Starting phenix.real_space_refine on Sun Feb 25 02:20:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fed_31553/02_2024/7fed_31553.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fed_31553/02_2024/7fed_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_31553/02_2024/7fed_31553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fed_31553/02_2024/7fed_31553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fed_31553/02_2024/7fed_31553.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fed_31553/02_2024/7fed_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: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 27.37, per 1000 atoms: 0.57 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: 18.86 Conformation dependent library (CDL) restraints added in 9.1 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: 5.44 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: 19.65 Time building geometry restraints manager: 20.22 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: 5.060 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: 16.480 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 124.520 Find NCS groups from input model: 3.430 Set up NCS constraints: 0.370 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.930 ------------------------------------------------------------------------------- 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 % Allowed : 0.52 % Favored : 98.84 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 654 HIS 0.004 0.002 HIS N 362 PHE 0.012 0.001 PHE G 410 TYR 0.058 0.005 TYR G 420 ARG 0.003 0.000 ARG K 568 *********************** 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 : 5.236 Fit side-chains REVERT: E 669 ILE cc_start: 0.8282 (mm) cc_final: 0.7978 (mt) REVERT: A 669 ILE cc_start: 0.8297 (mm) cc_final: 0.7959 (mt) REVERT: B 669 ILE cc_start: 0.8365 (mm) cc_final: 0.8061 (mt) REVERT: C 669 ILE cc_start: 0.8358 (mm) cc_final: 0.7986 (mt) REVERT: D 633 ASP cc_start: 0.6962 (t0) cc_final: 0.6756 (t0) REVERT: D 669 ILE cc_start: 0.8264 (mm) cc_final: 0.7950 (mt) REVERT: F 669 ILE cc_start: 0.8315 (mm) cc_final: 0.7969 (mt) REVERT: G 480 MET cc_start: 0.8850 (tpt) cc_final: 0.8548 (tpt) REVERT: G 669 ILE cc_start: 0.8318 (mm) cc_final: 0.7954 (mt) REVERT: H 480 MET cc_start: 0.8847 (tpt) cc_final: 0.8017 (tpt) REVERT: H 669 ILE cc_start: 0.8340 (mm) cc_final: 0.7937 (mt) REVERT: I 552 MET cc_start: 0.8231 (tpt) cc_final: 0.7807 (tpt) REVERT: I 598 MET cc_start: 0.8301 (mmm) cc_final: 0.7799 (mmt) REVERT: I 669 ILE cc_start: 0.8308 (mm) cc_final: 0.8011 (mt) REVERT: J 669 ILE cc_start: 0.8294 (mm) cc_final: 0.7985 (mt) REVERT: K 669 ILE cc_start: 0.8327 (mm) cc_final: 0.8008 (mt) REVERT: L 669 ILE cc_start: 0.8368 (mm) cc_final: 0.8051 (mt) REVERT: M 669 ILE cc_start: 0.8350 (mm) cc_final: 0.7965 (mt) REVERT: N 669 ILE cc_start: 0.8270 (mm) cc_final: 0.7946 (mt) REVERT: O 669 ILE cc_start: 0.8327 (mm) cc_final: 0.7982 (mt) REVERT: P 480 MET cc_start: 0.8829 (tpt) cc_final: 0.8504 (tpt) REVERT: P 669 ILE cc_start: 0.8359 (mm) cc_final: 0.7994 (mt) REVERT: Q 480 MET cc_start: 0.8827 (tpt) cc_final: 0.8134 (tpt) REVERT: Q 568 ARG cc_start: 0.7591 (ttt180) cc_final: 0.7391 (ttt90) REVERT: Q 669 ILE cc_start: 0.8341 (mm) cc_final: 0.7923 (mt) REVERT: R 552 MET cc_start: 0.8256 (tpt) cc_final: 0.7899 (tpt) REVERT: R 598 MET cc_start: 0.8285 (mmm) cc_final: 0.7808 (mmt) REVERT: R 633 ASP cc_start: 0.7078 (t0) cc_final: 0.6872 (t0) REVERT: R 669 ILE cc_start: 0.8304 (mm) cc_final: 0.7993 (mt) outliers start: 34 outliers final: 21 residues processed: 682 average time/residue: 0.6554 time to fit residues: 725.7745 Evaluate side-chains 606 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 585 time to evaluate : 4.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 360 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 360 THR Chi-restraints excluded: chain J residue 360 THR Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain R residue 347 VAL 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: 0.1980 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: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 362 HIS A 362 HIS C 362 HIS D 362 HIS F 362 HIS G 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 P 362 HIS ** P 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 362 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 48942 Z= 0.180 Angle : 0.517 5.834 66312 Z= 0.258 Chirality : 0.042 0.182 7848 Planarity : 0.003 0.038 8478 Dihedral : 4.669 56.433 6593 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.63 % Allowed : 5.31 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.11), residues: 6012 helix: 0.54 (0.10), residues: 2790 sheet: -1.38 (0.15), residues: 1134 loop : -1.40 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 445 HIS 0.006 0.002 HIS J 362 PHE 0.008 0.001 PHE R 410 TYR 0.006 0.001 TYR P 405 ARG 0.005 0.000 ARG D 478 *********************** 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 677 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 643 time to evaluate : 5.308 Fit side-chains REVERT: E 669 ILE cc_start: 0.8230 (mm) cc_final: 0.7980 (mt) REVERT: A 669 ILE cc_start: 0.8296 (mm) cc_final: 0.8023 (mt) REVERT: B 552 MET cc_start: 0.8174 (tpt) cc_final: 0.7787 (tpt) REVERT: B 598 MET cc_start: 0.8223 (mmm) cc_final: 0.7586 (mmt) REVERT: B 669 ILE cc_start: 0.8324 (mm) cc_final: 0.8053 (mt) REVERT: C 478 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7498 (mmm-85) REVERT: C 669 ILE cc_start: 0.8305 (mm) cc_final: 0.7970 (mt) REVERT: D 633 ASP cc_start: 0.7026 (t0) cc_final: 0.6576 (t0) REVERT: D 669 ILE cc_start: 0.8268 (mm) cc_final: 0.8014 (mt) REVERT: F 669 ILE cc_start: 0.8279 (mm) cc_final: 0.7971 (mt) REVERT: G 669 ILE cc_start: 0.8280 (mm) cc_final: 0.7950 (mt) REVERT: H 669 ILE cc_start: 0.8268 (mm) cc_final: 0.7895 (mt) REVERT: I 552 MET cc_start: 0.8160 (tpt) cc_final: 0.7688 (tpt) REVERT: I 598 MET cc_start: 0.8326 (mmm) cc_final: 0.7694 (mmt) REVERT: I 633 ASP cc_start: 0.7032 (t0) cc_final: 0.6805 (t0) REVERT: