Starting phenix.real_space_refine on Wed Jul 24 00:51:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4l_41035/07_2024/8t4l_41035.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4l_41035/07_2024/8t4l_41035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4l_41035/07_2024/8t4l_41035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4l_41035/07_2024/8t4l_41035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4l_41035/07_2024/8t4l_41035.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4l_41035/07_2024/8t4l_41035.cif" } resolution = 3.2 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= 0.021 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 144 5.16 5 C 15303 2.51 5 N 4107 2.21 5 O 4821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24375 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3437 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 411} Chain breaks: 4 Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "H" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 970 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 787 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "E" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3437 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 411} Chain breaks: 4 Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "G" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "O" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 970 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "Q" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 787 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "F" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3437 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 411} Chain breaks: 4 Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "N" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "P" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 970 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 787 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "S" 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" 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: "V" 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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: "Y" 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: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.37, per 1000 atoms: 0.59 Number of scatterers: 24375 At special positions: 0 Unit cell: (154.512, 157.644, 170.172, 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 144 16.00 O 4821 8.00 N 4107 7.00 C 15303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.04 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 301 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 386 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 289 " " NAG A 611 " - " ASN A 241 " " NAG B 701 " - " ASN B 611 " " NAG E 601 " - " ASN E 301 " " NAG E 602 " - " ASN E 88 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 386 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 289 " " NAG E 611 " - " ASN E 241 " " NAG F 601 " - " ASN F 301 " " NAG F 602 " - " ASN F 88 " " NAG F 603 " - " ASN F 160 " " NAG F 604 " - " ASN F 197 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 276 " " NAG F 607 " - " ASN F 295 " " NAG F 608 " - " ASN F 386 " " NAG F 609 " - " ASN F 448 " " NAG F 610 " - " ASN F 289 " " NAG F 611 " - " ASN F 241 " " NAG G 701 " - " ASN G 611 " " NAG I 701 " - " ASN I 611 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN E 156 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN F 156 " " NAG Z 1 " - " ASN F 262 " " NAG a 1 " - " ASN F 332 " Time building additional restraints: 10.44 Conformation dependent library (CDL) restraints added in 4.3 seconds 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 45 sheets defined 19.7% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.454A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.831A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.262A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.246A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (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 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.913A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' 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 83 through 87 Processing helix chain 'H' and resid 100I through 102 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.037A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.454A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.830A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.262A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.502A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 546 removed outlier: 3.913A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU G 545 " --> pdb=" O ALA G 541 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 Processing helix chain 'G' and resid 618 through 625 Processing helix chain 'G' and resid 627 through 636 Processing helix chain 'G' and resid 638 through 663 Processing helix chain 'O' and resid 28 through 30 No H-bonds generated for 'chain 'O' and resid 28 through 30' Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100I through 102 Processing helix chain 'Q' and resid 79 through 83 removed outlier: 4.036A pdb=" N GLU Q 83 " --> pdb=" O SER Q 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.454A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 354 removed outlier: 3.830A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.262A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 484 removed outlier: 4.247A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 546 removed outlier: 3.913A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU I 545 " --> pdb=" O ALA I 541 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 596 Processing helix chain 'I' and resid 618 through 625 Processing helix chain 'I' and resid 627 through 636 Processing helix chain 'I' and resid 638 through 663 Processing helix chain 'P' and resid 28 through 30 No H-bonds generated for 'chain 'P' and resid 28 through 30' Processing helix chain 'P' and resid 63 through 65 No H-bonds generated for 'chain 'P' and resid 63 through 65' Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100I through 102 Processing helix chain 'R' and resid 79 through 83 removed outlier: 4.037A pdb=" N GLU R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.258A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.019A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.578A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.110A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 4.009A pdb=" N ASN A 301 " --> pdb=" O LEU A 323A" (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS A 305 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N PHE A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 469 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 34 through 39 removed outlier: 6.930A pdb=" N MET C 