Starting phenix.real_space_refine on Mon Aug 25 02:54:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4a_41025/08_2025/8t4a_41025.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4a_41025/08_2025/8t4a_41025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4a_41025/08_2025/8t4a_41025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4a_41025/08_2025/8t4a_41025.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4a_41025/08_2025/8t4a_41025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4a_41025/08_2025/8t4a_41025.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.032 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 150 5.16 5 C 15660 2.51 5 N 4152 2.21 5 O 4962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24924 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3459 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 21, 'TRANS': 414} 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: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1019 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Restraints were copied for chains: E, F, G, I, J, K, M, N, O, P, Q, R, V, Y, W, Z, X, a Time building chain proxies: 4.71, per 1000 atoms: 0.19 Number of scatterers: 24924 At special positions: 0 Unit cell: (156.4, 147.2, 173.65, 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 150 16.00 O 4962 8.00 N 4152 7.00 C 15660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.00 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.00 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 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=2.00 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.00 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.00 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.00 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 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 - 3.00 Amino acid : True - 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 ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 301 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 156 " " NAG A 604 " - " ASN A 160 " " NAG A 605 " - " ASN A 197 " " NAG A 606 " - " ASN A 234 " " NAG A 607 " - " ASN A 276 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 339 " " 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 A 614 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG E 601 " - " ASN E 301 " " NAG E 602 " - " ASN E 88 " " NAG E 603 " - " ASN E 156 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 234 " " NAG E 607 " - " ASN E 276 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 339 " " 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 E 614 " - " ASN E 392 " " NAG F 601 " - " ASN F 301 " " NAG F 602 " - " ASN F 88 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 160 " " NAG F 605 " - " ASN F 197 " " NAG F 606 " - " ASN F 234 " " NAG F 607 " - " ASN F 276 " " NAG F 608 " - " ASN F 295 " " NAG F 609 " - " ASN F 339 " " 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 F 614 " - " ASN F 392 " " NAG G 701 " - " ASN G 611 " " NAG G 702 " - " ASN G 618 " " NAG G 703 " - " ASN G 637 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 618 " " NAG I 703 " - " ASN I 637 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 386 " " NAG V 1 " - " ASN E 332 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 386 " " NAG Y 1 " - " ASN F 332 " " NAG Z 1 " - " ASN F 262 " " NAG a 1 " - " ASN F 386 " Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 961.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 63 sheets defined 18.4% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.399A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 removed outlier: 3.513A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.855A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.378A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.500A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.795A 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: 3.639A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.709A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100F Processing helix chain 'L' and resid 27 through 31 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.399A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 removed outlier: 3.513A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.855A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.379A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.500A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.794A 