I 669 ILE cc_start: 0.8245 (mm) cc_final: 0.7983 (mt) REVERT: J 669 ILE cc_start: 0.8236 (mm) cc_final: 0.7986 (mt) REVERT: K 669 ILE cc_start: 0.8306 (mm) cc_final: 0.8042 (mt) REVERT: L 552 MET cc_start: 0.8195 (tpt) cc_final: 0.7781 (tpt) REVERT: L 598 MET cc_start: 0.8223 (mmm) cc_final: 0.7626 (mmt) REVERT: L 669 ILE cc_start: 0.8326 (mm) cc_final: 0.8048 (mt) REVERT: M 478 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7531 (mmm-85) REVERT: M 669 ILE cc_start: 0.8301 (mm) cc_final: 0.7967 (mt) REVERT: N 669 ILE cc_start: 0.8246 (mm) cc_final: 0.7986 (mt) REVERT: O 669 ILE cc_start: 0.8282 (mm) cc_final: 0.7983 (mt) REVERT: P 669 ILE cc_start: 0.8326 (mm) cc_final: 0.7986 (mt) REVERT: Q 669 ILE cc_start: 0.8270 (mm) cc_final: 0.7902 (mt) REVERT: R 552 MET cc_start: 0.8189 (tpt) cc_final: 0.7795 (tpt) REVERT: R 598 MET cc_start: 0.8320 (mmm) cc_final: 0.7715 (mmt) REVERT: R 633 ASP cc_start: 0.7105 (t0) cc_final: 0.6858 (t0) REVERT: R 669 ILE cc_start: 0.8269 (mm) cc_final: 0.7991 (mt) outliers start: 34 outliers final: 22 residues processed: 671 average time/residue: 0.6040 time to fit residues: 658.7156 Evaluate side-chains 631 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 607 time to evaluate : 5.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 478 ARG Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 572 GLU Chi-restraints excluded: chain H residue 634 THR Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 360 THR Chi-restraints excluded: chain I residue 634 THR Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 634 THR Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 478 ARG Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 572 GLU Chi-restraints excluded: chain Q residue 572 GLU Chi-restraints excluded: chain R residue 347 VAL 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: 1.9990 chunk 367 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 540 optimal weight: 2.9990 chunk 583 optimal weight: 0.2980 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: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS ** I 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7739 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 48942 Z= 0.282 Angle : 0.539 11.171 66312 Z= 0.264 Chirality : 0.043 0.169 7848 Planarity : 0.003 0.039 8478 Dihedral : 4.396 52.128 6585 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.16 % Allowed : 7.66 % Favored : 91.18 % 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: -0.74 (0.11), residues: 6012 helix: 0.64 (0.10), residues: 2790 sheet: -1.04 (0.16), residues: 954 loop : -1.62 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 445 HIS 0.006 0.002 HIS J 362 PHE 0.010 0.001 PHE E 410 TYR 0.008 0.001 TYR G 405 ARG 0.002 0.000 ARG M 568 *********************** 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 673 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 611 time to evaluate : 5.328 Fit side-chains REVERT: E 552 MET cc_start: 0.8257 (tpt) cc_final: 0.7774 (tpt) REVERT: E 669 ILE cc_start: 0.8321 (mm) cc_final: 0.8111 (mt) REVERT: B 598 MET cc_start: 0.8211 (mmm) cc_final: 0.7501 (mmt) REVERT: B 669 ILE cc_start: 0.8422 (mm) cc_final: 0.8199 (mt) REVERT: C 478 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7852 (mmm-85) REVERT: C 633 ASP cc_start: 0.7169 (t0) cc_final: 0.6791 (t0) REVERT: C 669 ILE cc_start: 0.8378 (mm) cc_final: 0.8062 (mt) REVERT: D 633 ASP cc_start: 0.7105 (t0) cc_final: 0.6898 (t0) REVERT: F 480 MET cc_start: 0.8816 (tpt) cc_final: 0.8332 (tpt) REVERT: F 669 ILE cc_start: 0.8349 (mm) cc_final: 0.8095 (mt) REVERT: G 669 ILE cc_start: 0.8345 (mm) cc_final: 0.8068 (mt) REVERT: H 480 MET cc_start: 0.8783 (tpt) cc_final: 0.8399 (tpt) REVERT: H 633 ASP cc_start: 0.7098 (t0) cc_final: 0.6893 (t0) REVERT: H 669 ILE cc_start: 0.8297 (mm) cc_final: 0.7987 (mt) REVERT: I 552 MET cc_start: 0.8256 (tpt) cc_final: 0.7845 (tpt) REVERT: I 598 MET cc_start: 0.8314 (mmm) cc_final: 0.7710 (mmt) REVERT: I 633 ASP cc_start: 0.7143 (t0) cc_final: 0.6842 (t0) REVERT: I 669 ILE cc_start: 0.8384 (mm) cc_final: 0.8178 (mt) REVERT: J 552 MET cc_start: 0.8267 (tpt) cc_final: 0.7774 (tpt) REVERT: J 669 ILE cc_start: 0.8330 (mm) cc_final: 0.8112 (mt) REVERT: L 598 MET cc_start: 0.8230 (mmm) cc_final: 0.7559 (mmt) REVERT: L 669 ILE cc_start: 0.8422 (mm) cc_final: 0.8191 (mt) REVERT: M 478 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7882 (mmm-85) REVERT: M 633 ASP cc_start: 0.7195 (t0) cc_final: 0.6819 (t0) REVERT: M 669 ILE cc_start: 0.8368 (mm) cc_final: 0.8051 (mt) REVERT: O 480 MET cc_start: 0.8828 (tpt) cc_final: 0.8259 (tpt) REVERT: O 669 ILE cc_start: 0.8357 (mm) cc_final: 0.8107 (mt) REVERT: P 669 ILE cc_start: 0.8381 (mm) cc_final: 0.8089 (mt) REVERT: Q 480 MET cc_start: 0.8747 (tpt) cc_final: 0.8350 (tpt) REVERT: Q 633 ASP cc_start: 0.7084 (t0) cc_final: 0.6869 (t0) REVERT: Q 669 ILE cc_start: 0.8310 (mm) cc_final: 0.7969 (mt) REVERT: R 552 MET cc_start: 0.8270 (tpt) cc_final: 0.7874 (tpt) REVERT: R 598 MET cc_start: 0.8297 (mmm) cc_final: 0.7749 (mmt) REVERT: R 633 ASP cc_start: 0.7244 (t0) cc_final: 0.6983 (t0) REVERT: R 669 ILE cc_start: 0.8381 (mm) cc_final: 0.8173 (mt) outliers start: 62 outliers final: 40 residues processed: 653 average time/residue: 0.6232 time to fit residues: 661.0963 Evaluate side-chains 620 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 578 time to evaluate : 5.