Starting phenix.real_space_refine on Wed Aug 7 01:27:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1c_41809/08_2024/8u1c_41809.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1c_41809/08_2024/8u1c_41809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1c_41809/08_2024/8u1c_41809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1c_41809/08_2024/8u1c_41809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1c_41809/08_2024/8u1c_41809.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1c_41809/08_2024/8u1c_41809.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 140 5.16 5 C 11632 2.51 5 N 3144 2.21 5 O 3464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 46": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18380 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 10, 'TRANS': 115} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 2757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2757 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 16, 'TRANS': 337} Chain breaks: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 10, 'TRANS': 115} Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 2757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2757 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 16, 'TRANS': 337} Chain breaks: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 10, 'TRANS': 115} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "J" Number of atoms: 2757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2757 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 16, 'TRANS': 337} Chain breaks: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 10, 'TRANS': 115} Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "O" Number of atoms: 2757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2757 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 16, 'TRANS': 337} Chain breaks: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.64, per 1000 atoms: 0.69 Number of scatterers: 18380 At special positions: 0 Unit cell: (157.325, 157.325, 99.325, 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 140 16.00 O 3464 8.00 N 3144 7.00 C 11632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.01 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 181 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 290 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 336 " distance=2.04 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 446 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.01 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 86 " - pdb=" SG CYS E 419 " distance=2.04 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 181 " - pdb=" SG CYS E 228 " distance=2.03 Simple disulfide: pdb=" SG CYS E 230 " - pdb=" SG CYS E 235 " distance=2.03 Simple disulfide: pdb=" SG CYS E 276 " - pdb=" SG CYS E 290 " distance=2.02 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 288 " distance=2.02 Simple disulfide: pdb=" SG CYS E 317 " - pdb=" SG CYS E 336 " distance=2.04 Simple disulfide: pdb=" SG CYS E 423 " - pdb=" SG CYS E 446 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.01 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 86 " - pdb=" SG CYS J 419 " distance=2.04 Simple disulfide: pdb=" SG CYS J 121 " - pdb=" SG CYS J 126 " distance=2.03 Simple disulfide: pdb=" SG CYS J 181 " - pdb=" SG CYS J 228 " distance=2.03 Simple disulfide: pdb=" SG CYS J 230 " - pdb=" SG CYS J 235 " distance=2.03 Simple disulfide: pdb=" SG CYS J 276 " - pdb=" SG CYS J 290 " distance=2.02 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 288 " distance=2.02 Simple disulfide: pdb=" SG CYS J 317 " - pdb=" SG CYS J 336 " distance=2.04 Simple disulfide: pdb=" SG CYS J 423 " - pdb=" SG CYS J 446 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.01 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 86 " - pdb=" SG CYS O 419 " distance=2.04 Simple disulfide: pdb=" SG CYS O 121 " - pdb=" SG CYS O 126 " distance=2.03 Simple disulfide: pdb=" SG CYS O 181 " - pdb=" SG CYS O 228 " distance=2.03 Simple disulfide: pdb=" SG CYS O 230 " - pdb=" SG CYS O 235 " distance=2.03 Simple disulfide: pdb=" SG CYS O 276 " - pdb=" SG CYS O 290 " distance=2.02 Simple disulfide: pdb=" SG CYS O 278 " - pdb=" SG CYS O 288 " distance=2.02 Simple disulfide: pdb=" SG CYS O 317 " - pdb=" SG CYS O 336 " distance=2.04 Simple disulfide: pdb=" SG CYS O 423 " - pdb=" SG CYS O 446 " distance=2.04 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG K 1 " - " NAG K 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG B 1 " - " ASN A 283 " " NAG F 1 " - " ASN E 283 " " NAG K 1 " - " ASN J 283 " " NAG P 1 " - " ASN O 283 " Time building additional restraints: 6.95 Conformation dependent library (CDL) restraints added in 3.2 seconds 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 52 sheets defined 5.3% alpha, 46.