --> pdb=" O LEU Q 588 " (cutoff:3.500A) Processing helix chain 'Q' and resid 605 through 621 removed outlier: 3.582A pdb=" N LYS Q 621 " --> pdb=" O GLU Q 617 " (cutoff:3.500A) Processing helix chain 'Q' and resid 634 through 643 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 437 through 440 Processing helix chain 'R' and resid 447 through 458 removed outlier: 3.523A pdb=" N GLY R 458 " --> pdb=" O ALA R 454 " (cutoff:3.500A) Processing helix chain 'R' and resid 465 through 479 removed outlier: 3.618A pdb=" N LEU R 471 " --> pdb=" O ARG R 467 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS R 474 " --> pdb=" O ALA R 470 " (cutoff:3.500A) Processing helix chain 'R' and resid 480 through 484 removed outlier: 4.063A pdb=" N ILE R 484 " --> pdb=" O GLY R 481 " (cutoff:3.500A) Processing helix chain 'R' and resid 485 through 497 Processing helix chain 'R' and resid 500 through 511 Processing helix chain 'R' and resid 512 through 525 Processing helix chain 'R' and resid 532 through 544 Processing helix chain 'R' and resid 549 through 561 Processing helix chain 'R' and resid 561 through 570 removed outlier: 4.041A pdb=" N ASN R 570 " --> pdb=" O LEU R 566 " (cutoff:3.500A) Processing helix chain 'R' and resid 582 through 592 removed outlier: 3.681A pdb=" N SER R 592 " --> pdb=" O LEU R 588 " (cutoff:3.500A) Processing helix chain 'R' and resid 605 through 621 removed outlier: 3.582A pdb=" N LYS R 621 " --> pdb=" O GLU R 617 " (cutoff:3.500A) Processing helix chain 'R' and resid 634 through 643 Processing sheet with id=AA1, first strand: chain 'E' and resid 388 through 392 removed outlier: 6.441A 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 435 Processing sheet with id=AA3, first strand: chain 'E' and resid 651 through 653 removed outlier: 6.297A pdb=" N ILE E 628 " --> pdb=" O LEU E 652 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU E 579 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE E 578 " --> pdb=" O VAL E 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER E 668 " --> pdb=" O ILE E 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG E 580 " --> pdb=" O SER E 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 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 388 through 392 removed outlier: 6.441A 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 435 Processing sheet with id=AA7, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.297A pdb=" N ILE A 628 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU A 579 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE A 578 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER A 668 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG A 580 " --> pdb=" O SER A 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 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 388 through 392 removed outlier: 6.440A 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 435 Processing sheet with id=AB2, first strand: chain 'B' and resid 651 through 653 removed outlier: 6.296A pdb=" N ILE B 628 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU B 579 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE B 578 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER B 668 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG B 580 " --> pdb=" O SER B 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 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 388 through 392 removed outlier: 6.441A 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 435 Processing sheet with id=AB6, first strand: chain 'C' and resid 651 through 653 removed outlier: 6.297A pdb=" N ILE C 628 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU C 579 " --> pdb=" O VAL C 629 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE C 578 " --> pdb=" O VAL C 666 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER C 668 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG C 580 " --> pdb=" O SER C 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 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 388 through 392 removed outlier: 6.440A 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 435 Processing sheet with id=AC1, first strand: chain 'D' and resid 651 through 653 removed outlier: 6.297A pdb=" N ILE D 628 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU D 579 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE D 578 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER D 668 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG D 580 " --> pdb=" O SER D 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 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 388 through 392 removed outlier: 6.441A 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 435 Processing sheet with id=AC5, first strand: chain 'F' and resid 651 through 653 removed outlier: 6.297A pdb=" N ILE F 628 " --> pdb=" O LEU F 652 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU F 579 " --> pdb=" O VAL F 629 