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 478 ARG Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain H residue 409 VAL Chi-restraints excluded: chain H residue 572 GLU Chi-restraints excluded: chain H residue 634 THR Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 360 THR Chi-restraints excluded: chain I residue 409 VAL Chi-restraints excluded: chain I residue 630 THR Chi-restraints excluded: chain I residue 634 THR Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 409 VAL Chi-restraints excluded: chain K residue 634 THR Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 409 VAL Chi-restraints excluded: chain M residue 478 ARG Chi-restraints excluded: chain N residue 409 VAL Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain O residue 409 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 572 GLU Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 572 GLU Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 409 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 533 optimal weight: 5.9990 chunk 406 optimal weight: 9.9990 chunk 280 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 257 optimal weight: 6.9990 chunk 362 optimal weight: 8.9990 chunk 542 optimal weight: 0.9990 chunk 574 optimal weight: 1.9990 chunk 283 optimal weight: 0.9990 chunk 513 optimal weight: 2.9990 chunk 154 optimal weight: 0.0970 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 611 GLN ** D 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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** ** K 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 611 GLN N 611 GLN ** O 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7689 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 48942 Z= 0.169 Angle : 0.486 12.532 66312 Z= 0.237 Chirality : 0.042 0.171 7848 Planarity : 0.003 0.038 8478 Dihedral : 4.123 49.153 6584 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.71 % Allowed : 9.82 % Favored : 89.47 % 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: -0.49 (0.11), residues: 6012 helix: 0.94 (0.10), residues: 2790 sheet: -1.11 (0.16), residues: 1062 loop : -1.53 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 445 HIS 0.004 0.001 HIS I 608 PHE 0.005 0.001 PHE E 410 TYR 0.007 0.001 TYR N 420 ARG 0.001 0.000 ARG M 478 *********************** 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 622 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 584 time to evaluate : 6.013 Fit side-chains REVERT: E 552 MET cc_start: 0.8147 (tpt) cc_final: 0.7672 (tpt) REVERT: B 552 MET cc_start: 0.8170 (tpt) cc_final: 0.7834 (tpt) REVERT: B 598 MET cc_start: 0.8176 (mmm) cc_final: 0.7516 (mmt) REVERT: C 478 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7698 (mmm-85) REVERT: C 633 ASP cc_start: 0.7176 (t0) cc_final: 0.6796 (t0) REVERT: C 669 ILE cc_start: 0.8352 (mm) cc_final: 0.8064 (mt) REVERT: D 633 ASP cc_start: 0.7100 (t0) cc_final: 0.6807 (t0) REVERT: F 552 MET cc_start: 0.8185 (tpt) cc_final: 0.7819 (tpt) REVERT: F 669 ILE cc_start: 0.8373 (mm) cc_final: 0.8163 (mt) REVERT: G 669 ILE cc_start: 0.8360 (mm) cc_final: 0.8095 (mt) REVERT: H 633 ASP cc_start: 0.7119 (t0) cc_final: 0.6896 (t0) REVERT: H 669 ILE cc_start: 0.8292 (mm) cc_final: 0.8035 (mt) REVERT: I 552 MET cc_start: 0.8197 (tpt) cc_final: 0.7752 (tpt) REVERT: I 598 MET cc_start: 0.8271 (mmm) cc_final: 0.7801 (mmt) REVERT: I 633 ASP cc_start: 0.7196 (t0) cc_final: 0.6914 (t0) REVERT: J 552 MET cc_start: 0.8162 (tpt) cc_final: 0.7676 (tpt) REVERT: L 552 MET cc_start: 0.8173 (tpt) cc_final: 0.7828 (tpt) REVERT: L 598 MET cc_start: 0.8198 (mmm) cc_final: 0.7579 (mmt) REVERT: L 669 ILE cc_start: 0.8393 (mm) cc_final: 0.8187 (mt) REVERT: M 478 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7699 (mmm-85) REVERT: M 552 MET cc_start: 0.8226 (tpt) cc_final: 0.7743 (tpt) REVERT: M 633 ASP cc_start: 0.7167 (t0) cc_final: 0.6784 (t0) REVERT: M 669 ILE cc_start: 0.8352 (mm) cc_final: 0.8077 (mt) REVERT: N 633 ASP cc_start: 0.6997 (t0) cc_final: 0.6705 (t0) REVERT: O 552 MET cc_start: 0.8182 (tpt) cc_final: 0.7808 (tpt) REVERT: O 669 ILE cc_start: 0.8378 (mm) cc_final: 0.8161 (mt) REVERT: P 669 ILE cc_start: 0.8379 (mm) cc_final: 0.8111 (mt) REVERT: Q 633 ASP cc_start: 0.7092 (t0) cc_final: 0.6832 (t0) REVERT: Q 669 ILE cc_start: 0.8343 (mm) cc_final: 0.8103 (mt) REVERT: R 552 MET cc_start: 0.8205 (tpt) cc_final: 0.7763 (tpt) REVERT: R 598 MET cc_start: 0.8279 (mmm) cc_final: 0.7773 (mmt) REVERT: R 633 ASP cc_start: 0.7221 (t0) cc_final: 0.6878 (t0) outliers start: 38 outliers final: 21 residues processed: 615 average time/residue: 0.5737 time to fit residues: 584.9216 Evaluate side-chains 589 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 566 time to evaluate : 5.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 478 ARG Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain H residue 572 GLU Chi-restraints excluded: chain H residue 634 THR Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 634 THR Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 634 THR Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 478 ARG Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 572 GLU Chi-restraints excluded: chain Q residue 572 GLU Chi-restraints excluded: chain R residue 347 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 478 optimal weight: 2.9990 chunk 325 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 427 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 chunk 489 optimal weight: 7.9990 chunk 396 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 293 optimal weight: 2.9990 chunk 515 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 611 GLN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 611 GLN ** K 434 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** ** M 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 611 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 48942 Z= 0.238 Angle : 0.518 13.166 66312 Z= 0.250 Chirality : 0.043 0.167 7848 Planarity : 0.003 0.038 8478 Dihedral : 4.073 35.981 6583 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.19 % Allowed : 10.27 % Favored : 88.53 % 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: -0.53 (0.11), residues: 6012 helix: 0.96 (0.10), residues: 2790 sheet: -1.22 (0.15), residues: 1062 loop : -1.57 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 445 HIS 0.005 0.002 HIS N 362 PHE 0.008 0.001 PHE E 410 TYR 0.008 0.001 TYR P 405 ARG 0.002 0.000 ARG M 478 *********************** 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 616 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 552 time to evaluate : 5.338 Fit side-chains REVERT: E 552 MET cc_start: 0.8224 (tpt) cc_final: 0.7732 (tpt) REVERT: A 400 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7031 (pt) REVERT: B 400 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7167 (pt) REVERT: B 552 MET cc_start: 0.8260 (tpt) cc_final: 0.7945 (tpt) REVERT: B 598 MET cc_start: 0.8167 (mmm) cc_final: 0.7518 (mmt) REVERT: C 400 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7063 (pt) REVERT: C 478 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7720 (mmm-85) REVERT: C 633 ASP cc_start: 0.7243 (t0) cc_final: 0.6828 (t0) REVERT: C 669 ILE cc_start: 0.8363 (mm) cc_final: 0.8092 (mt) REVERT: D 633 ASP cc_start: 0.7179 (t0) cc_final: 0.6886 (t0) REVERT: F 400 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7025 (pt) REVERT: F 669 ILE cc_start: 0.8389 (mm) cc_final: 0.8171 (mt) REVERT: G 400 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7162 (pt) REVERT: G 669 ILE cc_start: 0.8356 (mm) cc_final: 0.8083 (mt) REVERT: H 633 ASP cc_start: 0.7185 (t0) cc_final: 0.6939 (t0) REVERT: H 669 ILE cc_start: 0.8320 (mm) cc_final: 0.8081 (mt) REVERT: I 552 MET cc_start: 0.8244 (tpt) cc_final: 0.7835 (tpt) REVERT: I 598 MET cc_start: 0.8273 (mmm) cc_final: 0.7817 (mmt) REVERT: I 633 ASP cc_start: 0.7345 (t0) cc_final: 0.7062 (t0) REVERT: J 552 MET cc_start: 0.8235 (tpt) cc_final: 0.7732 (tpt) REVERT: K 400 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6966 (pt) REVERT: L 400 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7086 (pt) REVERT: L 478 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7045 (mmm-85) REVERT: L 552 MET cc_start: 0.8227 (tpt) cc_final: 0.7915 (tpt) REVERT: L 598 MET cc_start: 0.8213 (mmm) cc_final: 0.7552 (mmt) REVERT: L 669 ILE cc_start: 0.8396 (mm) cc_final: 0.8186 (mt) REVERT: M 400 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7007 (pt) REVERT: M 478 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7749 (mmm-85) REVERT: M 633 ASP cc_start: 0.7201 (t0) cc_final: 0.6816 (t0) REVERT: M 669 ILE cc_start: 0.8366 (mm) cc_final: 0.8092 (mt) REVERT: N 633 ASP cc_start: 0.7128 (t0) cc_final: 0.6785 (t0) REVERT: O 400 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7031 (pt) REVERT: O 669 ILE cc_start: 0.8394 (mm) cc_final: 0.8184 (mt) REVERT: P 400 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7204 (pt) REVERT: P 669 ILE cc_start: 0.8375 (mm) cc_final: 0.8104 (mt) REVERT: Q 633 ASP cc_start: 0.7164 (t0) cc_final: 0.6928 (t0) REVERT: Q 669 ILE cc_start: 0.8365 (mm) cc_final: 0.8131 (mt) REVERT: R 552 MET cc_start: 0.8253 (tpt) cc_final: 0.7849 (tpt) REVERT: R 598 MET cc_start: 0.8264 (mmm) cc_final: 0.7805 (mmt) REVERT: R 633 ASP cc_start: 0.7294 (t0) cc_final: 0.6922 (t0) outliers start: 64 outliers final: 28 residues processed: 601 average time/residue: 0.6068 time to fit residues: 612.3328 Evaluate side-chains 589 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 548 time to evaluate : 5.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 478 ARG Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 595 GLN Chi-restraints excluded: chain H residue 572 GLU Chi-restraints excluded: chain H residue 634 THR Chi-restraints excluded: chain I residue 630 THR Chi-restraints excluded: chain I residue 634 THR Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 634 THR Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 400 LEU Chi-restraints excluded: chain L residue 478 ARG Chi-restraints excluded: chain L residue 578 ILE Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 400 LEU Chi-restraints excluded: chain M residue 478 ARG Chi-restraints excluded: chain N residue 400 LEU Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain O residue 400 LEU Chi-restraints excluded: chain O residue 578 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 400 LEU Chi-restraints excluded: chain P residue 572 GLU Chi-restraints excluded: chain P residue 595 GLN Chi-restraints excluded: chain Q residue 572 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 193 optimal weight: 0.9980 chunk 517 optimal weight: 0.0670 chunk 113 optimal weight: 0.5980 chunk 337 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 574 optimal weight: 1.9990 chunk 477 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- 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 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 611 GLN ** G 611 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** K 611 GLN ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 611 GLN P 611 GLN Q 611 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 48942 Z= 0.164 Angle : 0.487 13.806 66312 Z= 0.233 Chirality : 0.041 0.164 7848 Planarity : 0.003 0.037 8478 Dihedral : 3.860 35.842 6580 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.08 % Allowed : 11.28 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.27 (0.11), residues: 6012 helix: 1.19 (0.10), residues: 2790 sheet: -1.23 (0.15), residues: 1062 loop : -1.39 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 445 HIS 0.004 0.001 HIS N 608 PHE 0.004 0.001 PHE E 410 TYR 0.007 0.001 TYR D 420 ARG 0.001 0.000 ARG M 478 *********************** 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 611 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 553 time to evaluate : 5.265 Fit side-chains revert: symmetry clash REVERT: E 552 MET cc_start: 0.8160 (tpt) cc_final: 0.7647 (tpt) REVERT: A 400 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6974 (pt) REVERT: A 478 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8036 (tpt90) REVERT: B 400 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7185 (pt) REVERT: B 552 MET cc_start: 0.8160 (tpt) cc_final: 0.7879 (tpt) REVERT: B 598 MET cc_start: 0.8154 (mmm) cc_final: 0.7392 (mmt) REVERT: C 400 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7108 (pt) REVERT: C 478 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7508 (mmm-85) REVERT: C 552 MET cc_start: 0.8244 (tpt) cc_final: 0.7765 (tpt) REVERT: C 629 VAL cc_start: 0.8839 (t) cc_final: 0.8635 (m) REVERT: C 633 ASP cc_start: 0.7188 (t0) cc_final: 0.6790 (t0) REVERT: C 669 ILE cc_start: 