Starting phenix.real_space_refine on Wed Jul 24 03:01:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4d_41027/07_2024/8t4d_41027.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4d_41027/07_2024/8t4d_41027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4d_41027/07_2024/8t4d_41027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4d_41027/07_2024/8t4d_41027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4d_41027/07_2024/8t4d_41027.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4d_41027/07_2024/8t4d_41027.cif" } resolution = 3.1 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= 0.027 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 159 5.16 5 C 15567 2.51 5 N 4167 2.21 5 O 4860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24753 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} 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: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 98} Chain: "E" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} 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: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "Q" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 98} Chain: "F" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} 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: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "R" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 98} 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: 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: "U" 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: "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: 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: "X" 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: "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: 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: 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 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: 14.19, per 1000 atoms: 0.57 Number of scatterers: 24753 At special positions: 0 Unit cell: (156.6, 152.424, 173.304, 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 159 16.00 O 4860 8.00 N 4167 7.00 C 15567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.03 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=2.03 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 A 501 " - pdb=" SG CYS B 605 " distance=2.02 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=2.04 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 H 99 " - pdb=" SG CYS H 100D" 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=2.03 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=2.03 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 E 501 " - pdb=" SG CYS G 605 " distance=2.02 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=2.04 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 O 99 " - pdb=" SG CYS O 100D" 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=2.03 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 F 501 " - pdb=" SG CYS I 605 " distance=2.02 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=2.04 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 P 99 " - pdb=" SG CYS P 100D" 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 U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " 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 339 " " NAG A 609 " - " ASN A 386 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 289 " " NAG A 612 " - " ASN A 241 " " NAG A 613 " - " ASN A 355 " " 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 339 " " NAG E 609 " - " ASN E 386 " " NAG E 610 " - " ASN E 448 " " NAG E 611 " - " ASN E 289 " " NAG E 612 " - " ASN E 241 " " NAG E 613 " - " ASN E 355 " " 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 339 " " NAG F 609 " - " ASN F 386 " " NAG F 610 " - " ASN F 448 " " NAG F 611 " - " ASN F 289 " " NAG F 612 " - " ASN F 241 " " NAG F 613 " - " ASN F 355 " " NAG G 701 " - " ASN G 611 " " NAG I 701 " - " ASN I 611 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN E 332 " " NAG W 1 " - " ASN E 156 " " NAG X 1 " - " ASN E 262 " " NAG Y 1 " - " ASN F 332 " " NAG Z 1 " - " ASN F 156 " " NAG a 1 " - " ASN F 262 " Time building additional restraints: 9.36 Conformation dependent library (CDL) restraints added in 4.2 seconds 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5598 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 48 sheets defined 17.8% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.320A 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 335 through 354 removed outlier: 3.837A 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 474 through 484 removed outlier: 4.117A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.791A 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 removed outlier: 3.599A pdb=" N THR C 87 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.523A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.813A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.159A 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 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.182A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.597A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.320A 