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE F 578 " --> pdb=" O VAL F 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER F 668 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG F 580 " --> pdb=" O SER F 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 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 388 through 392 removed outlier: 6.441A 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 435 Processing sheet with id=AC9, first strand: chain 'G' and resid 651 through 653 removed outlier: 6.297A pdb=" N ILE G 628 " --> pdb=" O LEU G 652 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU G 579 " --> pdb=" O VAL G 629 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE G 578 " --> pdb=" O VAL G 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER G 668 " --> pdb=" O ILE G 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG G 580 " --> pdb=" O SER G 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 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 388 through 392 removed outlier: 6.440A 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 435 Processing sheet with id=AD4, first strand: chain 'H' and resid 651 through 653 removed outlier: 6.296A pdb=" N ILE H 628 " --> pdb=" O LEU H 652 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU H 579 " --> pdb=" O VAL H 629 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE H 578 " --> pdb=" O VAL H 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER H 668 " --> pdb=" O ILE H 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG H 580 " --> pdb=" O SER H 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 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 388 through 392 removed outlier: 6.441A 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 435 Processing sheet with id=AD8, first strand: chain 'I' and resid 651 through 653 removed outlier: 6.297A pdb=" N ILE I 628 " --> pdb=" O LEU I 652 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU I 579 " --> pdb=" O VAL I 629 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE I 578 " --> pdb=" O VAL I 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER I 668 " --> pdb=" O ILE I 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG I 580 " --> pdb=" O SER I 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'I' and resid 593 through 596 Processing sheet with id=AE1, first strand: chain 'J' and resid 388 through 392 removed outlier: 6.441A pdb=" N LEU J 404 " --> pdb=" O PRO J 408 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 433 through 435 Processing sheet with id=AE3, first strand: chain 'J' and resid 651 through 653 removed outlier: 6.297A pdb=" N ILE J 628 " --> pdb=" O LEU J 652 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU J 579 " --> pdb=" O VAL J 629 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE J 578 " --> pdb=" O VAL J 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER J 668 " --> pdb=" O ILE J 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG J 580 " --> pdb=" O SER J 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'J' and resid 593 through 596 Processing sheet with id=AE5, first strand: chain 'K' and resid 388 through 392 removed outlier: 6.441A pdb=" N LEU K 404 " --> pdb=" O PRO K 408 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 433 through 435 Processing sheet with id=AE7, first strand: chain 'K' and resid 651 through 653 removed outlier: 6.296A pdb=" N ILE K 628 " --> pdb=" O LEU K 652 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU K 579 " --> pdb=" O VAL K 629 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE K 578 " --> pdb=" O VAL K 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER K 668 " --> pdb=" O ILE K 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG K 580 " --> pdb=" O SER K 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'K' and resid 593 through 596 Processing sheet with id=AE9, first strand: chain 'L' and resid 388 through 392 removed outlier: 6.440A pdb=" N LEU L 404 " --> pdb=" O PRO L 408 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 433 through 435 Processing sheet with id=AF2, first strand: chain 'L' and resid 651 through 653 removed outlier: 6.297A pdb=" N ILE L 628 " --> pdb=" O LEU L 652 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU L 579 " --> pdb=" O VAL L 629 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE L 578 " --> pdb=" O VAL L 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER L 668 " --> pdb=" O ILE L 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG L 580 " --> pdb=" O SER L 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'L' and resid 593 through 596 Processing sheet with id=AF4, first strand: chain 'M' and resid 388 through 392 removed outlier: 6.440A pdb=" N LEU M 404 " --> pdb=" O PRO M 408 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 433 through 435 Processing sheet with id=AF6, first strand: chain 'M' and resid 651 through 653 removed