34 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 38 removed outlier: 6.432A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 48 current: chain 'D' and resid 96 through 98 Processing sheet with id=AB3, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 32 through 39 removed outlier: 7.467A pdb=" N PHE H 32 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN H 52 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100B through 100G Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 11 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 95B through 98 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB7, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.258A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.019A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.578A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 172 through 177 Processing sheet with id=AC3, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.110A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 4.009A pdb=" N ASN E 301 " --> pdb=" O LEU E 323A" (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS E 305 " --> pdb=" O PHE E 320 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N PHE E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 469 Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'J' and resid 34 through 39 removed outlier: 6.929A pdb=" N MET J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AC7, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC8, first strand: chain 'M' and resid 33 through 38 removed outlier: 6.433A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 96 through 98 Processing sheet with id=AC9, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'O' and resid 32 through 39 removed outlier: 7.466A pdb=" N PHE O 32 " --> pdb=" O ASN O 52 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN O 52 " --> pdb=" O PHE O 32 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP O 34 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100B through 100G Processing sheet with id=AD2, first strand: chain 'Q' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 10 through 11 current: chain 'Q' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 45 through 48 current: chain 'Q' and resid 95B through 98 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AD4, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.258A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'F' and resid 75 through 76 removed outlier: 4.019A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.578A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 172 through 177 Processing sheet with id=AD9, first strand: chain 'F' and resid 200 through 203 removed outlier: 6.110A pdb=" N ALA F 200 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR F 435 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 312 removed outlier: 4.009A pdb=" N ASN F 301 " --> pdb=" O LEU F 323A" (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS F 305 " --> pdb=" O PHE F 320 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N PHE F 320 " --> pdb=" O LYS F 305 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE F 307 " --> pdb=" O TYR F 318 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR F 318 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE F 309 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA F 316 " --> pdb=" O ILE F 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 315 through 323A current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 465 through 469 Processing sheet with id=AE2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'K' and resid 34 through 39 removed outlier: 6.929A pdb=" N MET K 34 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100H through 103 Processing sheet with id=AE4, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE5, first strand: chain 'N' and resid 33 through 38 removed outlier: 6.433A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 Processing sheet with id=AE6, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'P' and resid 32 through 39 removed outlier: 7.467A pdb=" N PHE P 32 " --> pdb=" O ASN P 52 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN P 52 " --> pdb=" O PHE P 32 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP P 34 " --> pdb=" O ASP P 50 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 100B through 100G Processing sheet with id=AE8, first strand: chain 'R' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 10 through 11 current: chain 'R' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 45 through 48 current: chain 'R' and resid 95B through 98 No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'R' and resid 19 through 24 693 hydrogen bonds defined for protein. 1755 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: 7.72 Time building geometry restraints manager: 11.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3921 1.32 - 1.45: 7170 1.45 - 1.58: 13602 1.58 - 1.71: 0 1.71 - 1.84: 198 Bond restraints: 24891 Sorted by residual: bond pdb=" C PRO R 8 " pdb=" O PRO R 8 " ideal model delta sigma weight residual 1.246 1.186 0.060 8.50e-03 1.38e+04 4.99e+01 bond pdb=" C PRO Q 8 " pdb=" O PRO Q 8 " ideal model delta sigma weight residual 1.246 1.186 0.060 8.50e-03 1.38e+04 4.96e+01 bond pdb=" C PRO L 8 " pdb=" O PRO L 8 " ideal model delta sigma weight residual 1.246 1.186 0.060 8.50e-03 1.38e+04 4.91e+01 bond pdb=" CA PRO R 8 " pdb=" C PRO R 8 " ideal model delta sigma weight residual 1.514 1.539 -0.025 5.50e-03 3.31e+04 2.04e+01 bond pdb=" CA PRO Q 8 " pdb=" C PRO Q 8 " ideal model delta sigma weight residual 1.514 1.539 -0.025 5.50e-03 3.31e+04 2.02e+01 ... (remaining 24886 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.45: 780 106.45 - 113.43: 13647 113.43 - 120.42: 9379 120.42 - 127.40: 9637 127.40 - 134.38: 328 Bond angle restraints: 33771 Sorted by residual: angle pdb=" C MET E 161 " pdb=" CA MET E 161 " pdb=" CB MET E 161 " ideal model delta sigma weight residual 116.54 109.29 7.25 1.15e+00 7.56e-01 3.98e+01 angle pdb=" C MET F 161 " pdb=" CA MET F 161 " pdb=" CB MET F 161 " ideal model delta sigma weight residual 116.54 109.29 7.25 1.15e+00 7.56e-01 3.97e+01 angle pdb=" C MET A 161 " pdb=" CA MET A 161 " pdb=" CB MET A 161 " ideal model delta sigma weight residual 116.54 109.30 7.24 1.15e+00 7.56e-01 3.97e+01 angle pdb=" N ARG J 83 " pdb=" CA ARG J 83 " pdb=" C ARG J 83 " ideal model delta sigma weight residual 110.14 101.40 8.74 1.47e+00 4.63e-01 3.53e+01 angle pdb=" N ARG C 83 " pdb=" CA ARG C 83 " pdb=" C ARG C 83 " ideal model delta sigma weight residual 110.14 101.41 8.73 1.47e+00 4.63e-01 3.53e+01 ... (remaining 33766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 14982 21.29 - 42.58: 363 42.58 - 63.86: 141 63.86 - 85.15: 30 85.15 - 106.44: 18 Dihedral angle restraints: 15534 sinusoidal: 6840 harmonic: 8694 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 155.94 -62.94 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual 93.00 155.94 -62.94 