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 335 through 354 removed outlier: 3.838A 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 474 through 484 removed outlier: 4.117A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.791A 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 removed outlier: 3.599A pdb=" N THR J 87 " --> pdb=" O ASP J 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.524A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 546 removed outlier: 3.813A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 4.159A 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 624 Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 638 through 662 Processing helix chain 'O' and resid 28 through 32 removed outlier: 4.183A pdb=" N HIS O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.597A pdb=" N VAL Q 83 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.320A 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 335 through 354 removed outlier: 3.838A 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 474 through 484 removed outlier: 4.117A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.791A 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 removed outlier: 3.599A pdb=" N THR K 87 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.524A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 546 removed outlier: 3.813A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 4.159A 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 624 Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 662 Processing helix chain 'P' and resid 28 through 32 removed outlier: 4.183A pdb=" N HIS P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.597A pdb=" N VAL R 83 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.229A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.081A 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 removed outlier: 3.693A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.794A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.892A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.532A 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: 6.780A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A 315 " --> 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: 5.644A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (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: 6.337A 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 95A through 98 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB4, first strand: chain 'H' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 9 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100M through 103 Processing sheet with id=AB5, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB6, first strand: chain 'L' and resid 27C through 27D removed outlier: 3.717A pdb=" N THR L 30 " --> pdb=" O ASP L 27D" (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.544A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.229A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.693A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.794A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'E' and resid 200 through 203 removed outlier: 5.892A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC5, 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: 6.780A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN E 315 " --> 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=AC6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'J' and resid 34 through 39 removed outlier: 5.645A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (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=AC8, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC9, first strand: chain 'M' and resid 33 through 38 removed outlier: 6.337A 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 95A through 98 Processing sheet with id=AD1, first strand: chain 'O' and resid 3 through 5 Processing sheet with id=AD2, first strand: chain 'O' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 9 through 12 current: chain 'O' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100M through 103 Processing sheet with id=AD3, first strand: chain 'Q' and resid 5 through 6 Processing sheet with id=AD4, first strand: chain 'Q' and resid 27C through 27D removed outlier: 3.717A pdb=" N THR Q 30 " --> pdb=" O ASP Q 27D" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 53 through 54 removed outlier: 6.543A pdb=" N ASN Q 53 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.229A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.693A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.794A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'F' and resid 200 through 203 removed outlier: 5.892A pdb=" N ALA F 200 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR F 435 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AE3, 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: 6.780A pdb=" N ASN F 301 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN F 315 " --> 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=AE4, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'K' and resid 34 through 39 removed outlier: 