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 100 through 100D Processing helix chain 'L' and resid 28 through 31 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.999A pdb=" N PHE A 102 " --> pdb=" O PRO A 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 100 through 100D Processing helix chain 'D' and resid 28 through 31 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.999A pdb=" N PHE E 102 " --> pdb=" O PRO E 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 100 through 100D Processing helix chain 'I' and resid 28 through 31 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 98 through 102 removed outlier: 3.999A pdb=" N PHE J 102 " --> pdb=" O PRO J 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 73 through 75 No H-bonds generated for 'chain 'M' and resid 73 through 75' Processing helix chain 'M' and resid 100 through 100D Processing helix chain 'N' and resid 28 through 31 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'O' and resid 98 through 102 removed outlier: 3.999A pdb=" N PHE O 102 " --> pdb=" O PRO O 99 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=2, first strand: chain 'H' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'H' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=5, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 91 through 97 removed outlier: 6.785A pdb=" N ILE A 444 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU A 96 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 442 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 113 through 122 removed outlier: 6.981A pdb=" N ILE A 114 " --> pdb=" O HIS A 133 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS A 133 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLU A 116 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A 131 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS A 154 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 155 " --> pdb=" O HIS A 172 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 177 through 182 removed outlier: 6.394A pdb=" N LEU A 201 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A 212 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL A 203 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 221 through 223 Processing sheet with id=11, first strand: chain 'A' and resid 221 through 223 removed outlier: 6.598A pdb=" N ARG A 256 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.578A pdb=" N THR A 267 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N LEU A 315 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR A 285 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE A 280 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU A 287 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS A 278 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA A 289 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N CYS A 276 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 351 through 356 removed outlier: 7.961A pdb=" N MET A 374 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL A 400 " --> pdb=" O MET A 374 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N MET A 376 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL A 398 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 378 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=15, first strand: chain 'C' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=18, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'E' and resid 91 through 97 removed outlier: 6.785A pdb=" N ILE E 444 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU E 96 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR E 442 " --> pdb=" O LEU E 96 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'E' and resid 113 through 122 removed outlier: 6.981A pdb=" N ILE E 114 " --> pdb=" O HIS E 133 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS E 133 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLU E 116 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU E 131 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS E 154 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU E 155 " --> pdb=" O HIS E 172 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 177 through 182 removed outlier: 6.394A pdb=" N LEU E 201 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR E 212 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL E 203 " --> pdb=" O THR E 210 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 221 through 223 Processing sheet with id=24, first strand: chain 'E' and resid 221 through 223 removed outlier: 6.598A pdb=" N ARG E 256 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 267 through 268 removed outlier: 6.578A pdb=" N THR E 267 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N LEU E 315 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR E 285 " --> pdb=" O PHE E 280 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE E 280 " --> pdb=" O THR E 285 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU E 287 " --> pdb=" O CYS E 278 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS E 278 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA E 289 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N