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: 3.639A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU G 545 " --> pdb=" O ALA G 541 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER G 546 " --> pdb=" O ARG G 542 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.709A pdb=" N MET G 626 " --> pdb=" O ILE G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 638 through 662 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100B through 100F Processing helix chain 'Q' and resid 27 through 31 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.399A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 removed outlier: 3.513A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 123 through 126' Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 354 removed outlier: 3.855A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.378A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.500A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.795A 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: 3.639A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU I 545 " --> pdb=" O ALA I 541 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER I 546 " --> pdb=" O ARG I 542 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 596 Processing helix chain 'I' and resid 618 through 626 removed outlier: 3.709A pdb=" N MET I 626 " --> pdb=" O ILE I 622 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 662 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100B through 100F Processing helix chain 'R' and resid 27 through 31 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.272A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.633A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.518A pdb=" N VAL A 120 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 9.909A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.213A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.747A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.213A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 312 removed outlier: 6.887A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 8 Processing sheet with id=AB2, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB5, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE D 95B" --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL H 35A" --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS H 96 " --> pdb=" O TYR H 100K" (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL H 35A" --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.273A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.633A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 120 through 121 removed outlier: 3.518A pdb=" N VAL E 120 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 172 through 177 Processing sheet with id=AD1, first strand: chain 'E' and resid 259 through 261 removed outlier: 9.910A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.747A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 301 through 312 removed outlier: 6.888A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 3 through 8 Processing sheet with id=AD5, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AD8, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE M 95B" --> pdb=" O ALA M 92 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG O 50 " --> pdb=" O VAL O 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL O 35A" --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS O 96 " --> pdb=" O TYR O 100K" (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG O 50 " --> pdb=" O VAL O 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL O 35A" --> pdb=" O ARG O 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP Q 35 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.273A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AE9, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AF1, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.634A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 120 through 121 removed outlier: 3.518A pdb=" N VAL F 120 " --> pdb=" O GLN F 203 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 172 through 177 Processing sheet with id=AF4, first strand: chain 'F' and resid 259 through 261 removed outlier: 9.909A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.746A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 301 through 312 removed outlier: 6.887A pdb=" N ASN F 301 