outlier: 6.297A pdb=" N ILE M 628 " --> pdb=" O LEU M 652 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU M 579 " --> pdb=" O VAL M 629 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE M 578 " --> pdb=" O VAL M 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER M 668 " --> pdb=" O ILE M 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG M 580 " --> pdb=" O SER M 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'M' and resid 593 through 596 Processing sheet with id=AF8, first strand: chain 'N' and resid 388 through 392 removed outlier: 6.440A pdb=" N LEU N 404 " --> pdb=" O PRO N 408 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 433 through 435 Processing sheet with id=AG1, first strand: chain 'N' and resid 651 through 653 removed outlier: 6.297A pdb=" N ILE N 628 " --> pdb=" O LEU N 652 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU N 579 " --> pdb=" O VAL N 629 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE N 578 " --> pdb=" O VAL N 666 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER N 668 " --> pdb=" O ILE N 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG N 580 " --> pdb=" O SER N 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'N' and resid 593 through 596 Processing sheet with id=AG3, first strand: chain 'O' and resid 388 through 392 removed outlier: 6.441A pdb=" N LEU O 404 " --> pdb=" O PRO O 408 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 433 through 435 Processing sheet with id=AG5, first strand: chain 'O' and resid 651 through 653 removed outlier: 6.297A pdb=" N ILE O 628 " --> pdb=" O LEU O 652 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU O 579 " --> pdb=" O VAL O 629 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE O 578 " --> pdb=" O VAL O 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER O 668 " --> pdb=" O ILE O 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG O 580 " --> pdb=" O SER O 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'O' and resid 593 through 596 Processing sheet with id=AG7, first strand: chain 'P' and resid 388 through 392 removed outlier: 6.441A pdb=" N LEU P 404 " --> pdb=" O PRO P 408 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 433 through 435 Processing sheet with id=AG9, first strand: chain 'P' and resid 651 through 653 removed outlier: 6.296A pdb=" N ILE P 628 " --> pdb=" O LEU P 652 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU P 579 " --> pdb=" O VAL P 629 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE P 578 " --> pdb=" O VAL P 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER P 668 " --> pdb=" O ILE P 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG P 580 " --> pdb=" O SER P 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'P' and resid 593 through 596 Processing sheet with id=AH2, first strand: chain 'Q' and resid 388 through 392 removed outlier: 6.441A pdb=" N LEU Q 404 " --> pdb=" O PRO Q 408 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 433 through 435 Processing sheet with id=AH4, first strand: chain 'Q' and resid 651 through 653 removed outlier: 6.296A pdb=" N ILE Q 628 " --> pdb=" O LEU Q 652 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU Q 579 " --> pdb=" O VAL Q 629 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE Q 578 " --> pdb=" O VAL Q 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER Q 668 " --> pdb=" O ILE Q 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG Q 580 " --> pdb=" O SER Q 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'Q' and resid 593 through 596 Processing sheet with id=AH6, first strand: chain 'R' and resid 388 through 392 removed outlier: 6.440A pdb=" N LEU R 404 " --> pdb=" O PRO R 408 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 433 through 435 Processing sheet with id=AH8, first strand: chain 'R' and resid 651 through 653 removed outlier: 6.297A pdb=" N ILE R 628 " --> pdb=" O LEU R 652 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU R 579 " --> pdb=" O VAL R 629 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE R 578 " --> pdb=" O VAL R 666 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER R 668 " --> pdb=" O ILE R 578 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG R 580 " --> pdb=" O SER R 668 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'R' and resid 593 through 596 2349 hydrogen bonds defined for protein. 6750 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: 19.54 Time building geometry restraints manager: 19.