CYS E 276 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 351 through 356 removed outlier: 7.961A pdb=" N MET E 374 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL E 400 " --> pdb=" O MET E 374 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N MET E 376 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL E 398 " --> pdb=" O MET E 376 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU E 378 " --> pdb=" O SER E 396 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=28, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=31, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'J' and resid 91 through 97 removed outlier: 6.785A pdb=" N ILE J 444 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU J 96 " --> pdb=" O THR J 442 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR J 442 " --> pdb=" O LEU J 96 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'J' and resid 113 through 122 removed outlier: 6.981A pdb=" N ILE J 114 " --> pdb=" O HIS J 133 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS J 133 " --> pdb=" O ILE J 114 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLU J 116 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU J 131 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS J 154 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU J 155 " --> pdb=" O HIS J 172 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'J' and resid 177 through 182 removed outlier: 6.394A pdb=" N LEU J 201 " --> pdb=" O THR J 212 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR J 212 " --> pdb=" O LEU J 201 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL J 203 " --> pdb=" O THR J 210 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'J' and resid 221 through 223 Processing sheet with id=37, first strand: chain 'J' and resid 221 through 223 removed outlier: 6.598A pdb=" N ARG J 256 " --> pdb=" O ILE J 260 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE J 260 " --> pdb=" O ARG J 256 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'J' and resid 267 through 268 removed outlier: 6.578A pdb=" N THR J 267 " --> pdb=" O ILE J 313 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N LEU J 315 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR J 285 " --> pdb=" O PHE J 280 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE J 280 " --> pdb=" O THR J 285 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU J 287 " --> pdb=" O CYS J 278 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS J 278 " --> pdb=" O GLU J 287 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA J 289 " --> pdb=" O CYS J 276 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N CYS J 276 " --> pdb=" O ALA J 289 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'J' and resid 351 through 356 removed outlier: 7.961A pdb=" N MET J 374 " --> pdb=" O VAL J 400 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL J 400 " --> pdb=" O MET J 374 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N MET J 376 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL J 398 " --> pdb=" O MET J 376 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU J 378 " --> pdb=" O SER J 396 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=41, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.567A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=44, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.890A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'O' and resid 91 through 97 removed outlier: 6.785A pdb=" N ILE O 444 " --> pdb=" O ALA O 94 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU O 96 " --> pdb=" O THR O 442 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR O 442 " --> pdb=" O LEU O 96 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'O' and resid 113 through 122 removed outlier: 6.981A pdb=" N ILE O 114 " --> pdb=" O HIS O 133 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS O 133 " --> pdb=" O ILE O 114 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLU O 116 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU O 131 " --> pdb=" O GLU O 116 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS O 154 " --> pdb=" O THR O 132 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU O 155 " --> pdb=" O HIS O 172 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'O' and resid 177 through 182 removed outlier: 6.394A pdb=" N LEU O 201 " --> pdb=" O THR O 212 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR O 212 " --> pdb=" O LEU O 201 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL O 203 " --> pdb=" O THR O 210 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'O' and resid 221 through 223 Processing sheet with id=50, first strand: chain 'O' and resid 221 through 223 removed outlier: 6.598A pdb=" N ARG O 256 " --> pdb=" O ILE O 260 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE O 260 " --> pdb=" O ARG O 256 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'O' and resid 267 through 268 removed outlier: 