5.644A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (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=AE6, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'N' and resid 33 through 38 removed outlier: 6.336A 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 95A through 98 Processing sheet with id=AE8, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AE9, first strand: chain 'P' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 9 through 12 current: chain 'P' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 100M through 103 Processing sheet with id=AF1, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AF2, first strand: chain 'R' and resid 27C through 27D removed outlier: 3.717A pdb=" N THR R 30 " --> pdb=" O ASP R 27D" (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.544A pdb=" N ASN R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 1872 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: 8.93 Time building geometry restraints manager: 10.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7814 1.34 - 1.47: 6439 1.47 - 1.59: 10806 1.59 - 1.71: 0 1.71 - 1.84: 222 Bond restraints: 25281 Sorted by residual: bond pdb=" N SER F 140 " pdb=" CA SER F 140 " ideal model delta sigma weight residual 1.459 1.496 -0.037 9.10e-03 1.21e+04 1.61e+01 bond pdb=" N SER A 140 " pdb=" CA SER A 140 " ideal model delta sigma weight residual 1.459 1.496 -0.036 9.10e-03 1.21e+04 1.61e+01 bond pdb=" N SER E 140 " pdb=" CA SER E 140 " ideal model delta sigma weight residual 1.459 1.496 -0.036 9.10e-03 1.21e+04 1.60e+01 bond pdb=" CB CYS J 92 " pdb=" SG CYS J 92 " ideal model delta sigma weight residual 1.808 1.736 0.072 3.30e-02 9.18e+02 4.79e+00 bond pdb=" CB CYS C 92 " pdb=" SG CYS C 92 " ideal model delta sigma weight residual 1.808 1.736 0.072 3.30e-02 9.18e+02 4.71e+00 ... (remaining 25276 not shown) Histogram of bond angle deviations from ideal: 97.46 - 104.82: 444 104.82 - 112.18: 12487 112.18 - 119.54: 8960 119.54 - 126.90: 11997 126.90 - 134.26: 399 Bond angle restraints: 34287 Sorted by residual: angle pdb=" N GLY D 100 " pdb=" CA GLY D 100 " pdb=" C GLY D 100 " ideal model delta sigma weight residual 112.85 106.41 6.44 1.61e+00 3.86e-01 1.60e+01 angle pdb=" N GLY N 100 " pdb=" CA GLY N 100 " pdb=" C GLY N 100 " ideal model delta sigma weight residual 112.85 106.42 6.43 1.61e+00 3.86e-01 1.59e+01 angle pdb=" N GLY M 100 " pdb=" CA GLY M 100 " pdb=" C GLY M 100 " ideal model delta sigma weight residual 112.85 106.43 6.42 1.61e+00 3.86e-01 1.59e+01 angle pdb=" N THR P 100 " pdb=" CA THR P 100 " pdb=" C THR P 100 " ideal model delta sigma weight residual 108.76 102.95 5.81 1.58e+00 4.01e-01 1.35e+01 angle pdb=" N THR O 100 " pdb=" CA THR O 100 " pdb=" C THR O 100 " ideal model delta sigma weight residual 108.76 102.96 5.80 1.58e+00 4.01e-01 1.35e+01 ... (remaining 34282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 15330 21.14 - 42.28: 367 42.28 - 63.42: 119 63.42 - 84.56: 39 84.56 - 105.70: 18 Dihedral angle restraints: 15873 sinusoidal: 7119 harmonic: 8754 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 134.73 -41.73 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 92 " pdb=" CB CYS J 92 " ideal model delta sinusoidal sigma weight residual 93.00 134.72 -41.72 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 92 " pdb=" CB CYS K 92 " ideal model delta sinusoidal sigma weight residual 93.00 134.70 -41.70 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 15870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2817 0.061 - 0.122: 968 0.122 - 0.183: 159 0.183 - 0.244: 13 0.244 - 0.305: 6 Chirality restraints: 3963 Sorted by residual: chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 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 ... (remaining 3960 not shown) Planarity restraints: 4350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 480 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ARG F 480 " 0.065 2.00e-02 2.50e+03 pdb=" O ARG F 480 " -0.024 2.00e-02 2.50e+03 pdb=" N SER F 481 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 480 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ARG E 480 " 0.065 2.00e-02 2.50e+03 pdb=" O ARG E 480 " -0.024 2.00e-02 2.50e+03 pdb=" N SER E 481 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 480 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ARG A 480 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG A 480 " 0.024 2.00e-02 2.50e+03 pdb=" N SER A 481 " 0.022 2.00e-02 2.50e+03 ... (remaining 4347 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 158 2.58 - 3.16: 19636 3.16 - 3.74: 37292 3.74 - 4.32: 55255 4.32 - 4.90: 90546 Nonbonded interactions: 202887 Sorted by model distance: nonbonded pdb=" NH1 ARG E 151 " pdb=" OE2 GLU O 97 " model vdw 2.005 2.520 nonbonded pdb=" NH1 ARG A 151 " pdb=" OE2 GLU H 97 " model vdw 2.071 2.520 nonbonded pdb=" NH1 ARG F 151 " pdb=" OE2 GLU P 97 " model vdw 2.073 2.520 nonbonded pdb=" O GLY C 96 " pdb=" OH TYR D 96 " model vdw 2.162 2.440 nonbonded pdb=" O GLY K 96 " pdb=" OH TYR N 96 " model vdw 2.162 2.440 ... (remaining 202882 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 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'U' selection = chain 'X' selection = chain 'a' } 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: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 