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 155.94 -62.94 1 1.00e+01 1.00e-02 5.23e+01 ... (remaining 15531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2850 0.061 - 0.122: 844 0.122 - 0.183: 185 0.183 - 0.243: 12 0.243 - 0.304: 12 Chirality restraints: 3903 Sorted by residual: chirality pdb=" C5 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" C6 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C5 BMA Z 3 " pdb=" C4 BMA Z 3 " pdb=" C6 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 3900 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 477 " -0.018 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C ASP F 477 " 0.061 2.00e-02 2.50e+03 pdb=" O ASP F 477 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN F 478 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 477 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C ASP E 477 " -0.060 2.00e-02 2.50e+03 pdb=" O ASP E 477 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN E 478 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 477 " -0.018 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ASP A 477 " 0.060 2.00e-02 2.50e+03 pdb=" O ASP A 477 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 478 " -0.020 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5356 2.79 - 3.32: 21544 3.32 - 3.85: 41079 3.85 - 4.37: 49003 4.37 - 4.90: 82525 Nonbonded interactions: 199507 Sorted by model distance: nonbonded pdb=" OE1 GLN L 89 " pdb=" NE2 GLN L 96 " model vdw 2.269 2.520 nonbonded pdb=" OE1 GLN Q 89 " pdb=" NE2 GLN Q 96 " model vdw 2.269 2.520 nonbonded pdb=" OE1 GLN R 89 " pdb=" NE2 GLN R 96 " model vdw 2.269 2.520 nonbonded pdb=" OE2 GLU A 106 " pdb=" NZ LYS B 574 " model vdw 2.283 2.520 nonbonded pdb=" OE2 GLU F 106 " pdb=" NZ LYS I 574 " model vdw 2.283 2.520 ... (remaining 199502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' } ncs_group { reference = chain 'T' selection = chain 'W' selection = chain 'Z' } 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.210 Set scattering table: 0.210 Process input model: 65.590 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 24891 Z= 0.398 Angle : 1.045 8.986 33771 Z= 0.614 Chirality : 0.061 0.304 3903 Planarity : 0.006 0.041 4236 Dihedral : 11.469 106.438 9846 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.34 % Allowed : 1.15 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.15), residues: 2973 helix: 0.30 (0.24), residues: 429 sheet: 1.27 (0.17), residues: 873 loop : 0.64 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP H 47 HIS 0.008 0.002 HIS A 374 PHE 0.036 0.003 PHE O 78 TYR 0.019 0.003 TYR Q 36 ARG 0.006 0.001 ARG F 500 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 764 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8316 (mmtm) REVERT: A 211 GLU cc_start: 0.7573 (tt0) cc_final: 0.7220 (pt0) REVERT: A 217 TYR cc_start: 0.8680 (m-80) cc_final: 0.7849 (m-80) REVERT: C 27 TYR cc_start: 0.7867 (p90) cc_final: 0.7602 (p90) REVERT: C 81 GLN cc_start: 0.8284 (tp40) cc_final: 0.7746 (tp40) REVERT: C 101 ASP cc_start: 0.8032 (t0) cc_final: 0.7769 (t0) REVERT: C 102 PHE cc_start: 0.7549 (m-80) cc_final: 0.7242 (m-80) REVERT: D 21 ILE cc_start: 0.8170 (mt) cc_final: 0.7832 (mp) REVERT: D 27 ILE cc_start: 0.8287 (mm) cc_final: 0.7991 (mm) REVERT: D 69 ASN cc_start: 0.8493 (m-40) cc_final: 0.8290 (m-40) REVERT: B 632 ASP cc_start: 0.8834 (t70) cc_final: 0.8588 (t0) REVERT: H 22 CYS cc_start: 0.5118 (m) cc_final: 0.3899 (m) REVERT: H 60 ASN cc_start: 0.7924 (t0) cc_final: 0.7608 (t0) REVERT: H 66 ARG cc_start: 0.6920 (mtm180) cc_final: 0.6617 (mtm110) REVERT: H 100 MET cc_start: 0.8112 (mmm) cc_final: 0.7747 (mpp) REVERT: L 69 THR cc_start: 0.8328 (p) cc_final: 0.7900 (t) REVERT: L 89 GLN cc_start: 0.7059 (mt0) cc_final: 0.6607 (tt0) REVERT: E 97 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8451 (mmtm) REVERT: E 99 ASN cc_start: 0.8997 (t0) cc_final: 0.8448 (t0) REVERT: E 167 ASP cc_start: 0.7640 (m-30) cc_final: 0.7339 (m-30) REVERT: E 211 GLU cc_start: 0.7667 (tt0) cc_final: 0.7208 (pt0) REVERT: E 302 ASN cc_start: 0.8392 (m-40) cc_final: 0.7917 (m-40) REVERT: E 333 ILE cc_start: 0.8564 (mt) cc_final: 0.8324 (tt) REVERT: E 375 SER cc_start: 0.9061 (t) cc_final: 0.8773 (m) REVERT: E 475 MET cc_start: 0.8294 (mmm) cc_final: 0.7732 (tpp) REVERT: J 81 GLN cc_start: 0.8182 (tp40) cc_final: 0.7690 (tp40) REVERT: M 21 ILE cc_start: 0.8387 (mt) cc_final: 0.8093 (mp) REVERT: O 100 GLU cc_start: 0.8129 (pm20) cc_final: 0.7477 (pm20) REVERT: Q 69 THR cc_start: 0.8219 (p) cc_final: 0.7789 (t) REVERT: F 97 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8524 (mmtm) REVERT: F 99 ASN cc_start: 0.8992 (t0) cc_final: 0.8525 (t0) REVERT: F 211 GLU cc_start: 0.7812 (tt0) cc_final: 0.7220 (pt0) REVERT: K 81 GLN cc_start: 0.8171 (tp40) cc_final: 0.7751 (tp40) REVERT: K 101 ASP cc_start: 0.7999 (t0) cc_final: 0.7758 (t0) REVERT: N 91 TYR cc_start: 0.9044 (t80) cc_final: 0.8719 (t80) REVERT: P 60 ASN cc_start: 0.7800 (t0) cc_final: 0.7503 (t0) REVERT: P 66 ARG cc_start: 0.6981 (mtm180) cc_final: 0.6669 (tmm-80) REVERT: P 100 MET cc_start: 0.8174 (mmm) cc_final: 0.7822 (mpp) REVERT: R 27 ASN cc_start: 0.8758 (p0) cc_final: 0.8443 (p0) REVERT: R 69 THR cc_start: 0.8269 (p) cc_final: 0.7878 (t) REVERT: R 89 GLN cc_start: 0.7069 (mt0) cc_final: 0.6725 (tt0) outliers start: 9 outliers final: 3 residues processed: 773 average time/residue: 0.3537 time to fit residues: 423.3622 Evaluate side-chains 532 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 529 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 5 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 230 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 170 GLN A 425 ASN C 100BGLN ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 630 GLN B 653 GLN L 89 GLN E 170 GLN E 425 ASN J 100BGLN ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 GLN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN I 543 ASN ** R 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 24891 Z= 0.312 Angle : 0.656 10.665 33771 Z= 0.347 Chirality : 0.046 0.200 3903 Planarity : 0.004 0.038 4236 Dihedral : 7.461 66.054 4451 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.71 % Allowed : 8.37 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.15), residues: 2973 helix: 1.48 (0.26), residues: 429 sheet: 1.19 (0.17), residues: 909 loop : 0.32 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP O 33 HIS 0.005 0.001 HIS N 39 PHE 0.018 0.002 PHE O 78 TYR 0.026 0.002 TYR E 217 ARG 0.005 0.001 ARG E 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 555 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8459 (mmtm) REVERT: A 137 LYS cc_start: 0.8489 (mttp) cc_final: 0.8220 (mttt) REVERT: A 211 GLU cc_start: 0.8070 (tt0) cc_final: 0.7358 (pt0) REVERT: A 215 ILE cc_start: 0.8939 (tp) cc_final: 0.8650 (tp) REVERT: A 217 TYR cc_start: 0.8768 (m-80) cc_final: 0.8018 (m-80) REVERT: A 308 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7843 (mtp85) REVERT: C 27 TYR cc_start: 