6.578A pdb=" N THR O 267 " --> pdb=" O ILE O 313 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N LEU O 315 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR O 285 " --> pdb=" O PHE O 280 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE O 280 " --> pdb=" O THR O 285 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU O 287 " --> pdb=" O CYS O 278 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS O 278 " --> pdb=" O GLU O 287 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA O 289 " --> pdb=" O CYS O 276 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N CYS O 276 " --> pdb=" O ALA O 289 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'O' and resid 351 through 356 removed outlier: 7.961A pdb=" N MET O 374 " --> pdb=" O VAL O 400 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL O 400 " --> pdb=" O MET O 374 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N MET O 376 " --> pdb=" O VAL O 398 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL O 398 " --> pdb=" O MET O 376 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU O 378 " --> pdb=" O SER O 396 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.93 Time building geometry restraints manager: 7.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4568 1.32 - 1.46: 6292 1.46 - 1.60: 7788 1.60 - 1.74: 48 1.74 - 1.88: 172 Bond restraints: 18868 Sorted by residual: bond pdb=" CB ILE D 106 " pdb=" CG1 ILE D 106 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" CB ILE L 106 " pdb=" CG1 ILE L 106 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" CB ILE N 106 " pdb=" CG1 ILE N 106 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" CB ILE I 106 " pdb=" CG1 ILE I 106 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" NE ARG J 149 " pdb=" CZ ARG J 149 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.03e+01 ... (remaining 18863 not shown) Histogram of bond angle deviations from ideal: 97.62 - 105.00: 568 105.00 - 112.38: 8332 112.38 - 119.76: 7780 119.76 - 127.14: 8580 127.14 - 134.52: 280 Bond angle restraints: 25540 Sorted by residual: angle pdb=" N ILE G 40 " pdb=" CA ILE G 40 " pdb=" C ILE G 40 " ideal model delta sigma weight residual 108.95 100.35 8.60 9.80e-01 1.04e+00 7.70e+01 angle pdb=" N ILE H 40 " pdb=" CA ILE H 40 " pdb=" C ILE H 40 " ideal model delta sigma weight residual 108.95 100.35 8.60 9.80e-01 1.04e+00 7.70e+01 angle pdb=" N ILE C 40 " pdb=" CA ILE C 40 " pdb=" C ILE C 40 " ideal model delta sigma weight residual 108.95 100.35 8.60 9.80e-01 1.04e+00 7.70e+01 angle pdb=" N ILE M 40 " pdb=" CA ILE M 40 " pdb=" C ILE M 40 " ideal model delta sigma weight residual 108.95 100.35 8.60 9.80e-01 1.04e+00 7.70e+01 angle pdb=" N PRO G 52A" pdb=" CA PRO G 52A" pdb=" C PRO G 52A" ideal model delta sigma weight residual 111.21 97.62 13.59 1.59e+00 3.96e-01 7.30e+01 ... (remaining 25535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 10828 17.04 - 34.09: 348 34.09 - 51.13: 68 51.13 - 68.17: 28 68.17 - 85.22: 16 Dihedral angle restraints: 11288 sinusoidal: 4644 harmonic: 6644 Sorted by residual: dihedral pdb=" N THR J 324 " pdb=" C THR J 324 " pdb=" CA THR J 324 " pdb=" CB THR J 324 " ideal model delta harmonic sigma weight residual 123.40 133.38 -9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" N THR E 324 " pdb=" C THR E 324 " pdb=" CA THR E 324 " pdb=" CB THR E 324 " ideal model delta harmonic sigma weight residual 123.40 133.38 -9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" N THR O 324 " pdb=" C THR O 324 " pdb=" CA THR O 324 " pdb=" CB THR O 324 " ideal model delta harmonic sigma weight residual 123.40 133.38 -9.98 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 11285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1896 0.102 - 0.203: 636 0.203 - 0.305: 124 0.305 - 0.407: 32 0.407 - 0.508: 20 Chirality restraints: 2708 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 ... (remaining 2705 not shown) Planarity restraints: 3256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 99 " -0.060 2.00e-02 2.50e+03 2.96e-02 2.20e+01 pdb=" CG TRP M 99 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP M 99 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP M 99 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP M 99 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 99 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP M 99 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 99 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 99 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP M 99 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 99 " -0.060 2.00e-02 2.50e+03 2.96e-02 2.20e+01 pdb=" CG TRP H 99 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP H 99 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP H 99 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP H 99 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 99 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP H 99 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 