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10077 1.33 - 1.45: 9693 1.45 - 1.57: 28794 1.57 - 1.69: 0 1.69 - 1.81: 378 Bond restraints: 48942 Sorted by residual: bond pdb=" N VAL N 347 " pdb=" CA VAL N 347 " ideal model delta sigma weight residual 1.458 1.483 -0.025 7.70e-03 1.69e+04 1.07e+01 bond pdb=" N VAL B 347 " pdb=" CA VAL B 347 " ideal model delta sigma weight residual 1.460 1.485 -0.025 7.60e-03 1.73e+04 1.06e+01 bond pdb=" N VAL A 347 " pdb=" CA VAL A 347 " ideal model delta sigma weight residual 1.460 1.485 -0.025 7.60e-03 1.73e+04 1.05e+01 bond pdb=" N VAL R 347 " pdb=" CA VAL R 347 " ideal model delta sigma weight residual 1.460 1.484 -0.024 7.60e-03 1.73e+04 1.02e+01 bond pdb=" N VAL L 347 " pdb=" CA VAL L 347 " ideal model delta sigma weight residual 1.460 1.484 -0.024 7.60e-03 1.73e+04 1.01e+01 ... (remaining 48937 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.45: 1386 106.45 - 113.33: 27703 113.33 - 120.22: 18082 120.22 - 127.10: 18663 127.10 - 133.99: 478 Bond angle restraints: 66312 Sorted by residual: angle pdb=" CA TYR C 420 " pdb=" C TYR C 420 " pdb=" O TYR C 420 " ideal model delta sigma weight residual 120.36 114.24 6.12 1.08e+00 8.57e-01 3.21e+01 angle pdb=" CA TYR L 420 " pdb=" C TYR L 420 " pdb=" O TYR L 420 " ideal model delta sigma weight residual 120.36 114.27 6.09 1.08e+00 8.57e-01 3.18e+01 angle pdb=" CA TYR O 420 " pdb=" C TYR O 420 " pdb=" O TYR O 420 " ideal model delta sigma weight residual 120.36 114.28 6.08 1.08e+00 8.57e-01 3.17e+01 angle pdb=" CA TYR Q 420 " pdb=" C TYR Q 420 " pdb=" O TYR Q 420 " ideal model delta sigma weight residual 120.36 114.28 6.08 1.08e+00 8.57e-01 3.17e+01 angle pdb=" CA TYR P 420 " pdb=" C TYR P 420 " pdb=" O TYR P 420 " ideal model delta sigma weight residual 120.36 114.28 6.08 1.08e+00 8.57e-01 3.17e+01 ... (remaining 66307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 26516 15.96 - 31.92: 2956 31.92 - 47.87: 654 47.87 - 63.83: 132 63.83 - 79.79: 18 Dihedral angle restraints: 30276 sinusoidal: 12654 harmonic: 17622 Sorted by residual: dihedral pdb=" CA LEU H 671 " pdb=" C LEU H 671 " pdb=" N SER H 672 " pdb=" CA SER H 672 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU A 671 " pdb=" C LEU A 671 " pdb=" N SER A 672 " pdb=" CA SER A 672 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU Q 671 " pdb=" C LEU Q 671 " pdb=" N SER Q 672 " pdb=" CA SER Q 672 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 30273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 6491 0.063 - 0.127: 1104 0.127 - 0.190: 175 0.190 - 0.254: 41 0.254 - 0.317: 37 Chirality restraints: 7848 Sorted by residual: chirality pdb=" CB ILE I 484 " pdb=" CA ILE I 484 " pdb=" CG1 ILE I 484 " pdb=" CG2 ILE I 484 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.51e+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 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB ILE L 484 " pdb=" CA ILE L 484 " pdb=" CG1 ILE L 484 " pdb=" CG2 ILE L 484 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 7845 not shown) Planarity restraints: 8478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 420 " 0.058 2.00e-02 2.50e+03 3.07e-02 1.88e+01 pdb=" CG TYR G 420 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR G 420 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR G 420 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR G 420 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR G 420 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR G 420 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 420 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 420 " 0.058 2.00e-02 2.50e+03 3.06e-02 1.87e+01 pdb=" CG TYR L 420 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR L 420 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR L 420 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR L 420 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR L 420 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR L 420 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 420 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 420 " 0.058 2.00e-02 2.50e+03 3.06e-02 1.87e+01 pdb=" CG TYR H 420 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR H 420 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR H 420 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR H 420 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR H 420 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR H 420 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 420 " 0.033 2.00e-02 2.50e+03 ... (remaining 8475 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 18026 2.90 - 3.40: 46502 3.40 - 3.90: 76484 3.90 - 4.40: 85462 4.40 - 4.90: 147409 Nonbonded interactions: 373883 Sorted by model distance: nonbonded pdb=" OG SER G 529 " pdb=" NE2 HIS G 564 " model vdw 2.394 2.520 nonbonded pdb=" OG SER I 529 " pdb=" NE2 HIS I 564 " model vdw 2.394 2.520 nonbonded pdb=" OG SER R 529 " pdb=" NE2 HIS R 564 " model vdw 2.394 2.520 nonbonded pdb=" OG SER M 529 " pdb=" NE2 HIS M 564 " model vdw 2.394 2.520 nonbonded pdb=" OG SER K 529 " pdb=" NE2 HIS K 564 " model vdw 2.395 2.520 ... (remaining 373878 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' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 4.190 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: 0.040 Extract box with map and model: 18.100 Check model and map are aligned: 0.690 Set scattering table: 0.410 Process input