66.530 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.200 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 0.072 25281 Z= 0.402 Angle : 1.011 8.962 34287 Z= 0.577 Chirality : 0.059 0.305 3963 Planarity : 0.005 0.038 4299 Dihedral : 11.136 105.699 10131 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.23 % Allowed : 0.57 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 2994 helix: 0.53 (0.25), residues: 429 sheet: 1.24 (0.16), residues: 948 loop : 0.41 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 614 HIS 0.006 0.002 HIS F 374 PHE 0.024 0.003 PHE P 100B TYR 0.023 0.003 TYR O 98 ARG 0.014 0.001 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 600 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7718 (mtm110) REVERT: D 47 MET cc_start: 0.8575 (mmm) cc_final: 0.8304 (mmp) REVERT: D 52 THR cc_start: 0.8510 (p) cc_final: 0.8202 (m) REVERT: D 66 LYS cc_start: 0.8262 (ttpp) cc_final: 0.8056 (tttt) REVERT: B 575 GLN cc_start: 0.7721 (mt0) cc_final: 0.7454 (tt0) REVERT: B 652 GLN cc_start: 0.8642 (mt0) cc_final: 0.8414 (mt0) REVERT: B 653 GLN cc_start: 0.8340 (tt0) cc_final: 0.7540 (mt0) REVERT: E 110 SER cc_start: 0.8511 (t) cc_final: 0.8274 (m) REVERT: E 166 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7710 (mtm110) REVERT: E 198 THR cc_start: 0.8800 (m) cc_final: 0.8474 (m) REVERT: M 52 THR cc_start: 0.8462 (p) cc_final: 0.8174 (m) REVERT: F 110 SER cc_start: 0.8559 (t) cc_final: 0.8291 (m) REVERT: F 166 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7645 (mtm110) REVERT: F 198 THR cc_start: 0.8760 (m) cc_final: 0.8407 (m) REVERT: F 212 PRO cc_start: 0.8957 (Cg_exo) cc_final: 0.8601 (Cg_endo) REVERT: N 47 MET cc_start: 0.8517 (mmm) cc_final: 0.8284 (mmm) REVERT: N 52 THR cc_start: 0.8443 (p) cc_final: 0.8170 (m) outliers start: 6 outliers final: 4 residues processed: 606 average time/residue: 0.3852 time to fit residues: 356.2022 Evaluate side-chains 404 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 400 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain F residue 241 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 230 optimal weight: 0.0570 chunk 89 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN B 577 GLN B 630 GLN B 637 ASN H 39 GLN E 94 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100BGLN M 95 GLN O 39 GLN Q 38 GLN F 428 GLN N 95 GLN I 637 ASN P 39 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25281 Z= 0.228 Angle : 0.583 9.543 34287 Z= 0.308 Chirality : 0.048 0.588 3963 Planarity : 0.004 0.037 4299 Dihedral : 7.293 63.105 4618 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.31 % Allowed : 5.86 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.43 (0.15), residues: 2994 helix: 2.02 (0.27), residues: 411 sheet: 1.44 (0.16), residues: 897 loop : 0.50 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 35 HIS 0.003 0.001 HIS F 105 PHE 0.013 0.002 PHE E 233 TYR 0.024 0.001 TYR H 98 ARG 0.005 0.001 ARG M 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 417 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8551 (tttm) cc_final: 0.8285 (mttm) REVERT: A 166 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7694 (mtm110) REVERT: C 18 LEU cc_start: 0.8438 (tp) cc_final: 0.8213 (tp) REVERT: H 39 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: L 54 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7341 (ttm110) REVERT: E 110 SER cc_start: 0.8588 (t) cc_final: 0.8285 (m) REVERT: E 166 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7649 (ttp80) REVERT: E 358 ILE cc_start: 0.7487 (mt) cc_final: 0.7260 (mm) REVERT: M 47 MET cc_start: 0.8574 (mmm) cc_final: 0.8286 (mmt) REVERT: M 52 THR cc_start: 0.8488 (p) cc_final: 0.8217 (m) REVERT: O 39 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6992 (tt0) REVERT: O 77 THR cc_start: 0.8634 (m) cc_final: 0.7932 (p) REVERT: Q 28 ASP cc_start: 0.8645 (m-30) cc_final: 0.7997 (m-30) REVERT: Q 33 LEU cc_start: 0.8634 (tp) cc_final: 0.8430 (tp) REVERT: Q 54 ARG cc_start: 0.7697 (ttm110) cc_final: 0.7408 (ttm110) REVERT: F 110 SER cc_start: 0.8622 (t) cc_final: 0.8261 (m) REVERT: F 166 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7668 (mtm110) REVERT: F 212 PRO cc_start: 0.8969 (Cg_exo) cc_final: 0.8717 (Cg_endo) REVERT: K 4 LEU cc_start: 0.8257 (mt) cc_final: 0.8048 (mp) REVERT: N 47 MET cc_start: 0.8508 (mmm) cc_final: 0.8155 (mmm) REVERT: I 624 ASP cc_start: 0.8707 (m-30) cc_final: 0.8419 (m-30) REVERT: P 105 ARG cc_start: 0.7545 (ptp90) cc_final: 0.7203 (ptp90) REVERT: R 28 ASP cc_start: 0.8442 (m-30) cc_final: 0.7863 (m-30) outliers start: 61 outliers final: 42 residues processed: 455 average time/residue: 0.3533 time to fit residues: 250.8102 Evaluate side-chains 419 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 375 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain R residue 58 VAL 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: 0.6980 chunk 222 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 267 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 238 optimal weight: 0.6980 chunk 265 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 543 ASN G 637 ASN O 39 GLN Q 38 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25281 Z= 0.233 Angle : 0.544 7.686 34287 Z= 0.287 