0.8343 (mm) cc_final: 0.8088 (mt) REVERT: D 633 ASP cc_start: 0.7168 (t0) cc_final: 0.6865 (t0) REVERT: F 400 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7029 (pt) REVERT: F 552 MET cc_start: 0.8178 (tpt) cc_final: 0.7863 (tpt) REVERT: G 400 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7207 (pt) REVERT: G 669 ILE cc_start: 0.8301 (mm) cc_final: 0.8031 (mt) REVERT: H 480 MET cc_start: 0.8734 (tpt) cc_final: 0.8478 (tpt) REVERT: I 552 MET cc_start: 0.8201 (tpt) cc_final: 0.7766 (tpt) REVERT: I 598 MET cc_start: 0.8244 (mmm) cc_final: 0.7791 (mmt) REVERT: I 633 ASP cc_start: 0.7218 (t0) cc_final: 0.6949 (t0) REVERT: J 552 MET cc_start: 0.8171 (tpt) cc_final: 0.7640 (tpt) REVERT: K 400 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6959 (pt) REVERT: K 478 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8039 (tpt90) REVERT: L 400 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7020 (pt) REVERT: L 478 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8099 (tpt90) REVERT: L 552 MET cc_start: 0.8175 (tpt) cc_final: 0.7875 (tpt) REVERT: L 598 MET cc_start: 0.8139 (mmm) cc_final: 0.7459 (mmt) REVERT: L 669 ILE cc_start: 0.8390 (mm) cc_final: 0.8095 (mt) REVERT: M 400 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7073 (pt) REVERT: M 478 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7607 (mmm-85) REVERT: M 552 MET cc_start: 0.8230 (tpt) cc_final: 0.7809 (tpt) REVERT: M 633 ASP cc_start: 0.7187 (t0) cc_final: 0.6799 (t0) REVERT: M 669 ILE cc_start: 0.8354 (mm) cc_final: 0.8098 (mt) REVERT: N 633 ASP cc_start: 0.7133 (t0) cc_final: 0.6771 (t0) REVERT: O 400 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6924 (pt) REVERT: O 552 MET cc_start: 0.8175 (tpt) cc_final: 0.7849 (tpt) REVERT: P 400 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7183 (pt) REVERT: P 669 ILE cc_start: 0.8344 (mm) cc_final: 0.8075 (mt) REVERT: Q 480 MET cc_start: 0.8716 (tpt) cc_final: 0.8470 (tpt) REVERT: Q 633 ASP cc_start: 0.7167 (t0) cc_final: 0.6940 (t0) REVERT: R 552 MET cc_start: 0.8203 (tpt) cc_final: 0.7770 (tpt) REVERT: R 598 MET cc_start: 0.8242 (mmm) cc_final: 0.7781 (mmt) REVERT: R 633 ASP cc_start: 0.7244 (t0) cc_final: 0.6890 (t0) outliers start: 58 outliers final: 27 residues processed: 597 average time/residue: 0.5828 time to fit residues: 577.2581 Evaluate side-chains 579 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 537 time to evaluate : 5.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 478 ARG Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain H residue 572 GLU Chi-restraints excluded: chain H residue 595 GLN Chi-restraints excluded: chain H residue 634 THR Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 630 THR Chi-restraints excluded: chain I residue 634 THR Chi-restraints excluded: chain J residue 630 THR Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 478 ARG Chi-restraints excluded: chain K residue 634 THR Chi-restraints excluded: chain L residue 400 LEU Chi-restraints excluded: chain L residue 478 ARG Chi-restraints excluded: chain L residue 595 GLN Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 400 LEU Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain M residue 478 ARG Chi-restraints excluded: chain N residue 400 LEU Chi-restraints excluded: chain O residue 400 LEU Chi-restraints excluded: chain O residue 595 GLN Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 400 LEU Chi-restraints excluded: chain P residue 572 GLU Chi-restraints excluded: chain Q residue 572 GLU Chi-restraints excluded: chain Q residue 595 GLN Chi-restraints excluded: chain Q residue 638 LEU Chi-restraints excluded: chain R residue 347 VAL 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: 7.9990 chunk 327 optimal weight: 2.9990 chunk 419 optimal weight: 9.9990 chunk 325 optimal weight: 2.9990 chunk 483 optimal weight: 3.9990 chunk 320 optimal weight: 6.9990 chunk 572 optimal weight: 7.9990 chunk 358 optimal weight: 8.9990 chunk 349 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 GLN ** I 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 664 GLN ** K 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 664 GLN ** M 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 GLN ** 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** ** R 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 48942 Z= 0.485 Angle : 0.647 13.537 66312 Z= 0.311 Chirality : 0.047 0.147 7848 Planarity : 0.004 0.041 8478 Dihedral : 4.238 38.239 6576 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.58 % Allowed : 11.47 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.10), residues: 6012 helix: 0.58 (0.10), residues: 2772 sheet: -1.33 (0.15), residues: 1062 loop : -1.67 (0.12), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 445 HIS 0.008 0.002 HIS M 362 PHE 0.016 0.001 PHE B 637 TYR 0.013 0.002 TYR B 420 ARG 0.003 0.000 ARG C 478 *********************** 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 647 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 562 time to evaluate : 6.148 Fit side-chains revert: symmetry clash REVERT: E 552 MET cc_start: 0.8333 (tpt) cc_final: 0.7838 (tpt) REVERT: A 400 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7032 (pt) REVERT: A 478 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7246 (mmm-85) REVERT: B 400 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7212 (pt) REVERT: B 598 MET cc_start: 0.8171 (mmm) cc_final: 0.7525 (mmt) REVERT: C 400 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7069 (pt) REVERT: C 478 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7937 (mmm-85) REVERT: C 633 ASP cc_start: 0.7300 (t0) cc_final: 0.6877 (t0) REVERT: C 669 ILE cc_start: 0.8510 (mm) cc_final: 0.8217 (mt) REVERT: D 373 MET cc_start: 0.8374 (tmm) cc_final: 0.8062 (tmm) REVERT: D 633 ASP cc_start: 0.7290 (t0) cc_final: 0.6965 (t0) REVERT: F 400 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7126 (pt) REVERT: G 669 ILE cc_start: 0.8415 (mm) cc_final: 0.8015 (mt) REVERT: I 434 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7167 (pt0) REVERT: I 598 MET cc_start: 0.8255 (mmm) cc_final: 0.7776 (mmt) REVERT: I 633 ASP cc_start: 0.7421 (t0) cc_final: 0.7056 (t0) REVERT: J 552 MET cc_start: 0.8342 (tpt) cc_final: 0.7842 (tpt) REVERT: K 400 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7070 (pt) REVERT: K 478 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7286 (mmm-85) REVERT: L 400 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7179 (pt) REVERT: L 478 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7235 (mmm-85) REVERT: L 598 MET cc_start: 0.8190 (mmm) cc_final: 0.7600 (mmt) REVERT: L 669 ILE cc_start: 0.8489 (mm) cc_final: 0.8242 (mt) REVERT: M 400 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7016 (pt) REVERT: M 478 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7968 (mmm-85) REVERT: M 633 ASP cc_start: 0.7301 (t0) cc_final: 0.6885 (t0) REVERT: M 669 ILE cc_start: 0.8501 (mm) cc_final: 0.8202 (mt) REVERT: N 434 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6948 (pt0) REVERT: N 633 ASP cc_start: 0.7210 (t0) cc_final: 0.6823 (t0) REVERT: O 400 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7099 (pt) REVERT: P 669 ILE cc_start: 0.8434 (mm) cc_final: 0.8028 (mt) REVERT: Q 633 ASP cc_start: 0.7338 (t0) cc_final: 0.7086 (t0) REVERT: R 598 MET cc_start: 0.8237 (mmm) cc_final: 0.7745 (mmt) REVERT: R 633 ASP cc_start: 0.7400 (t0) cc_final: 0.7017 (t0) outliers start: 85 outliers final: 34 residues processed: 627 average time/residue: 0.6242 time to fit residues: 637.2975 Evaluate side-chains 605 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 556 time to evaluate : 5.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 478 ARG Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain H residue 409 VAL Chi-restraints excluded: chain H residue 572 GLU Chi-restraints excluded: chain H residue 634 THR Chi-restraints excluded: chain I residue 434 GLN Chi-restraints excluded: chain I residue 630 THR Chi-restraints excluded: chain I residue 634 THR Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 630 THR Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 478 ARG Chi-restraints excluded: chain K residue 634 THR Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 400 LEU Chi-restraints excluded: chain L residue 409 VAL Chi-restraints excluded: chain L residue 478 ARG Chi-restraints excluded: chain L residue 578 ILE Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 400 LEU Chi-restraints excluded: chain M residue 409 VAL Chi-restraints excluded: chain M residue 478 ARG Chi-restraints excluded: chain N residue 409 VAL Chi-restraints excluded: chain N residue 434 GLN Chi-restraints excluded: chain O residue 400 LEU Chi-restraints excluded: chain O residue 409 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 572 GLU Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain Q residue 572 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 354 optimal weight: 9.9990 chunk 228 optimal weight: 0.7980 chunk 341 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 363 optimal weight: 0.0070 chunk 390 optimal weight: 1.9990 chunk 283 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 450 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 611 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 H 611 GLN ** I 442 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** L 614 GLN L 664 GLN ** M 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 611 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 48942 Z= 0.134 Angle : 0.519 15.756 66312 Z= 0.245 Chirality : 0.041 0.170 7848 Planarity : 0.003 0.038 8478 Dihedral : 3.908 37.238 6576 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.78 % Allowed : 12.71 % Favored : 86.50 % 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: 1.13 (0.10), residues: 2790 sheet: -1.28 (0.15), residues: 1062 loop : -1.37 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 445 HIS 0.003 0.001 HIS L 608 PHE 0.018 0.001 PHE B 637 TYR 0.007 0.001 TYR N 420 ARG 0.002 0.000 ARG E 527 *********************** 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 590 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 548 time to evaluate : 5.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 552 MET cc_start: 0.8132 (tpt) cc_final: 0.7738 (tpt) REVERT: A 400 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6990 (pt) REVERT: A 478 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.6966 (mmm-85) REVERT: B 400 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7189 (pt) REVERT: B 552 MET cc_start: 0.8157 (tpt) cc_final: 0.7887 (tpt) REVERT: B 598 MET cc_start: 0.8123 (mmm) cc_final: 0.7545 (mmt) REVERT: C 400 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7044 (pt) REVERT: C 478 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7557 (mmm-85) REVERT: C 552 MET cc_start: 0.8230 (tpt) cc_final: 0.7766 (tpt) REVERT: C 633 ASP cc_start: 0.7212 (t0) cc_final: 0.6807 (t0) REVERT: C 669 ILE cc_start: 0.8426 (mm) cc_final: 0.8166 (mt) REVERT: D 633 ASP cc_start: 0.7212 (t0) cc_final: 0.6902 (t0) REVERT: F 400 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7076 (pt) REVERT: F 552 MET cc_start: 0.8164 (tpt) cc_final: 0.7818 (tpt) REVERT: G 669 ILE cc_start: 0.8208 (mm) cc_final: 0.7976 (mt) REVERT: H 480 MET cc_start: 0.8733 (tpt) cc_final: 0.8511 (tpt) REVERT: I 552 MET cc_start: 0.8172 (tpt) cc_final: 0.7723 (tpt) REVERT: I 633 ASP cc_start: 0.7333 (t0) cc_final: 0.7048 (t0) REVERT: J 552 MET cc_start: 0.8141 (tpt) cc_final: 0.7737 (tpt) REVERT: K 400 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6979 (pt) REVERT: K 478 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.6965 (mmm-85) REVERT: L 400 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7077 (pt) REVERT: L 478 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7019 (mmm-85) REVERT: L 552 MET cc_start: 0.8146 (tpt) cc_final: 0.7801 (tpt) REVERT: L 598 MET cc_start: 0.8156 (mmm) cc_final: 0.7491 (mmt) REVERT: L 669 ILE cc_start: 0.8394 (mm) cc_final: 0.8100 (mt) REVERT: M 400 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7102 (pt) REVERT: M 478 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7586 (mmm-85) REVERT: M 552 MET cc_start: 0.8204 (tpt) cc_final: 0.7788 (tpt) REVERT: M 633 ASP cc_start: 0.7187 (t0) cc_final: 0.6764 (t0) REVERT: M 669 ILE cc_start: 0.8425 (mm) cc_final: 0.8162 (mt) REVERT: N 633 ASP cc_start: 0.7186 (t0) cc_final: 0.6810 (t0) REVERT: O 400 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6987 (pt) REVERT: O 552 MET cc_start: 0.8172 (tpt) cc_final: 0.7819 (tpt) REVERT: P 669 ILE cc_start: 0.8182 (mm) cc_final: 0.7932 (mt) REVERT: Q 480 MET cc_start: 0.8713 (tpt) cc_final: 0.8501 (tpt) REVERT: Q 633 ASP cc_start: 0.7181 (t0) cc_final: 0.6960 (t0) REVERT: R 552 MET cc_start: 0.8176 (tpt) cc_final: 0.7738 (tpt) REVERT: R 633 ASP cc_start: 0.7254 (t0) cc_final: 0.6884 (t0) outliers start: 42 outliers final: 25 residues processed: 584 average time/residue: 0.6236 time to fit residues: 603.2863 Evaluate side-chains 584 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 546 time to evaluate : 5.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain E residue 662 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 478 ARG Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 595 GLN Chi-restraints excluded: chain H residue 572 GLU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 630 THR Chi-restraints excluded: chain J residue 662 LEU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 478 ARG Chi-restraints excluded: chain K residue 634 THR Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 400 LEU Chi-restraints excluded: chain L residue 478 ARG Chi-restraints excluded: chain L residue 578 ILE Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 400 LEU Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain M residue 478 ARG Chi-restraints excluded: chain O residue 400 LEU Chi-restraints excluded: chain O residue 662 LEU Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 572 GLU Chi-restraints excluded: chain Q residue 572 GLU Chi-restraints excluded: chain R residue 347 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 520 optimal weight: 0.9980 chunk 548 optimal weight: 2.9990 chunk 500 optimal weight: 7.9990 chunk 533 optimal weight: 4.9990 chunk 321 optimal weight: 0.9990 chunk 232 optimal weight: 3.9990 chunk 418 optimal weight: 0.0170 chunk 163 optimal weight: 7.9990 chunk 482 optimal weight: 0.5980 chunk 504 optimal weight: 0.9980 chunk 531 optimal weight: 0.0980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 614 GLN J 611 GLN J 664 GLN ** K 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 48942 Z= 0.132 Angle : 0.503 16.003 66312 Z= 0.235 Chirality : 0.041 0.180 7848 Planarity : 0.003 0.036 8478 Dihedral : 3.629 35.582 6576 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.80 % Allowed : 12.62 % Favored : 86.58 % 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: 0.02 (0.11), residues: 6012 helix: 1.50 (0.10), residues: 2790 sheet: -1.25 (0.15), residues: 1062 loop : -1.25 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 445 HIS 0.003 0.001 HIS H 608 PHE 0.015 0.001 PHE B 637 TYR 0.011 0.001 TYR D 420 ARG 0.002 0.000 ARG H 527 *********************** 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 615 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 572 time to evaluate : 5.696 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: E 552 MET cc_start: 0.8120 (tpt) cc_final: 0.7606 (tpt) REVERT: A 400 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6963 (pt) REVERT: B 400 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7137 (pt) REVERT: B 552 MET cc_start: 0.8126 (tpt) cc_final: 0.7808 (tpt) REVERT: C 400 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6995 (pt) REVERT: C 552 MET cc_start: 0.8196 (tpt) cc_final: 0.7749 (tpt) REVERT: C 633 ASP cc_start: 0.7188 (t0) cc_final: 0.6787 (t0) REVERT: C 669 ILE cc_start: 0.8396 (mm) cc_final: 0.8165 (mt) REVERT: D 633 ASP cc_start: 0.7178 (t0) cc_final: 0.6880 (t0) REVERT: F 400 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6909 (pt) REVERT: F 552 MET cc_start: 0.8146 (tpt) cc_final: 0.7846 (tpt) REVERT: I 552 MET cc_start: 0.8181 (tpt) cc_final: 0.7745 (tpt) REVERT: I 598 MET cc_start: 0.8162 (mmm) cc_final: 0.7820 (mmt) REVERT: I 633 ASP cc_start: 0.7243 (t0) cc_final: 0.6922 (t0) REVERT: J 552 MET cc_start: 0.8136 (tpt) cc_final: 0.7606 (tpt) REVERT: K 400 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6987 (pt) REVERT: L 552 MET cc_start: 0.8113 (tpt) cc_final: 0.7799 (tpt) REVERT: L 669 ILE cc_start: 0.8412 (mm) cc_final: 0.8196 (mt) REVERT: M 400 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7032 (pt) REVERT: M 552 MET cc_start: 0.8173 (tpt) cc_final: 0.7777 (tpt) REVERT: M 633 ASP cc_start: 0.7099 (t0) cc_final: 0.6676 (t0) REVERT: M 669 ILE cc_start: 0.8386 (mm) cc_final: 0.8171 (mt) REVERT: N 633 ASP cc_start: 0.7124 (t0) cc_final: 0.6802 (t0) REVERT: O 400 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6926 (pt) REVERT: O 552 MET cc_start: 0.8157 (tpt) cc_final: 0.7837 (tpt) REVERT: R 552 MET cc_start: 0.8181 (tpt) cc_final: 0.7767 (tpt) REVERT: R 598 MET cc_start: 0.8177 (mmm) cc_final: 0.7811 (mmt) REVERT: R 629 VAL cc_start: 0.8817 (t) cc_final: 0.8587 (m) REVERT: R 633 ASP cc_start: 0.7234 (t0) cc_final: 0.6902 (t0) outliers start: 43 outliers final: 21 residues processed: 606 average time/residue: 0.5881 time to fit residues: 590.1421 Evaluate side-chains 582 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 554 time to evaluate : 5.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain E residue 662 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 595 GLN Chi-restraints excluded: chain H residue 572 GLU Chi-restraints excluded: chain J residue 662 LEU Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 634 THR Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 578 ILE Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 400 LEU Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain O residue 400 LEU Chi-restraints excluded: chain O residue 662 LEU Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 572 GLU Chi-restraints excluded: chain P residue 595 GLN Chi-restraints excluded: chain Q residue 572 GLU 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: 0.6980 chunk 267 optimal weight: 3.9990 chunk 392 optimal weight: 0.6980 chunk 591 optimal weight: 3.9990 chunk 544 optimal weight: 0.8980 chunk 471 optimal weight: 0.0970 chunk 48 optimal weight: 3.9990 chunk 363 optimal weight: 0.4980 chunk 288 optimal weight: 7.