model: 118.410 Find NCS groups from input model: 3.320 Set up NCS constraints: 0.360 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 : 0.006 0.041 48942 Z= 0.374 Angle : 0.810 7.079 66312 Z= 0.505 Chirality : 0.056 0.317 7848 Planarity : 0.004 0.042 8478 Dihedral : 13.873 79.791 18792 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.77 % Rotamer Outliers : 0.63 % 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: -1.53 (0.10), residues: 6012 helix: -0.17 (0.09), residues: 2718 sheet: -1.37 (0.15), residues: 1026 loop : -1.75 (0.12), residues: 2268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 649 time to evaluate : 5.649 Fit side-chains outliers start: 34 outliers final: 21 residues processed: 682 average time/residue: 0.6322 time to fit residues: 694.1749 Evaluate side-chains 588 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 567 time to evaluate : 5.666 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4083 time to fit residues: 24.6041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 501 optimal weight: 3.9990 chunk 450 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 303 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 chunk 465 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 283 optimal weight: 0.6980 chunk 346 optimal weight: 0.7980 chunk 539 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 362 HIS ** E 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS C 362 HIS D 362 HIS F 362 HIS G 362 HIS ** G 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS ** I 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 362 HIS L 362 HIS ** L 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 362 HIS N 362 HIS ** N 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 362 HIS ** O 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 362 HIS R 362 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 48942 Z= 0.218 Angle : 0.535 5.887 66312 Z= 0.266 Chirality : 0.043 0.194 7848 Planarity : 0.003 0.040 8478 Dihedral : 4.289 21.426 6570 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.32 % 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: -0.91 (0.11), residues: 6012 helix: 0.44 (0.10), residues: 2790 sheet: -1.06 (0.17), residues: 954 loop : -1.64 (0.12), residues: 2268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 610 time to evaluate : 5.594 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 621 average time/residue: 0.6479 time to fit residues: 651.6267 Evaluate side-chains 586 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 579 time to evaluate : 5.502 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4610 time to fit residues: 13.8724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 299 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 448 optimal weight: 0.9980 chunk 367 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 540 optimal weight: 3.9990 chunk 583 optimal weight: 0.3980 chunk 481 optimal weight: 1.9990 chunk 535 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 433 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 611 GLN ** M 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 362 HIS ** R 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.022 48942 Z= 0.232 Angle : 0.515 11.516 66312 Z= 0.252 Chirality : 0.043 0.162 7848 Planarity : 0.003 0.038 8478 Dihedral : 4.068 20.365 6570 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 0.67 % 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: -0.67 (0.11), residues: 6012 helix: 0.71 (0.10), residues: 2790 sheet: -0.99 (0.17), residues: 954 loop : -1.60 (0.12), residues: 2268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 593 time to evaluate : 5.694 Fit side-chains outliers start: 36 outliers final: 14 residues processed: 624 average time/residue: 0.6441 time to fit residues: 651.1982 Evaluate side-chains 584 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 570 time to evaluate : 5.854 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4013 time to fit residues: 18.9904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 533 optimal weight: 4.9990 chunk 406 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 362 optimal weight: 6.9990 chunk 542 optimal weight: 1.9990 chunk 574 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 chunk 513 optimal weight: 1.9990 chunk 154 optimal weight: 0.0470 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 611 GLN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 611 GLN ** G 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 48942 Z= 0.197 Angle : 0.497 7.891 66312 Z= 0.242 Chirality : 0.042 0.163 7848 Planarity : 0.003 0.037 8478 Dihedral : 3.921 19.605 6570 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.47 % 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: -0.54 (0.11), residues: 6012 helix: 0.91 (0.10), residues: 2790 sheet: -1.12 (0.16), residues: 1062 loop : -1.57 (0.13), residues: 2160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 