99 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 99 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 99 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 99 " -0.060 2.00e-02 2.50e+03 2.96e-02 2.20e+01 pdb=" CG TRP C 99 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP C 99 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 99 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP C 99 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 99 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 99 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 99 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 99 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 99 " -0.034 2.00e-02 2.50e+03 ... (remaining 3253 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 6668 2.86 - 3.37: 15572 3.37 - 3.88: 33236 3.88 - 4.39: 40212 4.39 - 4.90: 67092 Nonbonded interactions: 162780 Sorted by model distance: nonbonded pdb=" O MET J 399 " pdb=" OH TYR J 445 " model vdw 2.353 3.040 nonbonded pdb=" O MET A 399 " pdb=" OH TYR A 445 " model vdw 2.353 3.040 nonbonded pdb=" O MET E 399 " pdb=" OH TYR E 445 " model vdw 2.353 3.040 nonbonded pdb=" O MET O 399 " pdb=" OH TYR O 445 " model vdw 2.353 3.040 nonbonded pdb=" N PRO M 52A" pdb=" O PRO M 52A" model vdw 2.378 2.496 ... (remaining 162775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'L' selection = chain 'N' } 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 individual isotropic 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: 23.060 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: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 56.310 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.023 0.159 18868 Z= 1.532 Angle : 1.847 13.590 25540 Z= 1.227 Chirality : 0.109 0.508 2708 Planarity : 0.010 0.055 3252 Dihedral : 10.037 85.218 6960 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.52 % Favored : 95.13 % Rotamer: Outliers : 0.20 % Allowed : 1.63 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.65 (0.17), residues: 892 loop : -0.38 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.013 TRP C 99 HIS 0.014 0.003 HIS H 100C PHE 0.028 0.006 PHE L 98 TYR 0.055 0.009 TYR E 321 ARG 0.009 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 480 time to evaluate : 2.396 Fit side-chains REVERT: J 417 LYS cc_start: 0.7185 (mmtt) cc_final: 0.6970 (mppt) outliers start: 4 outliers final: 4 residues processed: 484 average time/residue: 1.2342 time to fit residues: 674.6161 Evaluate side-chains 296 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 292 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain M residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 272 HIS E 133 HIS E 272 HIS J 133 HIS J 272 HIS O 133 HIS O 272 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18868 Z= 0.299 Angle : 0.712 8.841 25540 Z= 0.385 Chirality : 0.049 0.151 2708 Planarity : 0.005 0.036 3252 Dihedral : 5.836 27.960 2728 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.78 % Favored : 97.04 % Rotamer: Outliers : 4.07 % Allowed : 11.20 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.70 (0.16), residues: 2300 helix: None (None), residues: 0 sheet: 0.39 (0.17), residues: 876 loop : -1.06 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 47 HIS 0.004 0.001 HIS I 91 PHE 0.016 0.002 PHE D 83 TYR 0.018 0.002 TYR O 321 ARG 0.004 0.001 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 344 time to evaluate : 1.949 Fit side-chains REVERT: A 390 SER cc_start: 0.8914 (p) cc_final: 0.8690 (t) REVERT: E 390 SER cc_start: 0.8913 (p) cc_final: 0.8686 (t) REVERT: J 390 SER cc_start: 0.8911 (p) cc_final: 0.8681 (t) REVERT: O 390 SER cc_start: 0.8916 (p) cc_final: 0.8693 (t) outliers start: 80 outliers final: 40 residues processed: 372 average time/residue: 1.1069 time to fit residues: 469.6934 Evaluate side-chains 324 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 284 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 124 ASN Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 359 LYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 73 LYS Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 124 ASN Chi-restraints excluded: chain O residue 125 GLU Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 166 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 HIS D 90 HIS ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 HIS I 91 HIS N 90 HIS N 91 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18868 Z= 0.246 Angle : 0.616 5.554 25540 Z= 0.333 Chirality : 0.046 0.149 2708 Planarity : 0.004 0.037 3252 Dihedral : 5.173 25.411 2724 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 96.00 % Rotamer: Outliers : 4.58 % Allowed : 14.56 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.64 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.59 (0.17), residues: 916 loop : -1.19 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 47 HIS 0.004 0.001 HIS O 272 PHE 0.013 0.002 PHE J 118 TYR 0.014 0.001 TYR L 32 ARG 0.003 