0.7957 (p90) cc_final: 0.7552 (p90) REVERT: C 81 GLN cc_start: 0.8227 (tp40) cc_final: 0.7589 (tp40) REVERT: D 21 ILE cc_start: 0.8181 (mt) cc_final: 0.7890 (mp) REVERT: D 69 ASN cc_start: 0.8613 (m-40) cc_final: 0.8143 (m110) REVERT: D 91 TYR cc_start: 0.9141 (t80) cc_final: 0.8779 (t80) REVERT: B 632 ASP cc_start: 0.8847 (t70) cc_final: 0.8617 (t0) REVERT: H 3 GLN cc_start: 0.7129 (tm-30) cc_final: 0.6772 (tm-30) REVERT: H 60 ASN cc_start: 0.7901 (t0) cc_final: 0.7551 (t0) REVERT: H 66 ARG cc_start: 0.7161 (mtm180) cc_final: 0.6801 (mtm110) REVERT: H 100 MET cc_start: 0.8274 (mmm) cc_final: 0.8017 (mpp) REVERT: L 53 LYS cc_start: 0.8313 (mttm) cc_final: 0.7998 (mtmm) REVERT: L 66 GLN cc_start: 0.7805 (tt0) cc_final: 0.7345 (tt0) REVERT: L 67 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.7183 (p90) REVERT: E 97 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8491 (mmtm) REVERT: E 104 MET cc_start: 0.8453 (tpt) cc_final: 0.8229 (ttt) REVERT: E 137 LYS cc_start: 0.8526 (mttp) cc_final: 0.8280 (mttt) REVERT: E 211 GLU cc_start: 0.7958 (tt0) cc_final: 0.7276 (pt0) REVERT: E 375 SER cc_start: 0.9056 (t) cc_final: 0.8746 (m) REVERT: E 475 MET cc_start: 0.8411 (mmm) cc_final: 0.8052 (tpp) REVERT: J 17 SER cc_start: 0.8027 (p) cc_final: 0.7801 (m) REVERT: J 81 GLN cc_start: 0.8143 (tp40) cc_final: 0.7530 (tp40) REVERT: O 60 ASN cc_start: 0.7974 (t0) cc_final: 0.7568 (t0) REVERT: Q 67 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7217 (p90) REVERT: Q 96 GLN cc_start: 0.8504 (mt0) cc_final: 0.8153 (mt0) REVERT: F 97 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8596 (mmtm) REVERT: F 211 GLU cc_start: 0.7999 (tt0) cc_final: 0.7200 (pt0) REVERT: F 215 ILE cc_start: 0.8923 (tp) cc_final: 0.8616 (tt) REVERT: F 475 MET cc_start: 0.8480 (mmm) cc_final: 0.8000 (tpp) REVERT: K 81 GLN cc_start: 0.8150 (tp40) cc_final: 0.7518 (tp-100) REVERT: P 60 ASN cc_start: 0.7862 (t0) cc_final: 0.7498 (t0) REVERT: P 66 ARG cc_start: 0.7114 (mtm180) cc_final: 0.6901 (mtm110) REVERT: P 100 GLU cc_start: 0.8712 (pm20) cc_final: 0.8452 (pm20) REVERT: P 100 MET cc_start: 0.8339 (mmm) cc_final: 0.8028 (mpp) REVERT: R 89 GLN cc_start: 0.6939 (mt0) cc_final: 0.6637 (tt0) outliers start: 97 outliers final: 60 residues processed: 608 average time/residue: 0.3341 time to fit residues: 321.8757 Evaluate side-chains 546 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 484 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 90 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 267 optimal weight: 0.5980 chunk 288 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 265 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN Q 7 GLN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 24891 Z= 0.278 Angle : 0.619 13.651 33771 Z= 0.324 Chirality : 0.044 0.199 3903 Planarity : 0.004 0.043 4236 Dihedral : 6.240 42.849 4451 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.05 % Allowed : 9.63 % Favored : 86.31 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 2973 helix: 1.86 (0.27), residues: 417 sheet: 0.98 (0.17), residues: 882 loop : 0.17 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 36 HIS 0.005 0.001 HIS C 82A PHE 0.022 0.002 PHE K 102 TYR 0.014 0.002 TYR N 91 ARG 0.006 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 499 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8493 (mmtm) REVERT: A 106 GLU cc_start: 0.7781 (tt0) cc_final: 0.7489 (tt0) REVERT: A 211 GLU cc_start: 0.8082 (tt0) cc_final: 0.7439 (pt0) REVERT: A 217 TYR cc_start: 0.8772 (m-80) cc_final: 0.7796 (m-80) REVERT: C 27 TYR cc_start: 0.8047 (p90) cc_final: 0.7570 (p90) REVERT: C 81 GLN cc_start: 0.8236 (tp40) cc_final: 0.7533 (tp40) REVERT: C 101 ASP cc_start: 0.8099 (t0) cc_final: 0.7725 (t0) REVERT: D 21 ILE cc_start: 0.8274 (mt) cc_final: 0.8021 (mp) REVERT: D 69 ASN cc_start: 0.8888 (m-40) cc_final: 0.8492 (m110) REVERT: B 632 ASP cc_start: 0.8879 (t70) cc_final: 0.8594 (t0) REVERT: H 3 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6732 (tm-30) REVERT: H 60 ASN cc_start: 0.8042 (t0) cc_final: 0.7687 (t0) REVERT: H 66 ARG cc_start: 0.7210 (mtm180) cc_final: 0.6874 (mtm110) REVERT: H 94 LEU cc_start: 0.8693 (tt) cc_final: 0.8443 (tt) REVERT: H 100 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7563 (mp0) REVERT: H 100 MET cc_start: 0.8315 (mmm) cc_final: 0.7952 (mpp) REVERT: H 102 PHE cc_start: 0.8520 (m-80) cc_final: 0.8197 (m-10) REVERT: H 105 GLN cc_start: 0.8055 (mp10) cc_final: 0.7847 (mm-40) REVERT: L 53 LYS cc_start: 0.8297 (mttm) cc_final: 0.8043 (mtmm) REVERT: L 89 GLN cc_start: 0.7190 (mt0) cc_final: 0.6552 (tt0) REVERT: E 97 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8514 (mmtm) REVERT: E 141 MET cc_start: 0.8041 (mtt) cc_final: 0.7821 (mtt) REVERT: E 211 GLU cc_start: 0.7957 (tt0) cc_final: 0.7248 (pt0) REVERT: E 375 SER cc_start: 0.9029 (t) cc_final: 0.8730 (m) REVERT: E 475 MET cc_start: 0.8404 (mmm) cc_final: 0.7956 (tpp) REVERT: J 81 GLN cc_start: 0.8048 (tp40) cc_final: 0.7407 (tp40) REVERT: G 625 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8372 (m110) REVERT: O 39 GLN cc_start: 0.6842 (pt0) cc_final: 0.6607 (pp30) REVERT: O 81 LYS cc_start: 0.7624 (ttmm) cc_final: 0.6397 (ttpp) REVERT: Q 36 TYR cc_start: 0.7705 (m-80) cc_final: 0.7337 (m-80) REVERT: Q 69 THR cc_start: 0.8436 (p) cc_final: 0.8010 (t) REVERT: F 97 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8636 (mmtm) REVERT: F 112 TRP cc_start: 0.8648 (t-100) cc_final: 0.8366 (t-100) REVERT: F 141 MET cc_start: 0.7827 (mtt) cc_final: 0.7449 (tpp) REVERT: F 215 ILE cc_start: 0.8850 (tp) cc_final: 0.8599 (tt) REVERT: F 475 MET cc_start: 0.8451 (mmm) cc_final: 0.8156 (tpp) REVERT: F 492 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8123 (mt-10) REVERT: K 81 GLN cc_start: 0.8026 (tp40) cc_final: 0.7653 (tp40) REVERT: N 79 GLN cc_start: 0.7105 (pt0) cc_final: 0.6741 (pp30) REVERT: P 100 MET cc_start: 0.8383 (mmm) cc_final: 0.8148 (mpp) REVERT: P 102 PHE cc_start: 0.8367 (m-80) cc_final: 0.8163 (m-10) REVERT: R 89 GLN cc_start: 0.7041 (mt0) cc_final: 0.6735 (tt0) outliers start: 106 outliers final: 72 residues processed: 565 average time/residue: 0.3341 time to fit residues: 301.1296 Evaluate side-chains 541 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 468 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 625 ASN Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 613 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 90 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 4.9990 chunk 201 optimal weight: 0.2980 chunk 138 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 268 optimal weight: 0.9990 chunk 284 optimal weight: 0.5980 chunk 140 optimal weight: 0.6980 chunk 254 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN D 79 GLN H 52 ASN E 33 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AHIS M 79 GLN O 52 ASN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN N 69 ASN P 52 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 24891 Z= 0.215 Angle : 0.576 11.858 33771 Z= 