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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** ** C 434 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** ** I 442 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** ** O 434 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: 0.7651 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 48942 Z= 0.135 Angle : 0.524 16.202 66312 Z= 0.244 Chirality : 0.041 0.172 7848 Planarity : 0.003 0.035 8478 Dihedral : 3.545 34.862 6575 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.58 % Allowed : 13.24 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.11), residues: 6012 helix: 1.59 (0.10), residues: 2772 sheet: -1.25 (0.15), residues: 1062 loop : -1.20 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 445 HIS 0.004 0.001 HIS I 608 PHE 0.006 0.001 PHE L 637 TYR 0.013 0.001 TYR H 420 ARG 0.002 0.000 ARG H 527 ********************** 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 602 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 571 time to evaluate : 5.301 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: E 552 MET cc_start: 0.8131 (tpt) cc_final: 0.7633 (tpt) REVERT: E 598 MET cc_start: 0.8114 (mmm) cc_final: 0.7724 (mmt) REVERT: A 400 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6953 (pt) REVERT: B 400 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7121 (pt) REVERT: B 552 MET cc_start: 0.8135 (tpt) cc_final: 0.7826 (tpt) REVERT: C 400 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6987 (pt) REVERT: C 552 MET cc_start: 0.8214 (tpt) cc_final: 0.7766 (tpt) REVERT: C 633 ASP cc_start: 0.7117 (t0) cc_final: 0.6723 (t0) REVERT: D 633 ASP cc_start: 0.7161 (t0) cc_final: 0.6869 (t0) REVERT: F 400 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6910 (pt) REVERT: F 552 MET cc_start: 0.8175 (tpt) cc_final: 0.7862 (tpt) REVERT: I 552 MET cc_start: 0.8198 (tpt) cc_final: 0.7714 (tpt) REVERT: I 598 MET cc_start: 0.8114 (mmm) cc_final: 0.7856 (mmt) REVERT: I 633 ASP cc_start: 0.7283 (t0) cc_final: 0.6986 (t0) REVERT: J 552 MET cc_start: 0.8145 (tpt) cc_final: 0.7632 (tpt) REVERT: J 598 MET cc_start: 0.8107 (mmm) cc_final: 0.7711 (mmt) REVERT: K 400 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6988 (pt) REVERT: L 552 MET cc_start: 0.8137 (tpt) cc_final: 0.7812 (tpt) REVERT: L 593 ILE cc_start: 0.9200 (mm) cc_final: 0.8815 (mm) REVERT: M 400 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7024 (pt) REVERT: M 552 MET cc_start: 0.8182 (tpt) cc_final: 0.7782 (tpt) REVERT: M 633 ASP cc_start: 0.7088 (t0) cc_final: 0.6662 (t0) REVERT: N 633 ASP cc_start: 0.7152 (t0) cc_final: 0.6841 (t0) REVERT: O 400 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6899 (pt) REVERT: O 552 MET cc_start: 0.8171 (tpt) cc_final: 0.7851 (tpt) REVERT: R 552 MET cc_start: 0.8208 (tpt) cc_final: 0.7731 (tpt) REVERT: R 598 MET cc_start: 0.8125 (mmm) cc_final: 0.7850 (mmt) REVERT: R 629 VAL cc_start: 0.8802 (t) cc_final: 0.8597 (m) REVERT: R 633 ASP cc_start: 0.7275 (t0) cc_final: 0.6957 (t0) outliers start: 31 outliers final: 19 residues processed: 594 average time/residue: 0.5824 time to fit residues: 575.9686 Evaluate side-chains 585 residues out of total 5364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 559 time to evaluate : 5.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 630 THR Chi-restraints excluded: chain E residue 662 LEU Chi-restraints excluded: chain E residue 664 GLN Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain H residue 572 GLU Chi-restraints excluded: chain J residue 662 LEU Chi-restraints excluded: chain J residue 664 GLN Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 634 THR Chi-restraints excluded: chain L residue 578 ILE Chi-restraints excluded: chain M residue 400 LEU Chi-restraints excluded: chain O residue 347 VAL Chi-restraints excluded: chain O residue 400 LEU Chi-restraints excluded: chain O residue 662 LEU Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 572 GLU Chi-restraints excluded: chain Q residue 572 GLU Chi-restraints excluded: chain Q residue 578 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 374 optimal weight: 10.0000 chunk 501 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 434 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 471 optimal weight: 0.9990 chunk 197 optimal weight: 20.0000 chunk 484 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 434 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** ** O 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.189984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.179707 restraints weight = 45580.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.179137 restraints weight = 102380.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.147474 restraints weight = 111881.219| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.280 48942 Z= 0.241 Angle : 0.696 59.101 66312 Z= 0.374 Chirality : 0.042 0.552 7848 Planarity : 0.003 0.035 8478 Dihedral : 3.512 34.859 6573 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.48 % Allowed : 13.31 % Favored : 86.20 % Cbeta Deviations : 0.03 % 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: 0.09 (0.11), residues: 6012 helix: 1.58 (0.10), residues: 2772 sheet: -1.25 (0.15), residues: 1062 loop : -1.19 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 445 HIS 0.003 0.001 HIS E 608 PHE 0.006 0.001 PHE L 637 TYR 0.010 0.001 TYR D 420 ARG 0.002 0.000 ARG B 527 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10360.99 seconds wall clock time: 188 minutes 28.40 seconds (11308.40 seconds total)