Chirality : 0.046 0.488 3963 Planarity : 0.004 0.037 4299 Dihedral : 6.074 54.869 4614 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.08 % Allowed : 7.38 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.42 (0.15), residues: 2994 helix: 2.13 (0.27), residues: 411 sheet: 1.42 (0.16), residues: 897 loop : 0.46 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.004 0.001 HIS E 105 PHE 0.017 0.002 PHE H 100B TYR 0.015 0.001 TYR J 27 ARG 0.004 0.000 ARG M 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 384 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8414 (tttm) cc_final: 0.8193 (mttm) REVERT: A 166 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7672 (ttp80) REVERT: B 616 ASN cc_start: 0.8446 (p0) cc_final: 0.8222 (p0) REVERT: H 77 THR cc_start: 0.8356 (m) cc_final: 0.7978 (p) REVERT: L 28 ASP cc_start: 0.8680 (m-30) cc_final: 0.8431 (m-30) REVERT: L 32 TYR cc_start: 0.8573 (m-80) cc_final: 0.8176 (m-80) REVERT: L 54 ARG cc_start: 0.7708 (ttm110) cc_final: 0.7412 (ttm110) REVERT: E 110 SER cc_start: 0.8646 (t) cc_final: 0.8275 (m) REVERT: E 166 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7740 (ttp80) REVERT: M 52 THR cc_start: 0.8593 (p) cc_final: 0.8311 (m) REVERT: O 77 THR cc_start: 0.8330 (m) cc_final: 0.8082 (p) REVERT: Q 33 LEU cc_start: 0.8740 (tp) cc_final: 0.8499 (tp) REVERT: Q 54 ARG cc_start: 0.7745 (ttm110) cc_final: 0.7399 (ttm110) REVERT: F 110 SER cc_start: 0.8609 (t) cc_final: 0.8264 (m) REVERT: F 166 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7596 (ttp80) REVERT: N 47 MET cc_start: 0.8497 (mmm) cc_final: 0.8138 (mmm) REVERT: I 624 ASP cc_start: 0.8744 (m-30) cc_final: 0.8428 (m-30) REVERT: P 39 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.7033 (tt0) REVERT: P 77 THR cc_start: 0.8365 (m) cc_final: 0.7991 (p) REVERT: P 105 ARG cc_start: 0.7541 (ptp90) cc_final: 0.7306 (ptp90) outliers start: 55 outliers final: 40 residues processed: 420 average time/residue: 0.3763 time to fit residues: 249.9071 Evaluate side-chains 400 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 359 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN 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 O residue 28 THR Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 268 optimal weight: 0.0770 chunk 284 optimal weight: 0.0010 chunk 140 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS C 39 GLN H 39 GLN H 100KASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100KASN N 95 GLN I 607 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25281 Z= 0.161 Angle : 0.483 6.336 34287 Z= 0.253 Chirality : 0.044 0.394 3963 Planarity : 0.003 0.037 4299 Dihedral : 5.448 58.552 4614 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.93 % Allowed : 8.06 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.45 (0.16), residues: 2994 helix: 2.23 (0.27), residues: 411 sheet: 1.37 (0.17), residues: 900 loop : 0.51 (0.16), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 50 HIS 0.003 0.001 HIS E 105 PHE 0.009 0.001 PHE Q 36 TYR 0.010 0.001 TYR J 27 ARG 0.005 0.000 ARG F 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 377 time to evaluate : 3.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7924 (ptm-80) REVERT: C 82 MET cc_start: 0.8766 (ptp) cc_final: 0.8547 (mtm) REVERT: B 616 ASN cc_start: 0.8427 (p0) cc_final: 0.8215 (p0) REVERT: H 48 MET cc_start: 0.8253 (mtp) cc_final: 0.8045 (mtp) REVERT: H 77 THR cc_start: 0.8166 (m) cc_final: 0.7780 (p) REVERT: L 54 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7490 (ttm110) REVERT: E 110 SER cc_start: 0.8623 (t) cc_final: 0.8286 (m) REVERT: E 166 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7575 (ttp80) REVERT: O 39 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6888 (tt0) REVERT: O 77 THR cc_start: 0.8149 (m) cc_final: 0.7939 (p) REVERT: Q 33 LEU cc_start: 0.8727 (tp) cc_final: 0.8497 (tp) REVERT: Q 54 ARG cc_start: 0.7703 (ttm110) cc_final: 0.7399 (ttm110) REVERT: F 110 SER cc_start: 0.8647 (t) cc_final: 0.8312 (m) REVERT: F 166 ARG cc_start: 0.8247 (mtp85) cc_final: 0.7696 (mtm110) REVERT: N 47 MET cc_start: 0.8450 (mmm) cc_final: 0.8185 (mmm) REVERT: I 616 ASN cc_start: 0.8526 (p0) cc_final: 0.8314 (p0) REVERT: I 624 ASP cc_start: 0.8764 (m-30) cc_final: 0.8452 (m-30) REVERT: P 77 THR cc_start: 0.8218 (m) cc_final: 0.7875 (p) REVERT: P 105 ARG cc_start: 0.7487 (ptp90) cc_final: 0.7214 (ptp90) outliers start: 51 outliers final: 34 residues processed: 412 average time/residue: 0.3527 time to fit residues: 229.4968 Evaluate side-chains 391 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 356 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS H 39 GLN L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS F 374 HIS N 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25281 Z= 0.344 Angle : 0.569 8.361 34287 Z= 0.295 Chirality : 0.047 0.458 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.602 55.159 4614 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.50 % Allowed : 8.13 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.13 (0.16), residues: 2994 helix: 1.88 (0.26), residues: 411 sheet: 1.25 (0.17), residues: 900 loop : 0.26 (0.16), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 96 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.002 