0.300 Chirality : 0.043 0.198 3903 Planarity : 0.004 0.033 4236 Dihedral : 5.434 37.113 4446 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.78 % Allowed : 10.51 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 2973 helix: 1.95 (0.27), residues: 417 sheet: 1.00 (0.17), residues: 858 loop : 0.03 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 36 HIS 0.008 0.001 HIS K 82A PHE 0.017 0.001 PHE K 102 TYR 0.015 0.001 TYR R 49 ARG 0.004 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 475 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8505 (mmtm) REVERT: A 106 GLU cc_start: 0.7823 (tt0) cc_final: 0.7477 (tt0) REVERT: A 211 GLU cc_start: 0.8010 (tt0) cc_final: 0.7386 (pt0) REVERT: A 217 TYR cc_start: 0.8669 (m-80) cc_final: 0.7711 (m-80) REVERT: C 27 TYR cc_start: 0.8126 (p90) cc_final: 0.7624 (p90) REVERT: C 81 GLN cc_start: 0.8296 (tp40) cc_final: 0.7580 (tp40) REVERT: C 101 ASP cc_start: 0.8134 (t0) cc_final: 0.7751 (t0) REVERT: D 69 ASN cc_start: 0.8911 (m-40) cc_final: 0.8502 (m110) REVERT: D 91 TYR cc_start: 0.9150 (t80) cc_final: 0.8648 (t80) REVERT: B 632 ASP cc_start: 0.8874 (t70) cc_final: 0.8570 (t0) REVERT: H 3 GLN cc_start: 0.7204 (tm-30) cc_final: 0.6863 (tm-30) REVERT: H 66 ARG cc_start: 0.7129 (mtm180) cc_final: 0.6759 (mtm110) REVERT: H 100 ASP cc_start: 0.8012 (t0) cc_final: 0.7596 (m-30) REVERT: H 100 MET cc_start: 0.8248 (mmm) cc_final: 0.7860 (mpp) REVERT: H 105 GLN cc_start: 0.8090 (mp10) cc_final: 0.7883 (mm-40) REVERT: L 53 LYS cc_start: 0.8243 (mttm) cc_final: 0.7982 (mtmm) REVERT: L 89 GLN cc_start: 0.7083 (mt0) cc_final: 0.6629 (tt0) REVERT: E 97 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8477 (mmtm) REVERT: E 117 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8109 (tptt) REVERT: E 211 GLU cc_start: 0.7967 (tt0) cc_final: 0.7256 (pt0) REVERT: E 375 SER cc_start: 0.9002 (t) cc_final: 0.8704 (m) REVERT: J 81 GLN cc_start: 0.8025 (tp40) cc_final: 0.7429 (tp40) REVERT: M 31 ASN cc_start: 0.8709 (p0) cc_final: 0.8508 (p0) REVERT: G 625 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8322 (m110) REVERT: O 39 GLN cc_start: 0.6796 (pt0) cc_final: 0.6540 (pp30) REVERT: O 81 LYS cc_start: 0.7568 (ttmm) cc_final: 0.6368 (ttpp) REVERT: O 102 PHE cc_start: 0.8405 (m-80) cc_final: 0.8019 (m-10) REVERT: Q 34 GLN cc_start: 0.7925 (mt0) cc_final: 0.7568 (mt0) REVERT: Q 69 THR cc_start: 0.8421 (p) cc_final: 0.8002 (t) REVERT: F 97 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8647 (mmtm) REVERT: F 112 TRP cc_start: 0.8635 (t-100) cc_final: 0.8315 (t-100) REVERT: F 117 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8217 (tptt) REVERT: F 475 MET cc_start: 0.8296 (mmm) cc_final: 0.7981 (tpp) REVERT: F 492 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8054 (mt-10) REVERT: K 81 GLN cc_start: 0.7985 (tp40) cc_final: 0.7475 (tp40) REVERT: N 79 GLN cc_start: 0.7056 (pt0) cc_final: 0.6714 (pp30) REVERT: P 39 GLN cc_start: 0.6888 (pt0) cc_final: 0.6458 (pp30) REVERT: P 81 LYS cc_start: 0.7928 (tttt) cc_final: 0.7695 (ttpp) REVERT: P 100 GLU cc_start: 0.8790 (pm20) cc_final: 0.8256 (pm20) REVERT: P 102 PHE cc_start: 0.8345 (m-80) cc_final: 0.8099 (m-80) REVERT: R 69 THR cc_start: 0.8382 (p) cc_final: 0.7981 (t) REVERT: R 89 GLN cc_start: 0.6860 (mt0) cc_final: 0.6648 (tt0) outliers start: 99 outliers final: 77 residues processed: 533 average time/residue: 0.3364 time to fit residues: 286.7888 Evaluate side-chains 529 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 451 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 625 ASN Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 90 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 242 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 255 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN D 6 GLN D 31 ASN D 79 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN J 100BGLN M 39 HIS ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 422 GLN K 100BGLN N 6 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24891 Z= 0.267 Angle : 0.585 13.017 33771 Z= 0.301 Chirality : 0.044 0.191 3903 Planarity : 0.004 0.036 4236 Dihedral : 5.267 36.611 4446 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.94 % Allowed : 11.43 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 2973 helix: 2.03 (0.27), residues: 411 sheet: 0.88 (0.17), residues: 879 loop : -0.07 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 36 HIS 0.005 0.001 HIS D 39 PHE 0.015 0.002 PHE K 102 TYR 0.018 0.001 TYR M 91 ARG 0.005 0.000 ARG G 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 457 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8531 (mmtm) REVERT: A 106 GLU cc_start: 0.7794 (tt0) cc_final: 0.7482 (tt0) REVERT: A 211 GLU cc_start: 0.8039 (tt0) cc_final: 0.7381 (pt0) REVERT: A 217 TYR cc_start: 0.8613 (m-80) cc_final: 0.7747 (m-80) REVERT: C 27 TYR cc_start: 0.8052 (p90) cc_final: 0.7690 (p90) REVERT: C 81 GLN cc_start: 0.8244 (tp40) cc_final: 0.7510 (tp40) REVERT: D 69 ASN cc_start: 0.8924 (m-40) cc_final: 0.8482 (m110) REVERT: D 79 GLN cc_start: 0.7165 (pt0) cc_final: 0.6573 (pp30) REVERT: B 632 ASP cc_start: 0.8890 (t70) cc_final: 0.8555 (t0) REVERT: B 647 GLU cc_start: 0.8312 (tt0) cc_final: 0.8073 (tt0) REVERT: H 66 ARG cc_start: 0.7076 (mtm180) cc_final: 0.6719 (mtm110) REVERT: L 53 LYS cc_start: 0.8322 (mttm) cc_final: 0.8054 (mtmm) REVERT: L 69 THR cc_start: 0.8543 (p) cc_final: 0.8134 (t) REVERT: L 89 GLN cc_start: 0.7008 (mt0) cc_final: 0.6693 (tt0) REVERT: E 97 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8499 (mmtm) REVERT: E 117 LYS cc_start: 0.8645 (ttmm) cc_final: 0.8126 (tptt) REVERT: E 141 MET cc_start: 0.7829 (mtt) cc_final: 0.7565 (ptp) REVERT: E 211 GLU cc_start: 0.7972 (tt0) cc_final: 0.7252 (pt0) REVERT: E 328 MET cc_start: 0.8476 (ttm) cc_final: 0.7708 (ttp) REVERT: E 375 SER cc_start: 0.9132 (t) cc_final: 0.8849 (m) REVERT: J 81 GLN cc_start: 0.7995 (tp40) cc_final: 0.7332 (tp40) REVERT: M 31 ASN cc_start: 0.8846 (p0) cc_final: 0.8632 (p0) REVERT: M 45 LYS cc_start: 0.8081 (tttt) cc_final: 0.7616 (ptmt) REVERT: G 625 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8330 (m110) REVERT: O 39 GLN cc_start: 0.6988 (pt0) cc_final: 0.6551 (pp30) REVERT: O 81 LYS cc_start: 0.7618 (ttmm) cc_final: 0.6410 (ttpp) REVERT: O 100 GLU cc_start: 0.8621 (pm20) cc_final: 0.8234 (pm20) REVERT: O 102 PHE cc_start: 0.8449 (m-80) cc_final: 0.8030 (m-10) REVERT: Q 34 GLN cc_start: 0.7985 (mt0) cc_final: 0.7549 (mt0) REVERT: Q 36 TYR cc_start: 0.7725 (m-80) cc_final: 0.7415 (m-80) REVERT: Q 69 THR cc_start: 0.8420 (p) cc_final: 0.8006 (t) REVERT: F 97 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8653 (mmtm) REVERT: F 117 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8251 (tptt) REVERT: F 475 MET cc_start: 0.8264 (mmm) cc_final: 0.7979 (tpp) REVERT: K 81 GLN cc_start: 0.7960 (tp40) cc_final: 0.7444 (tp40) REVERT: P 39 GLN cc_start: 0.6811 (pt0) cc_final: 0.6349 (pp30) REVERT: P 66 ARG cc_start: 0.6996 (mtm180) cc_final: 0.6744 (mtm110) REVERT: P 102 PHE