568 time to evaluate : 6.029 Fit side-chains outliers start: 25 outliers final: 6 residues processed: 581 average time/residue: 0.6247 time to fit residues: 594.1886 Evaluate side-chains 557 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 551 time to evaluate : 5.100 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4309 time to fit residues: 12.1742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 478 optimal weight: 0.0670 chunk 325 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 427 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 chunk 489 optimal weight: 10.0000 chunk 396 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 293 optimal weight: 0.9990 chunk 515 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 GLN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 HIS ** K 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 611 GLN N 611 GLN O 611 GLN ** P 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 48942 Z= 0.194 Angle : 0.495 11.558 66312 Z= 0.241 Chirality : 0.042 0.134 7848 Planarity : 0.003 0.037 8478 Dihedral : 3.826 18.842 6570 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.58 % 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 (0.11), residues: 6012 helix: 1.07 (0.10), residues: 2772 sheet: -1.17 (0.15), residues: 1062 loop : -1.50 (0.12), residues: 2178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 546 time to evaluate : 5.386 Fit side-chains outliers start: 31 outliers final: 4 residues processed: 568 average time/residue: 0.5961 time to fit residues: 561.1038 Evaluate side-chains 545 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 541 time to evaluate : 5.451 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4299 time to fit residues: 10.9987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 193 optimal weight: 2.9990 chunk 517 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 337 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 574 optimal weight: 1.9990 chunk 477 optimal weight: 3.9990 chunk 266 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 611 GLN ** K 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 611 GLN ** P 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 611 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 48942 Z= 0.195 Angle : 0.506 13.943 66312 Z= 0.242 Chirality : 0.042 0.164 7848 Planarity : 0.003 0.037 8478 Dihedral : 3.760 17.877 6570 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 0.69 % 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 (0.11), residues: 6012 helix: 1.14 (0.10), residues: 2772 sheet: -1.21 (0.15), residues: 1062 loop : -1.42 (0.13), residues: 2178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 537 time to evaluate : 5.607 Fit side-chains outliers start: 37 outliers final: 15 residues processed: 556 average time/residue: 0.6108 time to fit residues: 563.5280 Evaluate side-chains 556 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 541 time to evaluate : 5.400 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4267 time to fit residues: 20.0073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 554 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 419 optimal weight: 10.0000 chunk 325 optimal weight: 3.9990 chunk 483 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 chunk 572 optimal weight: 8.9990 chunk 358 optimal weight: 8.9990 chunk 349 optimal weight: 0.7980 chunk 264 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 664 GLN ** K 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 GLN ** O 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.036 48942 Z= 0.426 Angle : 0.636 14.392 66312 Z= 0.304 Chirality : 0.046 0.150 7848 Planarity : 0.004 0.041 8478 Dihedral : 4.163 18.066 6570 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.63 % 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: -0.87 (0.11), residues: 6012 helix: 0.58 (0.10), residues: 2790 sheet: -1.32 (0.15), residues: 1062 loop : -1.61 (0.13), residues: 2160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 563 time to evaluate : 5.309 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 586 average time/residue: 0.6230 time to fit residues: 590.8511 Evaluate side-chains 569 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 554 time to evaluate : 5.428 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4141 time to fit residues: 19.5260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 354 optimal weight: 5.9990 chunk 228 optimal weight: 0.4980 chunk 341 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 363 optimal weight: 3.9990 chunk 390 optimal weight: 9.9990 chunk 283 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 450 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 664 GLN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 GLN B 614 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 GLN D 611 GLN D 664 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 611 GLN I 611 GLN J 664 