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 3 through 8 Processing sheet with id=AF8, first strand: chain 'K' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AG2, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE N 95B" --> pdb=" O ALA N 92 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'P' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP P 36 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG P 50 " --> pdb=" O VAL P 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL P 35A" --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS P 96 " --> pdb=" O TYR P 100K" (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP P 36 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG P 50 " --> pdb=" O VAL P 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL P 35A" --> pdb=" O ARG P 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP R 35 " --> pdb=" O VAL R 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'R' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 19 through 24 1080 hydrogen bonds defined for protein. 2727 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: 4.61 Time building geometry restraints manager: 2.26 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: 7654 1.34 - 1.46: 6465 1.46 - 1.59: 11120 1.59 - 1.71: 0 1.71 - 1.83: 210 Bond restraints: 25449 Sorted by residual: bond pdb=" CG LEU L 4 " pdb=" CD1 LEU L 4 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.68e+00 bond pdb=" CG LEU Q 4 " pdb=" CD1 LEU Q 4 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.68e+00 bond pdb=" CG LEU R 4 " pdb=" CD1 LEU R 4 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.63e+00 bond pdb=" CA ASP H 55 " pdb=" CB ASP H 55 " ideal model delta sigma weight residual 1.532 1.567 -0.035 1.43e-02 4.89e+03 5.91e+00 bond pdb=" CB VAL H 79 " pdb=" CG2 VAL H 79 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.89e+00 ... (remaining 25444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 32318 2.17 - 4.34: 1920 4.34 - 6.51: 268 6.51 - 8.67: 48 8.67 - 10.84: 6 Bond angle restraints: 34560 Sorted by residual: angle pdb=" CA ASP O 55 " pdb=" CB ASP O 55 " pdb=" CG ASP O 55 " ideal model delta sigma weight residual 112.60 117.73 -5.13 1.00e+00 1.00e+00 2.63e+01 angle pdb=" CA ASP H 55 " pdb=" CB ASP H 55 " pdb=" CG ASP H 55 " ideal model delta sigma weight residual 112.60 117.73 -5.13 1.00e+00 1.00e+00 2.63e+01 angle pdb=" CA ASP P 55 " pdb=" CB ASP P 55 " pdb=" CG ASP P 55 " ideal model delta sigma weight residual 112.60 117.72 -5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" N THR P 31 " pdb=" CA THR P 31 " pdb=" C THR P 31 " ideal model delta sigma weight residual 112.12 105.63 6.49 1.34e+00 5.57e-01 2.34e+01 angle pdb=" N THR O 31 " pdb=" CA THR O 31 " pdb=" C THR O 31 " ideal model delta sigma weight residual 112.12 105.64 6.48 1.34e+00 5.57e-01 2.34e+01 ... (remaining 34555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 15405 22.19 - 44.38: 546 44.38 - 66.57: 153 66.57 - 88.75: 51 88.75 - 110.94: 24 Dihedral angle restraints: 16179 sinusoidal: 7407 harmonic: 8772 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.66 -65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.66 -65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.66 -65.66 1 1.00e+01 1.00e-02 5.64e+01 ... (remaining 16176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3588 0.097 - 0.194: 471 0.194 - 0.291: 24 0.291 - 0.388: 6 0.388 - 0.485: 3 Chirality restraints: 4092 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN A 386 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN F 386 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN E 386 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.83e+00 ... (remaining 4089 not shown) Planarity restraints: 4341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 476 " 0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C ARG A 476 " -0.079 2.00e-02 2.50e+03 pdb=" O ARG A 476 " 0.030 2.00e-02 2.50e+03 pdb=" N ASP A 477 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 476 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C ARG F 476 " 0.079 2.00e-02 2.50e+03 pdb=" O ARG F 476 " -0.030 2.00e-02 2.50e+03 pdb=" N ASP F 477 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 476 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C ARG E 476 " 0.079 2.00e-02 2.50e+03 pdb=" O ARG E 476 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP E 477 " -0.027 2.00e-02 2.50e+03 ... (remaining 4338 