PHE A 383 TYR 0.018 0.002 TYR P 59 ARG 0.004 0.001 ARG F 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 351 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7724 (ttp80) REVERT: B 616 ASN cc_start: 0.8488 (p0) cc_final: 0.8202 (p0) REVERT: L 54 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7523 (ttm110) REVERT: E 110 SER cc_start: 0.8737 (t) cc_final: 0.8320 (m) REVERT: E 166 ARG cc_start: 0.8295 (mtp85) cc_final: 0.7797 (ttp80) REVERT: E 358 ILE cc_start: 0.7811 (mt) cc_final: 0.7577 (mm) REVERT: G 616 ASN cc_start: 0.8625 (p0) cc_final: 0.8261 (p0) REVERT: Q 31 THR cc_start: 0.8331 (m) cc_final: 0.7726 (p) REVERT: Q 54 ARG cc_start: 0.7823 (ttm110) cc_final: 0.7545 (ttm110) REVERT: F 110 SER cc_start: 0.8737 (t) cc_final: 0.8389 (m) REVERT: F 166 ARG cc_start: 0.8330 (mtp85) cc_final: 0.7899 (ttp80) REVERT: N 47 MET cc_start: 0.8494 (mmm) cc_final: 0.8241 (mmm) REVERT: I 616 ASN cc_start: 0.8585 (p0) cc_final: 0.8315 (p0) REVERT: I 624 ASP cc_start: 0.8716 (m-30) cc_final: 0.8403 (m-30) REVERT: P 39 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7012 (tt0) REVERT: P 105 ARG cc_start: 0.7478 (ptp90) cc_final: 0.7148 (ptp90) REVERT: R 34 GLU cc_start: 0.7807 (tt0) cc_final: 0.7574 (tt0) REVERT: R 89 MET cc_start: 0.7833 (tpp) cc_final: 0.7554 (ttt) outliers start: 66 outliers final: 55 residues processed: 397 average time/residue: 0.3383 time to fit residues: 214.4782 Evaluate side-chains 394 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 338 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 10.0000 chunk 255 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 284 optimal weight: 0.0030 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 95 GLN B 637 ASN L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN M 95 GLN G 637 ASN O 39 GLN O 100KASN Q 38 GLN Q 45 GLN N 95 GLN ** P 100KASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25281 Z= 0.185 Angle : 0.489 6.972 34287 Z= 0.256 Chirality : 0.044 0.402 3963 Planarity : 0.003 0.036 4299 Dihedral : 5.349 58.082 4614 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.01 % Allowed : 9.12 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.25 (0.16), residues: 2994 helix: 2.06 (0.26), residues: 411 sheet: 1.17 (0.17), residues: 906 loop : 0.42 (0.16), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS A 105 PHE 0.014 0.001 PHE O 63 TYR 0.012 0.001 TYR D 49 ARG 0.003 0.000 ARG F 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 343 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7703 (ttp80) REVERT: B 616 ASN cc_start: 0.8470 (p0) cc_final: 0.8197 (p0) REVERT: L 54 ARG cc_start: 0.7654 (ttm110) cc_final: 0.7423 (ttm110) REVERT: E 110 SER cc_start: 0.8684 (t) cc_final: 0.8329 (m) REVERT: E 166 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7738 (ttp80) REVERT: E 358 ILE cc_start: 0.7788 (mt) cc_final: 0.7570 (mm) REVERT: G 616 ASN cc_start: 0.8615 (p0) cc_final: 0.8290 (p0) REVERT: O 39 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6911 (tt0) REVERT: Q 34 GLU cc_start: 0.7719 (tt0) cc_final: 0.7502 (tt0) REVERT: Q 54 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7542 (ttm110) REVERT: F 110 SER cc_start: 0.8735 (t) cc_final: 0.8392 (m) REVERT: F 166 ARG cc_start: 0.8326 (mtp85) cc_final: 0.7853 (ttp80) REVERT: N 47 MET cc_start: 0.8470 (mmm) cc_final: 0.8214 (mmm) REVERT: I 616 ASN cc_start: 0.8520 (p0) cc_final: 0.8267 (p0) REVERT: I 624 ASP cc_start: 0.8751 (m-30) cc_final: 0.8412 (m-30) REVERT: P 22 CYS cc_start: 0.7530 (t) cc_final: 0.7290 (t) REVERT: P 39 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: P 105 ARG cc_start: 0.7460 (ptp90) cc_final: 0.7120 (ptp90) REVERT: R 89 MET cc_start: 0.7824 (tpp) cc_final: 0.7233 (ttp) outliers start: 53 outliers final: 37 residues processed: 381 average time/residue: 0.3453 time to fit residues: 208.7702 Evaluate side-chains 368 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 329 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 25 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 239 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 GLN D 95 GLN B 637 ASN L 38 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 637 ASN O 39 GLN O 100KASN Q 38 GLN N 95 GLN I 637 ASN ** P 100KASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25281 Z= 0.307 Angle : 0.538 8.208 34287 Z= 0.278 Chirality : 0.046 0.448 3963 Planarity : 0.004 0.036 4299 Dihedral : 5.441 55.966 4614 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.31 % Allowed : 8.97 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.16), residues: 2994 helix: 1.93 (0.27), residues: 411 sheet: 0.98 (0.16), residues: 963 loop : 0.31 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 96 HIS 0.003 0.001 HIS E 105 PHE 0.018 0.002 PHE O 63 TYR 0.012 0.001 TYR F 319 ARG 0.006 0.000 ARG O 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 336 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7735 (ttp80) REVERT: B 616 ASN cc_start: 0.8480 (p0) cc_final: 0.8194 (p0) REVERT: L 54 ARG cc_start: 0.7689 (ttm110) cc_final: 0.7462 (ttm110) REVERT: E 110 SER cc_start: 0.8743 (t) cc_final: 0.8325 (m) REVERT: E 166 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7809 (ttp80) REVERT: G 616 ASN cc_start: 0.8655 (p0) cc_final: 0.8320 (p0) REVERT: Q 31 THR cc_start: 0.8348 (m) cc_final: 0.7833 (p) REVERT: Q 54 ARG cc_start: 0.7877 (ttm110) cc_final: 0.7616 (ttm110) REVERT: F 110 SER cc_start: 0.8713 (t) cc_final: 0.8359 (m) REVERT: F 166 ARG cc_start: 0.8312 (mtp85) cc_final: 0.7829 (ttp80) REVERT: N 47 MET cc_start: 0.8484 (mmm) cc_final: 0.8212 (mmm) REVERT: I 616 ASN cc_start: 0.8539 (p0) cc_final: 0.8256 (p0) REVERT: I 624 ASP cc_start: 0.8788 (m-30) cc_final: 0.8424 (m-30) REVERT: P 39 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6911 (tt0) REVERT: P 105 ARG cc_start: 0.7477 (ptp90) cc_final: 0.7111 (ptp90) outliers start: 61 outliers final: 51 residues processed: 376 average time/residue: 0.3605 time to fit residues: 214.2143 Evaluate side-chains 381 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 329 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 43 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 169 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 55 optimal weight: 0.0000 chunk 54 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 GLN B 637 ASN L 38 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 HIS M 95 GLN G 637 ASN O 39 GLN O 100KASN Q 38 GLN N 95 GLN I 637 ASN ** P 100KASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25281 Z= 0.273 Angle : 0.530 8.079 34287 Z= 0.276 Chirality : 0.045 0.528 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.484 59.089 4614 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.38 % Allowed : 9.16 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.00 (0.16), residues: 2994 helix: 1.93 (0.26), residues: 411 sheet: 0.97 (0.17), residues: 930 loop : 0.24 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.003 0.001 HIS E 105 PHE 0.024 0.002 PHE O 63 TYR 0.012 0.001 TYR M 49 ARG 0.007 0.000 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 334 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9053 (mtp) cc_final: 0.8756 (mtp) REVERT: A 166 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7818 (ttp80) REVERT: B 616 ASN cc_start: 0.8475 (p0) cc_final: 0.8189 (p0) REVERT: L 54 ARG cc_start: 0.7681 (ttm110) cc_final: 0.7472 (ttm110) REVERT: L 73 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7914 (tp) REVERT: L 89 MET cc_start: 0.8035 (ttt) cc_final: 0.7667 (ttp) REVERT: E 110 SER cc_start: 0.8752 (t) cc_final: 0.8328 (m) REVERT: E 166 ARG cc_start: 0.8284 (mtp85) cc_final: 0.7835 (ttp80) REVERT: E 358 ILE cc_start: 0.7890 (mt) cc_final: 0.7658 (mm) REVERT: G 616 ASN cc_start: 0.8606 (p0) cc_final: 0.8284 (p0) REVERT: O 39 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7108 (tt0) REVERT: Q 34 GLU cc_start: 0.7588 (tt0) cc_final: 0.7355 (tt0) REVERT: Q 54 ARG cc_start: 0.7868 (ttm110) cc_final: 0.7626 (ttm110) REVERT: F 110 SER cc_start: 0.8705 (t) cc_final: 0.8360 (m) REVERT: F 166 ARG cc_start: 0.8283 (mtp85) cc_final: 0.7846 (ttp80) REVERT: K 27 TYR cc_start: 0.8246 (p90) cc_final: 0.8027 (p90) REVERT: N 47 MET cc_start: 0.8507 (mmm) cc_final: 0.8248 (mmm) REVERT: I 616 ASN cc_start: 0.8479 (p0) cc_final: 0.8204 (p0) REVERT: I 624 ASP cc_start: 0.8818 (m-30) cc_final: 0.8439 (m-30) REVERT: P 31 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8125 (t0) REVERT: P 39 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6964 (tt0) outliers start: 63 outliers final: 50 residues processed: 380 average time/residue: 0.3536 time to fit residues: 213.4330 Evaluate side-chains 378 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 324 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 43 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 464 THR Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 31 ASP Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 8.9990 chunk 271 optimal weight: 0.6980 chunk 247 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 81 optimal weight: 0.0470 chunk 238 optimal weight: 0.6980 chunk 249 optimal weight: 0.7980 chunk 263 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 GLN B 637 ASN L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN G 637 ASN O 39 GLN ** O 100KASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN N 95 GLN I 637 ASN P 100KASN R 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25281 Z= 0.181 Angle : 0.493 8.365 34287 Z= 0.257 Chirality : 0.044 0.563 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.307 59.346 4614 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.89 % Allowed : 9.99 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.19 (0.16), residues: 2994 helix: 2.10 (0.27), residues: 411 sheet: 1.13 (0.17), residues: 906 loop : 0.35 (0.16), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 50 HIS 0.002 0.001 HIS E 105 PHE 0.017 0.001 PHE O 63 TYR 0.014 0.001 TYR D 49 ARG 0.007 0.000 ARG M 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 342 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8983 (mtp) cc_final: 0.8748 (mtp) REVERT: A 166 ARG cc_start: 0.8215 (mtp85) cc_final: 0.7804 (ttp80) REVERT: A 334 SER cc_start: 0.8653 (t) cc_final: 0.8349 (p) REVERT: B 616 ASN cc_start: 0.8457 (p0) cc_final: 0.8205 (p0) REVERT: L 89 MET cc_start: 0.7940 (ttt) cc_final: 0.7653 (ttp) REVERT: E 110 SER cc_start: 0.8713 (t) cc_final: 0.8291 (m) REVERT: E 166 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7639 (ttp80) REVERT: E 358 ILE cc_start: 0.7875 (mt) cc_final: 0.7635 (mm) REVERT: E 432 GLN cc_start: 0.8311 (mt0) cc_final: 0.8093 (mt0) REVERT: G 616 ASN cc_start: 0.8557 (p0) cc_final: 0.8216 (p0) REVERT: O 39 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: Q 31 THR cc_start: 0.8418 (m) cc_final: 0.7947 (p) REVERT: Q 34 GLU cc_start: 0.7459 (tt0) cc_final: 0.7225 (tt0) REVERT: Q 54 ARG cc_start: 0.7873 (ttm110) cc_final: 0.7650 (ttm110) REVERT: F 110 SER cc_start: 0.8668 (t) cc_final: 0.8340 (m) REVERT: F 166 ARG cc_start: 0.8322 (mtp85) cc_final: 0.7894 (ttp80) REVERT: K 27 TYR cc_start: 0.8225 (p90) cc_final: 0.7953 (p90) REVERT: N 47 MET cc_start: 0.8451 (mmm) cc_final: 0.8193 (mmm) REVERT: I 616 ASN cc_start: 0.8455 (p0) cc_final: 0.8182 (p0) REVERT: I 624 ASP cc_start: 0.8822 (m-30) cc_final: 0.8448 (m-30) REVERT: P 39 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6902 (tt0) outliers start: 50 outliers final: 46 residues processed: 380 average time/residue: 0.3703 time to fit residues: 225.4186 Evaluate side-chains 384 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 336 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 43 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 292 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 233 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 637 ASN L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 637 ASN O 39 GLN ** O 100KASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN N 95 GLN I 637 ASN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25281 Z= 0.355 Angle : 0.576 9.028 34287 Z= 0.297 Chirality : 0.047 0.578 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.556 56.492 4614 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.08 % Allowed : 9.88 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.92 (0.16), residues: 2994 helix: 1.84 (0.27), residues: 411 sheet: 1.05 (0.17), residues: 900 loop : 0.12 (0.16), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 419 HIS 0.004 0.001 HIS A 85 PHE 0.021 0.002 PHE O 63 TYR 0.015 0.002 TYR A 319 ARG 0.008 0.001 ARG M 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 333 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7732 (ttp80) REVERT: B 616 ASN cc_start: 0.8486 (p0) cc_final: 0.8198 (p0) REVERT: H 80 MET cc_start: 0.7501 (ttp) cc_final: 0.7251 (ttp) REVERT: L 54 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7446 (ttm110) REVERT: L 89 MET cc_start: 0.8095 (ttt) cc_final: 0.7832 (ttp) REVERT: E 110 SER cc_start: 0.8846 (t) cc_final: 0.8417 (m) REVERT: E 166 ARG cc_start: 0.8304 (mtp85) cc_final: 0.7911 (ttp80) REVERT: E 267 GLU cc_start: 0.7908 (mp0) cc_final: 0.7644 (mp0) REVERT: E 432 GLN cc_start: 0.8407 (mt0) cc_final: 0.8138 (mt0) REVERT: G 616 ASN cc_start: 0.8604 (p0) cc_final: 0.8234 (p0) REVERT: O 39 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: Q 34 GLU cc_start: 0.7608 (tt0) cc_final: 0.7213 (tt0) REVERT: Q 54 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7590 (ttm110) REVERT: F 110 SER cc_start: 0.8710 (t) cc_final: 0.8364 (m) REVERT: F 166 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7876 (ttp80) REVERT: N 47 MET cc_start: 0.8527 (mmm) cc_final: 0.8261 (mmm) REVERT: I 599 SER cc_start: 0.7802 (p) cc_final: 0.7562 (t) REVERT: I 616 ASN cc_start: 0.8488 (p0) cc_final: 0.8188 (p0) REVERT: I 624 ASP cc_start: 0.8817 (m-30) cc_final: 0.8424 (m-30) REVERT: P 31 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.7989 (t0) REVERT: P 39 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6965 (tt0) outliers start: 55 outliers final: 49 residues processed: 373 average time/residue: 0.3537 time to fit residues: 208.9295 Evaluate side-chains 381 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 329 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 43 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 31 ASP Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 chunk 215 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 233 optimal weight: 0.0040 chunk 97 optimal weight: 0.6980 chunk 239 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 53 GLN B 637 ASN ** H 100KASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN G 637 ASN O 39 GLN O 100KASN ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN I 637 ASN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.155608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117706 restraints weight = 30453.934| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.29 r_work: 0.3226 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 25281 Z= 0.161 Angle : 0.493 7.485 34287 Z= 0.257 Chirality : 0.044 0.532 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.324 59.678 4614 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.74 % Allowed : 10.33 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.12 (0.16), residues: 2994 helix: 2.11 (0.27), residues: 411 sheet: 1.13 (0.17), residues: 885 loop : 0.26 (0.16), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP O 36 HIS 0.002 0.001 HIS E 374 PHE 0.019 0.001 PHE O 63 TYR 0.015 0.001 TYR M 49 ARG 0.007 0.000 ARG M 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5898.70 seconds wall clock time: 105 minutes 56.38 seconds (6356.38 seconds total)