0.001 ARG O 299 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 289 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7318 (pt0) cc_final: 0.7083 (pm20) REVERT: A 438 HIS cc_start: 0.6106 (m-70) cc_final: 0.5835 (m-70) REVERT: E 125 GLU cc_start: 0.7320 (pt0) cc_final: 0.7113 (pm20) REVERT: E 438 HIS cc_start: 0.6111 (m-70) cc_final: 0.5844 (m-70) REVERT: J 125 GLU cc_start: 0.7309 (pt0) cc_final: 0.7076 (pm20) REVERT: J 438 HIS cc_start: 0.6102 (m-70) cc_final: 0.5839 (m-70) REVERT: O 125 GLU cc_start: 0.7303 (pt0) cc_final: 0.7067 (pm20) REVERT: O 438 HIS cc_start: 0.6095 (m-70) cc_final: 0.5830 (m-70) outliers start: 90 outliers final: 32 residues processed: 335 average time/residue: 1.0445 time to fit residues: 402.8930 Evaluate side-chains 285 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 253 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 228 CYS Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 352 VAL Chi-restraints excluded: chain J residue 371 THR Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 228 CYS Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 371 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 0.0010 chunk 98 optimal weight: 1.9990 chunk 139 optimal weight: 0.0770 chunk 208 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.5546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 GLN L 91 HIS D 42 GLN D 91 HIS I 42 GLN N 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18868 Z= 0.199 Angle : 0.577 5.629 25540 Z= 0.308 Chirality : 0.045 0.148 2708 Planarity : 0.004 0.034 3252 Dihedral : 5.108 25.219 2724 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.35 % Favored : 96.48 % Rotamer: Outliers : 4.53 % Allowed : 14.61 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.71 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.55 (0.17), residues: 924 loop : -1.25 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 100F HIS 0.003 0.001 HIS L 91 PHE 0.011 0.002 PHE E 118 TYR 0.011 0.001 TYR O 321 ARG 0.003 0.000 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 269 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.7051 (pm20) REVERT: E 125 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: J 125 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.7071 (pm20) REVERT: O 125 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.7054 (pm20) outliers start: 89 outliers final: 29 residues processed: 309 average time/residue: 0.9412 time to fit residues: 339.5503 Evaluate side-chains 290 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 257 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 228 CYS Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 125 GLU Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 228 CYS Chi-restraints excluded: chain O residue 243 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.0000 chunk 125 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN L 42 GLN A 100 HIS C 81 GLN D 42 GLN E 100 HIS G 81 GLN J 100 HIS M 81 GLN N 42 GLN O 100 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18868 Z= 0.316 Angle : 0.624 5.979 25540 Z= 0.331 Chirality : 0.046 0.160 2708 Planarity : 0.005 0.044 3252 Dihedral : 5.207 24.147 2724 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.70 % Favored : 95.13 % Rotamer: Outliers : 4.43 % Allowed : 14.92 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.81 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.46 (0.17), residues: 884 loop : -1.26 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 100F HIS 0.005 0.001 HIS L 90 PHE 0.012 0.002 PHE E 118 TYR 0.014 0.002 TYR I 32 ARG 0.003 0.000 ARG O 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 297 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.7536 (m) cc_final: 0.7292 (t) REVERT: A 403 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7920 (pttt) REVERT: D 74 THR cc_start: 0.7541 (m) cc_final: 0.7298 (t) REVERT: E 403 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7915 (pttt) REVERT: I 74 THR cc_start: 0.7543 (m) cc_final: 0.7298 (t) REVERT: J 359 LYS cc_start: 0.8450 (ttpp) cc_final: 0.7750 (tttp) REVERT: J 403 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7917 (pttt) REVERT: N 74 THR cc_start: 0.7536 (m) cc_final: 0.7294 (t) REVERT: O 403 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7915 (pttt) outliers start: 87 outliers final: 44 residues processed: 344 average time/residue: 0.9116 time to fit residues: 368.5194 Evaluate side-chains 328 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 280 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 228 CYS Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 371 THR Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 228 CYS Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 220 optimal weight: 0.9980 chunk 183 optimal weight: 0.0370 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 HIS A 430 HIS E 353 HIS E 430 HIS J 353 HIS J 430 HIS O 353 HIS O 430 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 18868 Z= 