GLN ** K 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 614 GLN ** M 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 GLN N 664 GLN ** O 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 611 GLN R 611 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 48942 Z= 0.166 Angle : 0.514 14.700 66312 Z= 0.244 Chirality : 0.042 0.168 7848 Planarity : 0.003 0.037 8478 Dihedral : 3.811 17.417 6570 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % 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: -0.37 (0.11), residues: 6012 helix: 1.06 (0.10), residues: 2790 sheet: -1.27 (0.16), residues: 1062 loop : -1.38 (0.13), residues: 2160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 553 time to evaluate : 5.568 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 562 average time/residue: 0.6216 time to fit residues: 573.8344 Evaluate side-chains 548 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 544 time to evaluate : 5.028 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4120 time to fit residues: 10.7012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 520 optimal weight: 0.8980 chunk 548 optimal weight: 0.9990 chunk 500 optimal weight: 2.9990 chunk 533 optimal weight: 5.9990 chunk 321 optimal weight: 0.5980 chunk 232 optimal weight: 4.9990 chunk 418 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 482 optimal weight: 1.9990 chunk 504 optimal weight: 2.9990 chunk 531 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 611 GLN J 664 GLN ** K 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 48942 Z= 0.168 Angle : 0.531 15.767 66312 Z= 0.247 Chirality : 0.042 0.160 7848 Planarity : 0.003 0.036 8478 Dihedral : 3.675 15.944 6570 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 0.21 % 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: -0.20 (0.11), residues: 6012 helix: 1.28 (0.10), residues: 2790 sheet: -1.26 (0.15), residues: 1062 loop : -1.34 (0.13), residues: 2160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 556 time to evaluate : 5.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 563 average time/residue: 0.6068 time to fit residues: 562.5183 Evaluate side-chains 552 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 546 time to evaluate : 5.903 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4207 time to fit residues: 13.1908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 350 optimal weight: 2.9990 chunk 564 optimal weight: 3.9990 chunk 344 optimal weight: 0.5980 chunk 267 optimal weight: 3.9990 chunk 392 optimal weight: 0.3980 chunk 591 optimal weight: 0.9990 chunk 544 optimal weight: 1.9990 chunk 471 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 363 optimal weight: 4.9990 chunk 288 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 48942 Z= 0.177 Angle : 0.535 15.375 66312 Z= 0.249 Chirality : 0.042 0.161 7848 Planarity : 0.003 0.037 8478 Dihedral : 3.616 15.276 6570 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.09 % 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: -0.12 (0.11), residues: 6012 helix: 1.36 (0.10), residues: 2790 sheet: -1.26 (0.15), residues: 1062 loop : -1.32 (0.13), residues: 2160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12024 Ramachandran restraints generated. 6012 Oldfield, 0 Emsley, 6012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 549 time to evaluate : 5.455 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 551 average time/residue: 0.6093 time to fit residues: 550.6564 Evaluate side-chains 547 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 544 time to evaluate : 5.431 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4767 time to fit residues: 10.4518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 374 optimal weight: 4.9990 chunk 501 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 434 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 471 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 484 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 GLN ** K 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 614 GLN ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.187018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.177027 restraints weight = 45281.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.150934 restraints weight = 100936.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.148842 restraints weight = 135253.620| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 48942 Z= 0.183 Angle : 0.535 15.448 66312 Z= 0.250 Chirality : 0.042 0.172 7848 Planarity : 0.003 0.037 8478 Dihedral : 3.590 14.644 6570 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 0.11 % 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: -0.12 (0.11), residues: 6012 helix: 1.32 (0.10), residues: 2808 sheet: -1.26 (0.15), residues: 1062 loop : -1.28 (0.13), residues: 2142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9969.09 seconds wall clock time: 181 minutes 22.98 seconds (10882.98 seconds total)