cc_start: 0.8359 (m-80) cc_final: 0.8033 (m-80) REVERT: R 69 THR cc_start: 0.8432 (p) cc_final: 0.8018 (t) outliers start: 103 outliers final: 84 residues processed: 521 average time/residue: 0.3282 time to fit residues: 272.8428 Evaluate side-chains 534 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 449 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 625 ASN Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 90 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 9.9990 chunk 255 optimal weight: 4.9990 chunk 56 optimal weight: 0.0980 chunk 166 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 284 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 39 HIS M 79 GLN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 422 GLN N 6 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN ** R 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24891 Z= 0.185 Angle : 0.549 11.192 33771 Z= 0.282 Chirality : 0.042 0.183 3903 Planarity : 0.003 0.039 4236 Dihedral : 4.960 35.597 4446 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.25 % Allowed : 12.58 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 2973 helix: 2.03 (0.27), residues: 417 sheet: 0.99 (0.17), residues: 846 loop : -0.12 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 36 HIS 0.004 0.001 HIS A 330 PHE 0.016 0.001 PHE O 78 TYR 0.013 0.001 TYR K 91 ARG 0.005 0.000 ARG F 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 466 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8535 (mmtm) REVERT: A 106 GLU cc_start: 0.7797 (tt0) cc_final: 0.7482 (tt0) REVERT: A 211 GLU cc_start: 0.8041 (tt0) cc_final: 0.7337 (pt0) REVERT: C 27 TYR cc_start: 0.7972 (p90) cc_final: 0.7540 (p90) REVERT: C 81 GLN cc_start: 0.8329 (tp40) cc_final: 0.7645 (tp40) REVERT: D 69 ASN cc_start: 0.8918 (m-40) cc_final: 0.8461 (m110) REVERT: D 79 GLN cc_start: 0.7007 (pt0) cc_final: 0.6389 (pp30) REVERT: B 632 ASP cc_start: 0.8883 (t70) cc_final: 0.8568 (t0) REVERT: H 66 ARG cc_start: 0.7069 (mtm180) cc_final: 0.6711 (mtm110) REVERT: H 100 GLU cc_start: 0.7599 (mp0) cc_final: 0.7376 (mp0) REVERT: L 53 LYS cc_start: 0.8266 (mttm) cc_final: 0.7999 (mtmm) REVERT: L 89 GLN cc_start: 0.6735 (mt0) cc_final: 0.6472 (tt0) REVERT: E 97 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8510 (mmtm) REVERT: E 117 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8195 (tptt) REVERT: E 141 MET cc_start: 0.7757 (mtt) cc_final: 0.6895 (tpt) REVERT: E 211 GLU cc_start: 0.7964 (tt0) cc_final: 0.7250 (pt0) REVERT: E 375 SER cc_start: 0.9068 (t) cc_final: 0.8804 (m) REVERT: J 2 VAL cc_start: 0.8245 (m) cc_final: 0.7886 (m) REVERT: J 81 GLN cc_start: 0.8006 (tp40) cc_final: 0.7346 (tp40) REVERT: M 32 TYR cc_start: 0.8767 (m-80) cc_final: 0.8494 (m-80) REVERT: M 79 GLN cc_start: 0.6833 (pt0) cc_final: 0.6539 (pp30) REVERT: G 625 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8248 (m110) REVERT: O 39 GLN cc_start: 0.6858 (pt0) cc_final: 0.6547 (pp30) REVERT: O 81 LYS cc_start: 0.7585 (ttmm) cc_final: 0.6401 (ttpp) REVERT: O 100 GLU cc_start: 0.8601 (pm20) cc_final: 0.8267 (pm20) REVERT: O 102 PHE cc_start: 0.8381 (m-80) cc_final: 0.7966 (m-10) REVERT: Q 36 TYR cc_start: 0.7615 (m-80) cc_final: 0.7328 (m-80) REVERT: Q 69 THR cc_start: 0.8391 (p) cc_final: 0.7980 (t) REVERT: F 97 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8652 (mmtm) REVERT: F 117 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8230 (tptt) REVERT: F 440 GLN cc_start: 0.8030 (tp40) cc_final: 0.7667 (tp-100) REVERT: K 81 GLN cc_start: 0.7989 (tp40) cc_final: 0.7490 (tp40) REVERT: N 79 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6631 (pp30) REVERT: N 82 ASP cc_start: 0.6420 (m-30) cc_final: 0.6096 (m-30) REVERT: P 39 GLN cc_start: 0.6699 (pt0) cc_final: 0.6289 (pp30) REVERT: P 66 ARG cc_start: 0.7032 (mtm180) cc_final: 0.6784 (mtm110) REVERT: P 68 THR cc_start: 0.8478 (m) cc_final: 0.8087 (m) REVERT: P 81 LYS cc_start: 0.7864 (tttt) cc_final: 0.7613 (ttpp) REVERT: P 100 GLU cc_start: 0.8827 (pm20) cc_final: 0.8287 (pm20) REVERT: P 102 PHE cc_start: 0.8296 (m-80) cc_final: 0.8031 (m-80) REVERT: R 35 TRP cc_start: 0.7316 (m100) cc_final: 0.6971 (m100) REVERT: R 69 THR cc_start: 0.8434 (p) cc_final: 0.8027 (t) REVERT: R 89 GLN cc_start: 0.7662 (tt0) cc_final: 0.7449 (tt0) outliers start: 85 outliers final: 63 residues processed: 513 average time/residue: 0.3364 time to fit residues: 273.9209 Evaluate side-chains 515 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 450 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 625 ASN Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 162 optimal weight: 0.3980 chunk 207 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 158 optimal weight: 0.5980 chunk 283 optimal weight: 5.9990 chunk 177 optimal weight: 0.1980 chunk 172 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 HIS F 422 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 39 HIS N 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24891 Z= 0.220 Angle : 0.557 12.784 33771 Z= 0.285 Chirality : 0.043 0.209 3903 Planarity : 0.004 0.043 4236 Dihedral : 4.938 34.105 4446 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.10 % Allowed : 13.23 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 2973 helix: 2.00 (0.27), residues: 417 sheet: 1.01 (0.17), residues: 843 loop : -0.16 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 36 HIS 0.004 0.001 HIS A 330 PHE 0.016 0.001 PHE F 53 TYR 0.017 0.001 TYR M 91 ARG 0.004 0.000 ARG F 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 457 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8561 (mmtm) REVERT: A 106 GLU cc_start: 0.7842 (tt0) cc_final: 0.7512 (tt0) REVERT: A 141 MET cc_start: 0.7762 (ptp) cc_final: 0.7479 (ptp) REVERT: A 211 GLU cc_start: 0.8005 (tt0) cc_final: 0.7356 (pt0) REVERT: A 217 TYR cc_start: 0.8557 (m-80) cc_final: 0.7758 (m-80) REVERT: A 328 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7948 (ttm) REVERT: C 27 TYR cc_start: 0.8021 (p90) cc_final: 0.7584 (p90) REVERT: C 81 GLN cc_start: 0.8386 (tp40) cc_final: 0.7565 (tp40) REVERT: D 69 ASN cc_start: 0.8920 (m-40) cc_final: 0.8453 (m110) REVERT: B 632 ASP cc_start: 0.8829 (t70) cc_final: 0.8546 (t0) REVERT: H 66 ARG cc_start: 0.7073 (mtm180) cc_final: 0.6718 (mtm110) REVERT: H 100 GLU cc_start: 0.7648 (mp0) cc_final: 0.7421 (mp0) REVERT: L 53 LYS cc_start: 0.8299 (mttm) cc_final: 0.8038 (mtmm) REVERT: E 97 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8512 (mmtm) REVERT: E 117 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8121 (tptt) REVERT: E 211 GLU cc_start: 0.7971 (tt0) cc_final: 0.7245 (pt0) REVERT: E 375 SER cc_start: 0.9064 (t) cc_final: 0.8790 (m) REVERT: J 2 VAL cc_start: 0.8197 (m) cc_final: 0.7828 (m) REVERT: J 81 GLN cc_start: 0.8000 (tp40) cc_final: 0.7283 (tp40) REVERT: M 79 GLN cc_start: 0.6800 (pt0) cc_final: 0.6414 (pp30) REVERT: G 625 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8247 (m110) REVERT: O 39 GLN cc_start: 0.6956 (pt0) cc_final: 0.6482 (pp30) REVERT: O 81 LYS cc_start: 