0.486 Angle : 0.712 5.580 25540 Z= 0.377 Chirality : 0.049 0.182 2708 Planarity : 0.006 0.068 3252 Dihedral : 5.635 24.760 2724 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.40 % Allowed : 15.84 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.06 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.17 (0.17), residues: 956 loop : -1.41 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP G 100F HIS 0.008 0.002 HIS N 90 PHE 0.016 0.003 PHE E 118 TYR 0.016 0.002 TYR N 32 ARG 0.005 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 259 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 69 THR cc_start: 0.8457 (p) cc_final: 0.8235 (m) REVERT: A 359 LYS cc_start: 0.8461 (ttpp) cc_final: 0.7721 (tttp) REVERT: D 69 THR cc_start: 0.8463 (p) cc_final: 0.8235 (m) REVERT: E 359 LYS cc_start: 0.8461 (ttpp) cc_final: 0.7720 (tttp) REVERT: I 69 THR cc_start: 0.8459 (p) cc_final: 0.8245 (m) REVERT: N 69 THR cc_start: 0.8467 (p) cc_final: 0.8253 (m) REVERT: O 359 LYS cc_start: 0.8461 (ttpp) cc_final: 0.7721 (tttp) outliers start: 106 outliers final: 56 residues processed: 324 average time/residue: 0.9607 time to fit residues: 358.2928 Evaluate side-chains 303 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 247 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 228 CYS Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 371 THR Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 222 ARG Chi-restraints excluded: chain O residue 228 CYS Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 185 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 219 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18868 Z= 0.232 Angle : 0.588 6.487 25540 Z= 0.313 Chirality : 0.045 0.144 2708 Planarity : 0.005 0.036 3252 Dihedral : 5.187 24.596 2724 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.16 % Allowed : 18.38 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.96 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.29 (0.18), residues: 884 loop : -1.31 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 100F HIS 0.002 0.001 HIS I 91 PHE 0.013 0.002 PHE G 100E TYR 0.011 0.001 TYR O 321 ARG 0.003 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 250 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 69 THR cc_start: 0.8411 (p) cc_final: 0.8207 (m) REVERT: A 359 LYS cc_start: 0.8357 (ttpp) cc_final: 0.7661 (tttp) REVERT: A 403 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7959 (pttt) REVERT: D 69 THR cc_start: 0.8412 (p) cc_final: 0.8204 (m) REVERT: E 359 LYS cc_start: 0.8365 (ttpp) cc_final: 0.7663 (tttp) REVERT: E 403 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7960 (pttt) REVERT: J 359 LYS cc_start: 0.8399 (ttpp) cc_final: 0.7661 (tttp) REVERT: J 403 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7956 (pttt) REVERT: O 359 LYS cc_start: 0.8360 (ttpp) cc_final: 0.7664 (tttp) REVERT: O 403 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7955 (pttt) outliers start: 62 outliers final: 43 residues processed: 287 average time/residue: 1.0355 time to fit residues: 343.2207 Evaluate side-chains 276 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 229 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 228 CYS Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 371 THR Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 228 CYS Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18868 Z= 0.325 Angle : 0.611 6.356 25540 Z= 0.324 Chirality : 0.046 0.143 2708 Planarity : 0.005 0.047 3252 Dihedral : 5.249 24.006 2724 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.92 % Allowed : 17.57 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.97 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.26 (0.17), residues: 944 loop : -1.36 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 100F HIS 0.005 0.001 HIS L 91 PHE 0.014 0.002 PHE M 100E TYR 0.010 0.002 TYR A 321 ARG 0.005 0.000 ARG O 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 229 time to evaluate : 2.004 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: L 69 THR cc_start: 0.8427 (p) cc_final: 0.8215 (m) REVERT: A 359 LYS cc_start: 0.8346 (ttpp) cc_final: 0.7663 (tttp) REVERT: A 403 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7976 (pttt) REVERT: D 69 THR cc_start: 0.8427 (p) cc_final: 0.8212 (m) REVERT: E 359 LYS cc_start: 0.8347 (ttpp) cc_final: 0.7664 (tttp) REVERT: E 403 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7977 (pttt) REVERT: J 403 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7965 (pttt) REVERT: O 359 LYS cc_start: 0.8349 (ttpp) cc_final: 0.7663 (tttp) REVERT: O 403 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7970 (pttt) outliers start: 77 outliers final: 54 residues processed: 273 average time/residue: 1.1240 time to fit residues: 350.8290 Evaluate side-chains 282 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 224 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 228 CYS Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 352 VAL Chi-restraints excluded: chain J residue 356 MET Chi-restraints excluded: chain J residue 371 THR Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 228 CYS Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 185 optimal weight: 7.9990 chunk 193 optimal weight: 0.0470 chunk 134 optimal weight: 0.9980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN E 328 ASN J 328 ASN O 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18868 Z= 0.232 Angle : 0.577 6.848 25540 Z= 0.306 Chirality : 0.044 0.144 2708 Planarity : 0.005 0.041 3252 Dihedral : 5.068 21.206 2724 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.48 % Favored : 94.35 % Rotamer: Outliers : 3.31 % Allowed : 18.08 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.25 (0.17), residues: 948 loop : -1.30 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 100F HIS 0.003 0.001 HIS I 91 PHE 0.013 0.002 PHE G 100E TYR 0.010 0.001 TYR E 321 ARG 0.006 0.000 ARG I 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 236 time to evaluate : 2.096 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: A 359 LYS cc_start: 0.8390 (ttpp) cc_final: 0.7686 (tttp) REVERT: A 403 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7949 (pttt) REVERT: E 359 LYS cc_start: 0.8389 (ttpp) cc_final: 0.7686 (tttp) REVERT: E 403 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7948 (pttt) REVERT: J 359 LYS cc_start: 0.8492 (ttpp) cc_final: 0.7513 (ttmt) REVERT: J 403 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7939 (pttt) REVERT: O 359 LYS cc_start: 0.8392 (ttpp) cc_final: 0.7687 (tttp) REVERT: O 403 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7949 (pttt) outliers start: 65 outliers final: 48 residues processed: 274 average time/residue: 1.1597 time to fit residues: 365.6194 Evaluate side-chains 263 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 211 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 228 CYS Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 371 THR Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 228 CYS Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 209 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 139 optimal weight: 0.0270 chunk 110 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18868 Z= 0.209 Angle : 0.562 7.091 25540 Z= 0.298 Chirality : 0.044 0.145 2708 Planarity : 0.004 0.035 3252 Dihedral : 4.983 21.583 2724 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.09 % Favored : 94.74 % Rotamer: Outliers : 3.41 % Allowed : 18.13 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.89 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.32 (0.17), residues: 960 loop : -1.33 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 100F HIS 0.002 0.001 HIS D 91 PHE 0.014 0.001 PHE C 100E TYR 0.009 0.001 TYR A 321 ARG 0.005 0.000 ARG I 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 229 time to evaluate : 2.049 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: A 359 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7626 (tttp) REVERT: A 403 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7937 (pttt) REVERT: E 359 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7626 (tttp) REVERT: E 403 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7939 (pttt) REVERT: J 403 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7932 (pttt) REVERT: O 359 LYS cc_start: 0.8318 (ttpp) cc_final: 0.7624 (tttp) REVERT: O 403 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7929 (pttt) outliers start: 67 outliers final: 48 residues processed: 268 average time/residue: 1.2427 time to fit residues: 377.3876 Evaluate side-chains 263 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 211 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 228 CYS Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 371 THR Chi-restraints excluded: chain J residue 403 LYS Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 228 CYS Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 403 LYS Chi-restraints excluded: chain O residue 442 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 75 optimal weight: 0.0470 chunk 186 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.113788 restraints weight = 20735.045| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.87 r_work: 0.3240 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18868 Z= 0.208 Angle : 0.561 7.276 25540 Z= 0.296 Chirality : 0.044 0.145 2708 Planarity : 0.004 0.036 3252 Dihedral : 4.931 21.282 2724 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.04 % Favored : 94.78 % Rotamer: Outliers : 2.65 % Allowed : 18.69 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.84 (0.17), residues: 2300 helix: None (None), residues: 0 sheet: 0.33 (0.17), residues: 948 loop : -1.26 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP M 100F HIS 0.002 0.001 HIS J 128 PHE 0.014 0.001 PHE M 100E TYR 0.009 0.001 TYR J 321 ARG 0.004 0.000 ARG O 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7381.67 seconds wall clock time: 135 minutes 10.69 seconds (8110.69 seconds total)