0.7588 (ttmm) cc_final: 0.6403 (ttpp) REVERT: O 100 GLU cc_start: 0.8618 (pm20) cc_final: 0.8269 (pm20) REVERT: O 102 PHE cc_start: 0.8432 (m-80) cc_final: 0.8006 (m-10) REVERT: Q 36 TYR cc_start: 0.7660 (m-80) cc_final: 0.7345 (m-80) REVERT: Q 69 THR cc_start: 0.8361 (p) cc_final: 0.7939 (t) REVERT: F 97 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8668 (mmtm) REVERT: F 117 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8238 (tptt) REVERT: K 81 GLN cc_start: 0.8044 (tp40) cc_final: 0.7489 (tp40) REVERT: N 79 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6324 (pp30) REVERT: N 82 ASP cc_start: 0.6484 (m-30) cc_final: 0.6237 (m-30) REVERT: P 39 GLN cc_start: 0.6720 (pt0) cc_final: 0.6292 (pp30) REVERT: P 66 ARG cc_start: 0.7031 (mtm180) cc_final: 0.6771 (mtm110) REVERT: P 100 GLU cc_start: 0.8922 (pm20) cc_final: 0.8310 (pm20) REVERT: R 35 TRP cc_start: 0.7363 (m100) cc_final: 0.7039 (m100) REVERT: R 69 THR cc_start: 0.8472 (p) cc_final: 0.8045 (t) outliers start: 81 outliers final: 72 residues processed: 511 average time/residue: 0.3407 time to fit residues: 277.3044 Evaluate side-chains 522 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 447 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 625 ASN Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 55 optimal weight: 0.0980 chunk 54 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 222 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS D 6 GLN D 79 GLN E 130 GLN E 188 ASN E 195 ASN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN F 422 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 HIS ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24891 Z= 0.200 Angle : 0.548 11.919 33771 Z= 0.281 Chirality : 0.043 0.180 3903 Planarity : 0.004 0.043 4236 Dihedral : 4.858 33.449 4446 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.40 % Allowed : 13.04 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 2973 helix: 2.03 (0.27), residues: 417 sheet: 0.98 (0.17), residues: 861 loop : -0.17 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 36 HIS 0.004 0.001 HIS F 216 PHE 0.015 0.001 PHE O 78 TYR 0.011 0.001 TYR L 49 ARG 0.005 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 457 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8566 (mmtm) REVERT: A 106 GLU cc_start: 0.7857 (tt0) cc_final: 0.7517 (tt0) REVERT: A 141 MET cc_start: 0.7784 (ptp) cc_final: 0.7336 (ptp) REVERT: A 211 GLU cc_start: 0.8032 (tt0) cc_final: 0.7323 (pt0) REVERT: A 217 TYR cc_start: 0.8548 (m-80) cc_final: 0.7841 (m-80) REVERT: A 328 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7866 (ttm) REVERT: C 27 TYR cc_start: 0.7904 (p90) cc_final: 0.7474 (p90) REVERT: C 36 TRP cc_start: 0.8521 (m100) cc_final: 0.8159 (m100) REVERT: C 81 GLN cc_start: 0.8414 (tp40) cc_final: 0.7581 (tp40) REVERT: D 69 ASN cc_start: 0.8914 (m-40) cc_final: 0.8437 (m110) REVERT: D 79 GLN cc_start: 0.7044 (pt0) cc_final: 0.6481 (pp30) REVERT: B 632 ASP cc_start: 0.8820 (t70) cc_final: 0.8610 (t0) REVERT: H 66 ARG cc_start: 0.7145 (mtm180) cc_final: 0.6789 (mtm110) REVERT: H 100 GLU cc_start: 0.7692 (mp0) cc_final: 0.7476 (mp0) REVERT: L 53 LYS cc_start: 0.8448 (mttm) cc_final: 0.8178 (mtmm) REVERT: L 69 THR cc_start: 0.8484 (p) cc_final: 0.8060 (t) REVERT: E 97 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8510 (mmtm) REVERT: E 117 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8179 (tptt) REVERT: E 211 GLU cc_start: 0.7972 (tt0) cc_final: 0.7255 (pt0) REVERT: E 303 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8314 (p) REVERT: E 375 SER cc_start: 0.9030 (t) cc_final: 0.8740 (m) REVERT: J 2 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7829 (m) REVERT: J 81 GLN cc_start: 0.7994 (tp40) cc_final: 0.7336 (tp40) REVERT: G 625 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8197 (m110) REVERT: O 39 GLN cc_start: 0.6870 (pt0) cc_final: 0.6531 (pp30) REVERT: O 81 LYS cc_start: 0.7578 (ttmm) cc_final: 0.6416 (ttpp) REVERT: O 102 PHE cc_start: 0.8407 (m-80) cc_final: 0.7974 (m-10) REVERT: Q 36 TYR cc_start: 0.7674 (m-80) cc_final: 0.7338 (m-80) REVERT: Q 69 THR cc_start: 0.8355 (p) cc_final: 0.7934 (t) REVERT: F 97 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8653 (mmtm) REVERT: F 117 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8236 (tptt) REVERT: F 328 MET cc_start: 0.8263 (ttm) cc_final: 0.7879 (ttp) REVERT: K 81 GLN cc_start: 0.7995 (tp40) cc_final: 0.7298 (tp40) REVERT: N 79 GLN cc_start: 0.6808 (pt0) cc_final: 0.6411 (pp30) REVERT: P 39 GLN cc_start: 0.6745 (pt0) cc_final: 0.6398 (pp30) REVERT: P 66 ARG cc_start: 0.7031 (mtm180) cc_final: 0.6769 (mtm110) REVERT: P 94 LEU cc_start: 0.8690 (tt) cc_final: 0.8480 (tt) REVERT: R 69 THR cc_start: 0.8471 (p) cc_final: 0.8039 (t) outliers start: 89 outliers final: 78 residues processed: 518 average time/residue: 0.3423 time to fit residues: 280.7337 Evaluate side-chains 524 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 442 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 625 ASN Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 90 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 264 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 115 optimal weight: 0.0980 chunk 207 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 249 optimal weight: 0.8980 chunk 263 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN M 79 GLN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24891 Z= 0.272 Angle : 0.615 17.510 33771 Z= 0.314 Chirality : 0.045 0.386 3903 Planarity : 0.004 0.048 4236 Dihedral : 5.103 34.026 4446 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.63 % Allowed : 13.00 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 2973 helix: 1.91 (0.27), residues: 417 sheet: 0.87 (0.18), residues: 846 loop : -0.23 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 112 HIS 0.007 0.001 HIS A 330 PHE 0.014 0.001 PHE A 53 TYR 0.019 0.001 TYR M 91 ARG 0.006 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 451 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8561 (mmtm) REVERT: A 141 MET cc_start: 0.7853 (ptp) cc_final: 0.7431 (ptp) REVERT: A 211 GLU cc_start: 0.8028 (tt0) cc_final: 0.7359 (pt0) REVERT: A 217 TYR cc_start: 0.8576 (m-80) cc_final: 0.7841 (m-80) REVERT: A 328 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7923 (ttm) REVERT: C 27 TYR cc_start: 0.7971 (p90) cc_final: 0.7559 (p90) REVERT: C 36 TRP cc_start: 0.8564 (m100) cc_final: 0.8334 (m100) REVERT: C 81 GLN cc_start: 0.8372 (tp40) cc_final: 0.7585 (tp40) REVERT: D 69 ASN cc_start: 0.8923 (m-40) cc_final: 0.8431 (m110) REVERT: B 632 ASP cc_start: 0.8845 (t70) cc_final: 0.8613 (t0) REVERT: H 66 ARG cc_start: 0.7259 (mtm180) cc_final: 0.6906 (mtm110) REVERT: H 100 MET cc_start: 0.8285 (mpp) cc_final: 0.7587 (mpp) REVERT: L 53 LYS cc_start: 0.8515 (mttm) cc_final: 0.8211 (mtmm) REVERT: L 66 GLN cc_start: 0.8681 (tt0) cc_final: 0.8401 (tt0) REVERT: L 69 THR cc_start: 0.8463 (p) cc_final: 0.8024 (t) REVERT: E 97 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8522 (mmtm) REVERT: E 211 GLU cc_start: 0.7967 (tt0) cc_final: 0.7231 (pt0) REVERT: E 303 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8311 (p) REVERT: E 328 MET cc_start: 0.8313 (ttm) cc_final: 0.7802 (ttp) REVERT: E 333 ILE cc_start: 0.8864 (mt) cc_final: 0.8473 (tt) REVERT: E 375 SER cc_start: 0.9067 (t) cc_final: 0.8750 (m) REVERT: J 2 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7854 (m) REVERT: J 36 TRP cc_start: 0.8793 (m100) cc_final: 0.8411 (m100) REVERT: J 81 GLN cc_start: 0.7961 (tp40) cc_final: 0.7306 (tp40) REVERT: M 79 GLN cc_start: 0.6827 (pt0) cc_final: 0.6487 (pp30) REVERT: G 625 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8182 (m110) REVERT: O 39 GLN cc_start: 0.6891 (pt0) cc_final: 0.6588 (pp30) REVERT: O 81 LYS cc_start: 0.7650 (ttmm) cc_final: 0.6488 (ttpp) REVERT: O 100 GLU cc_start: 0.8845 (pm20) cc_final: 0.8507 (pm20) REVERT: Q 36 TYR cc_start: 0.7701 (m-80) cc_final: 0.7352 (m-80) REVERT: Q 69 THR cc_start: 0.8365 (p) cc_final: 0.7929 (t) REVERT: F 97 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8650 (mmtm) REVERT: F 117 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8228 (tptt) REVERT: K 81 GLN cc_start: 0.8152 (tp40) cc_final: 0.7361 (tp40) REVERT: N 79 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6569 (pp30) REVERT: N 103 ARG cc_start: 0.8606 (tpt170) cc_final: 0.7721 (mmp-170) REVERT: P 39 GLN cc_start: 0.6768 (pt0) cc_final: 0.6404 (pp30) REVERT: P 91 TYR cc_start: 0.6616 (m-80) cc_final: 0.6345 (m-80) REVERT: P 100 GLU cc_start: 0.8818 (pm20) cc_final: 0.8219 (pm20) REVERT: P 100 GLU cc_start: 0.7576 (mp0) cc_final: 0.7262 (mp0) REVERT: R 35 TRP cc_start: 0.7393 (m100) cc_final: 0.7038 (m100) REVERT: R 69 THR cc_start: 0.8461 (p) cc_final: 0.8030 (t) outliers start: 95 outliers final: 81 residues processed: 518 average time/residue: 0.3377 time to fit residues: 278.1519 Evaluate side-chains 531 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 445 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 625 ASN Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 90 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 292 optimal weight: 10.0000 chunk 269 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82AHIS D 79 GLN L 79 GLN L 89 GLN E 188 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 GLN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 24891 Z= 0.377 Angle : 0.670 19.225 33771 Z= 0.344 Chirality : 0.047 0.322 3903 Planarity : 0.004 0.048 4236 Dihedral : 5.536 44.435 4446 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.36 % Allowed : 13.69 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 2973 helix: 1.82 (0.27), residues: 411 sheet: 0.71 (0.18), residues: 864 loop : -0.31 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 33 HIS 0.006 0.001 HIS E 330 PHE 0.018 0.002 PHE K 67 TYR 0.013 0.002 TYR N 32 ARG 0.006 0.001 ARG A 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 456 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8576 (mmtm) REVERT: A 141 MET cc_start: 0.8008 (ptp) cc_final: 0.7640 (ptp) REVERT: A 211 GLU cc_start: 0.8114 (tt0) cc_final: 0.7405 (pt0) REVERT: A 217 TYR cc_start: 0.8642 (m-80) cc_final: 0.7875 (m-80) REVERT: A 328 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7990 (ttm) REVERT: C 27 TYR cc_start: 0.8057 (p90) cc_final: 0.7671 (p90) REVERT: C 81 GLN cc_start: 0.8394 (tp40) cc_final: 0.7732 (tp40) REVERT: D 69 ASN cc_start: 0.8926 (m-40) cc_final: 0.8399 (m110) REVERT: D 79 GLN cc_start: 0.6888 (pt0) cc_final: 0.6363 (pp30) REVERT: B 632 ASP cc_start: 0.8881 (t70) cc_final: 0.8611 (t0) REVERT: H 39 GLN cc_start: 0.6810 (pp30) cc_final: 0.6441 (pp30) REVERT: H 66 ARG cc_start: 0.7353 (mtm180) cc_final: 0.6953 (mtm110) REVERT: H 100 ASP cc_start: 0.7912 (t0) cc_final: 0.7705 (m-30) REVERT: H 100 MET cc_start: 0.8216 (mpp) cc_final: 0.7740 (mpp) REVERT: L 53 LYS cc_start: 0.8589 (mttm) cc_final: 0.8258 (mtmm) REVERT: L 66 GLN cc_start: 0.8726 (tt0) cc_final: 0.8460 (tt0) REVERT: L 69 THR cc_start: 0.8474 (p) cc_final: 0.8016 (t) REVERT: E 97 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8518 (mmtm) REVERT: E 211 GLU cc_start: 0.7979 (tt0) cc_final: 0.7223 (pt0) REVERT: E 303 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8295 (p) REVERT: E 333 ILE cc_start: 0.8889 (mt) cc_final: 0.8501 (tt) REVERT: E 375 SER cc_start: 0.9141 (t) cc_final: 0.8792 (m) REVERT: J 2 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7851 (m) REVERT: J 36 TRP cc_start: 0.8801 (m100) cc_final: 0.8335 (m100) REVERT: J 81 GLN cc_start: 0.7861 (tp40) cc_final: 0.7161 (tp40) REVERT: G 625 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8199 (m110) REVERT: O 39 GLN cc_start: 0.6819 (pt0) cc_final: 0.6573 (pp30) REVERT: O 81 LYS cc_start: 0.7678 (ttmm) cc_final: 0.6507 (ttpp) REVERT: O 100 GLU cc_start: 0.8926 (pm20) cc_final: 0.8624 (pm20) REVERT: Q 6 THR cc_start: 0.7848 (m) cc_final: 0.7227 (p) REVERT: Q 69 THR cc_start: 0.8398 (p) cc_final: 0.7954 (t) REVERT: F 97 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8698 (mmtm) REVERT: K 81 GLN cc_start: 0.8385 (tp40) cc_final: 0.7646 (tp40) REVERT: N 45 LYS cc_start: 0.8186 (pttp) cc_final: 0.7774 (ptmm) REVERT: P 39 GLN cc_start: 0.6788 (pt0) cc_final: 0.6412 (pp30) REVERT: P 91 TYR cc_start: 0.6826 (m-80) cc_final: 0.6577 (m-80) REVERT: P 94 LEU cc_start: 0.8792 (tt) cc_final: 0.8543 (tt) REVERT: P 100 GLU cc_start: 0.8871 (pm20) cc_final: 0.8247 (pm20) REVERT: P 100 GLU cc_start: 0.7586 (mp0) cc_final: 0.7271 (mp0) REVERT: R 69 THR cc_start: 0.8500 (p) cc_final: 0.8039 (t) outliers start: 88 outliers final: 81 residues processed: 516 average time/residue: 0.3288 time to fit residues: 270.3989 Evaluate side-chains 528 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 443 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 625 ASN Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 90 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 233 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 239 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 195 ASN C 76 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN N 79 GLN ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110052 restraints weight = 37320.242| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.67 r_work: 0.3205 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.216 24891 Z= 0.373 Angle : 0.788 59.200 33771 Z= 0.432 Chirality : 0.046 0.316 3903 Planarity : 0.004 0.049 4236 Dihedral : 5.533 44.352 4446 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.44 % Allowed : 14.07 % Favored : 82.49 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 2973 helix: 1.83 (0.27), residues: 411 sheet: 0.70 (0.18), residues: 864 loop : -0.32 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 33 HIS 0.007 0.001 HIS E 330 PHE 0.019 0.002 PHE K 67 TYR 0.012 0.001 TYR Q 49 ARG 0.005 0.000 ARG P 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6654.28 seconds wall clock time: 118 minutes 46.12 seconds (7126.12 seconds total)