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4092 2.77 - 3.31: 22717 3.31 - 3.84: 40823 3.84 - 4.37: 48738 4.37 - 4.90: 82792 Nonbonded interactions: 199162 Sorted by model distance: nonbonded pdb=" NH2 ARG E 500 " pdb=" OG SER J 98 " model vdw 2.243 3.120 nonbonded pdb=" NH2 ARG F 500 " pdb=" OG SER K 98 " model vdw 2.243 3.120 nonbonded pdb=" NH2 ARG A 500 " pdb=" OG SER C 98 " model vdw 2.244 3.120 nonbonded pdb=" OD1 ASN L 27 " pdb=" OG SER L 30 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASN Q 27 " pdb=" OG SER Q 30 " model vdw 2.244 3.040 ... (remaining 199157 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 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: 6.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.270 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.007 0.091 25575 Z= 0.319 Angle : 1.294 52.146 34893 Z= 0.697 Chirality : 0.064 0.485 4092 Planarity : 0.007 0.046 4281 Dihedral : 13.266 110.943 10422 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.23 % Allowed : 4.30 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.15), residues: 2991 helix: 1.09 (0.24), residues: 393 sheet: 1.39 (0.17), residues: 924 loop : 0.61 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 139 TYR 0.024 0.003 TYR L 95B PHE 0.023 0.003 PHE R 62 TRP 0.036 0.004 TRP O 100H HIS 0.015 0.002 HIS J 82A Details of bonding type rmsd covalent geometry : bond 0.00715 (25449) covalent geometry : angle 1.15184 (34560) SS BOND : bond 0.01201 ( 45) SS BOND : angle 10.71533 ( 90) hydrogen bonds : bond 0.13325 ( 957) hydrogen bonds : angle 7.56354 ( 2727) link_ALPHA1-3 : bond 0.00643 ( 6) link_ALPHA1-3 : angle 3.97668 ( 18) link_BETA1-4 : bond 0.00701 ( 15) link_BETA1-4 : angle 3.31728 ( 45) link_NAG-ASN : bond 0.00482 ( 60) link_NAG-ASN : angle 2.80924 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 435 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.8215 (mtm) cc_final: 0.7913 (mtm) REVERT: H 64 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7679 (mttm) REVERT: L 27 ASN cc_start: 0.7741 (t0) cc_final: 0.7422 (t0) REVERT: L 54 ARG cc_start: 0.7167 (ttm110) cc_final: 0.6494 (mtp85) REVERT: L 58 ILE cc_start: 0.6773 (mm) cc_final: 0.6354 (mm) REVERT: L 92 ASP cc_start: 0.7074 (t0) cc_final: 0.6859 (t70) REVERT: J 87 THR cc_start: 0.8978 (m) cc_final: 0.8690 (p) REVERT: M 70 THR cc_start: 0.9443 (m) cc_final: 0.9196 (t) REVERT: M 79 GLN cc_start: 0.7208 (mp10) cc_final: 0.6951 (mp10) REVERT: O 64 LYS cc_start: 0.7672 (mtpp) cc_final: 0.7443 (mttm) REVERT: Q 2 TYR cc_start: 0.3510 (t80) cc_final: 0.2708 (t80) REVERT: Q 58 ILE cc_start: 0.6535 (mm) cc_final: 0.6117 (mm) REVERT: Q 92 ASP cc_start: 0.6843 (t0) cc_final: 0.6625 (t70) REVERT: Q 95 LYS cc_start: 0.8328 (mmmm) cc_final: 0.8062 (mmmm) REVERT: N 70 THR cc_start: 0.9453 (m) cc_final: 0.9184 (p) REVERT: P 52 TYR cc_start: 0.7882 (m-80) cc_final: 0.7643 (m-80) REVERT: P 71 LYS cc_start: 0.7446 (ttpt) cc_final: 0.6729 (pttm) REVERT: P 72 ASP cc_start: 0.8296 (t0) cc_final: 0.8042 (t70) REVERT: R 27 ASN cc_start: 0.7768 (t0) cc_final: 0.7352 (t0) REVERT: R 58 ILE cc_start: 0.6501 (mm) cc_final: 0.5973 (mm) REVERT: R 92 ASP cc_start: 0.7052 (t0) cc_final: 0.6705 (t70) REVERT: R 95 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7895 (mmmm) outliers start: 6 outliers final: 2 residues processed: 441 average time/residue: 0.1652 time to fit residues: 108.7782 Evaluate side-chains 288 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 286 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain R residue 4 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82BASN L 37 GLN J 3 GLN K 3 GLN N 95 GLN P 82BASN ** R 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.096968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.070259 restraints weight = 62434.955| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.13 r_work: 0.3101 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25575 Z= 0.158 Angle : 0.662 8.317 34893 Z= 0.342 Chirality : 0.046 0.227 4092 Planarity : 0.004 0.042 4281 Dihedral : 8.753 70.871 4957 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.47 % Allowed : 6.91 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.15), residues: 2991 helix: 2.59 (0.26), residues: 393 sheet: 1.25 (0.17), residues: 942 loop : 0.20 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 38 TYR 0.020 0.002 TYR K 27 PHE 0.015 0.002 PHE K 29 TRP 0.017 0.001 TRP A 479 HIS 0.007 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00354 (25449) covalent geometry : angle 0.63451 (34560) SS BOND : bond 0.00456 ( 45) SS BOND : angle 0.94898 ( 90) hydrogen bonds : bond 0.04935 ( 957) hydrogen bonds : angle 5.78577 ( 2727) link_ALPHA1-3 : bond 0.01590 ( 6) link_ALPHA1-3 : angle 2.64255 ( 18) link_BETA1-4 : bond 0.00573 ( 15) link_BETA1-4 : angle 2.40407 ( 45) link_NAG-ASN : bond 0.00567 ( 60) link_NAG-ASN : angle 2.23755 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 327 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.8571 (mtm) cc_final: 0.8355 (mtm) REVERT: D 17 GLN cc_start: 0.7644 (mm-40) cc_final: 0.6917 (pt0) REVERT: H 38 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7728 (ptp-170) REVERT: H 55 ASP cc_start: 0.7913 (t0) cc_final: 0.7671 (t0) REVERT: H 64 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7851 (mttm) REVERT: L 46 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8301 (tt) REVERT: L 92 ASP cc_start: 0.7018 (t0) cc_final: 0.6784 (t70) REVERT: L 95 LYS cc_start: 0.8310 (mmmm) cc_final: 0.8099 (mmmm) REVERT: J 82 MET cc_start: 0.8678 (mtm) cc_final: 0.8443 (mtm) REVERT: M 17 GLN cc_start: 0.7540 (mm-40) cc_final: 0.6803 (pt0) REVERT: M 70 THR cc_start: 0.9524 (m) cc_final: 0.9294 (t) REVERT: M 79 GLN cc_start: 0.7077 (mp10) cc_final: 0.6567 (mp10) REVERT: O 43 LYS cc_start: 0.7403 (mttp) cc_final: 0.7082 (ptmm) REVERT: O 57 LYS cc_start: 0.8541 (mtpp) cc_final: 0.8284 (mtpp) REVERT: O 64 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7837 (mttm) REVERT: O 66 ARG cc_start: 0.6646 (mtp-110) cc_final: 0.6346 (mtp-110) REVERT: Q 95 LYS cc_start: 0.8321 (mmmm) cc_final: 0.8046 (mmmm) REVERT: K 72 ASP cc_start: 0.7272 (t0) cc_final: 0.6978 (t0) REVERT: K 75 LYS cc_start: 0.9141 (mtpp) cc_final: 0.8768 (mtpt) REVERT: N 42 LYS cc_start: 0.7880 (mttm) cc_final: 0.7457 (ptmm) REVERT: N 95 THR cc_start: 0.8228 (m) cc_final: 0.7959 (t) REVERT: I 648 GLU cc_start: 0.8308 (tp30) cc_final: 0.8040 (tp30) REVERT: P 38 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7587 (ptp-170) REVERT: P 82 MET cc_start: 0.6831 (ttp) cc_final: 0.6546 (ttp) REVERT: P 82 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8212 (t0) REVERT: P 96 LYS cc_start: 0.7494 (tttt) cc_final: 0.7180 (ttpt) REVERT: R 27 ASN cc_start: 0.7755 (t0) cc_final: 0.7438 (t0) REVERT: R 36 TYR cc_start: 0.7861 (m-80) cc_final: 0.7315 (m-10) REVERT: R 92 ASP cc_start: 0.6917 (t0) cc_final: 0.6671 (t70) REVERT: R 95 LYS cc_start: 0.8305 (mmmm) cc_final: 0.7996 (mmmm) outliers start: 39 outliers final: 24 residues processed: 345 average time/residue: 0.1676 time to fit residues: 85.9013 Evaluate side-chains 298 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 82 ASN Chi-restraints excluded: chain P residue 82 MET Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 20 optimal weight: 2.9990 chunk 284 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 259 optimal weight: 5.9990 chunk 271 optimal weight: 0.5980 chunk 236 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN M 37 GLN R 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.093781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.065829 restraints weight = 62850.734| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.19 r_work: 0.3027 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 25575 Z= 0.242 Angle : 0.681 8.726 34893 Z= 0.349 Chirality : 0.048 0.355 4092 Planarity : 0.004 0.041 4281 Dihedral : 7.755 56.587 4953 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.96 % Allowed : 6.61 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.15), residues: 2991 helix: 2.34 (0.26), residues: 393 sheet: 1.21 (0.17), residues: 888 loop : -0.05 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 66 TYR 0.021 0.002 TYR H 100K PHE 0.019 0.002 PHE R 62 TRP 0.017 0.002 TRP E 479 HIS 0.006 0.001 HIS J 82A Details of bonding type rmsd covalent geometry : bond 0.00576 (25449) covalent geometry : angle 0.65640 (34560) SS BOND : bond 0.00504 ( 45) SS BOND : angle 0.94686 ( 90) hydrogen bonds : bond 0.04840 ( 957) hydrogen bonds : angle 5.50919 ( 2727) link_ALPHA1-3 : bond 0.01343 ( 6) link_ALPHA1-3 : angle 2.76559 ( 18) link_BETA1-4 : bond 0.00470 ( 15) link_BETA1-4 : angle 2.31394 ( 45) link_NAG-ASN : bond 0.00370 ( 60) link_NAG-ASN : angle 2.14339 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 296 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8849 (mp) REVERT: C 23 ARG cc_start: 0.8462 (tpp-160) cc_final: 0.8209 (ttm110) REVERT: H 55 ASP cc_start: 0.7898 (t0) cc_final: 0.7655 (t0) REVERT: H 64 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7819 (mttm) REVERT: H 82 ASN cc_start: 0.8445 (t0) cc_final: 0.8234 (t0) REVERT: L 92 ASP cc_start: 0.7216 (t0) cc_final: 0.7001 (t70) REVERT: L 95 LYS cc_start: 0.8332 (mmmm) cc_final: 0.8063 (mmmm) REVERT: E 161 MET cc_start: 0.8866 (tpp) cc_final: 0.8636 (tpt) REVERT: M 79 GLN cc_start: 0.7146 (mp10) cc_final: 0.6589 (mp10) REVERT: O 57 LYS cc_start: 0.8547 (mtpp) cc_final: 0.8234 (mtpp) REVERT: O 64 LYS cc_start: 0.8053 (mtpp) cc_final: 0.7732 (mttm) REVERT: Q 92 ASP cc_start: 0.7477 (t70) cc_final: 0.6354 (p0) REVERT: Q 95 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8109 (mmmt) REVERT: F 111 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8756 (mt) REVERT: K 72 ASP cc_start: 0.7467 (t0) cc_final: 0.7167 (t0) REVERT: K 75 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8795 (mtpt) REVERT: R 27 ASN cc_start: 0.7660 (t0) cc_final: 0.7376 (t0) REVERT: R 36 TYR cc_start: 0.7962 (m-80) cc_final: 0.7355 (m-10) REVERT: R 92 ASP cc_start: 0.7076 (t0) cc_final: 0.6856 (t70) outliers start: 52 outliers final: 31 residues processed: 327 average time/residue: 0.1661 time to fit residues: 81.9136 Evaluate side-chains 296 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 263 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 657 GLU Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 82 MET Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 217 optimal weight: 0.8980 chunk 233 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 278 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN C 3 GLN D 6 GLN N 6 GLN N 39 HIS R 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.096871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069005 restraints weight = 62424.436| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.00 r_work: 0.3122 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25575 Z= 0.134 Angle : 0.598 8.185 34893 Z= 0.305 Chirality : 0.045 0.262 4092 Planarity : 0.004 0.048 4281 Dihedral : 6.938 53.810 4953 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.70 % Allowed : 7.40 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.15), residues: 2991 helix: 2.59 (0.27), residues: 393 sheet: 1.32 (0.17), residues: 861 loop : -0.14 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 66 TYR 0.019 0.001 TYR H 100K PHE 0.011 0.001 PHE F 176 TRP 0.012 0.001 TRP E 479 HIS 0.006 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00303 (25449) covalent geometry : angle 0.57272 (34560) SS BOND : bond 0.00316 ( 45) SS BOND : angle 0.76180 ( 90) hydrogen bonds : bond 0.04073 ( 957) hydrogen bonds : angle 5.25793 ( 2727) link_ALPHA1-3 : bond 0.01287 ( 6) link_ALPHA1-3 : angle 2.90369 ( 18) link_BETA1-4 : bond 0.00395 ( 15) link_BETA1-4 : angle 2.03958 ( 45) link_NAG-ASN : bond 0.00376 ( 60) link_NAG-ASN : angle 2.03393 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 303 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8665 (ttt180) REVERT: D 79 GLN cc_start: 0.6899 (mp10) cc_final: 0.6653 (mp10) REVERT: H 55 ASP cc_start: 0.7978 (t0) cc_final: 0.7742 (t0) REVERT: H 64 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7820 (mttm) REVERT: H 66 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.6988 (ttm110) REVERT: H 82 MET cc_start: 0.6239 (ppp) cc_final: 0.5860 (ppp) REVERT: H 82 ASN cc_start: 0.8494 (t0) cc_final: 0.8019 (t0) REVERT: L 54 ARG cc_start: 0.7744 (ttm110) cc_final: 0.7334 (tpp80) REVERT: L 95 LYS cc_start: 0.8435 (mmmm) cc_final: 0.8140 (mmmm) REVERT: M 70 THR cc_start: 0.9455 (p) cc_final: 0.9233 (t) REVERT: M 79 GLN cc_start: 0.7262 (mp10) cc_final: 0.6763 (mp10) REVERT: O 57 LYS cc_start: 0.8555 (mtpp) cc_final: 0.8272 (mtpp) REVERT: O 64 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7760 (mttm) REVERT: Q 95 LYS cc_start: 0.8564 (mmmm) cc_final: 0.8268 (mmmt) REVERT: F 111 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8854 (mt) REVERT: F 161 MET cc_start: 0.8722 (tpp) cc_final: 0.8469 (tpt) REVERT: K 72 ASP cc_start: 0.7653 (t0) cc_final: 0.7361 (t0) REVERT: K 75 LYS cc_start: 0.9239 (mtpp) cc_final: 0.8923 (mtpt) REVERT: P 5 LYS cc_start: 0.9298 (mttt) cc_final: 0.8801 (tptp) REVERT: P 86 ASP cc_start: 0.6038 (m-30) cc_final: 0.5837 (m-30) REVERT: R 36 TYR cc_start: 0.7866 (m-80) cc_final: 0.7315 (m-10) REVERT: R 79 GLU cc_start: 0.7156 (mp0) cc_final: 0.6950 (mp0) REVERT: R 92 ASP cc_start: 0.7207 (t0) cc_final: 0.7002 (t70) REVERT: R 95 LYS cc_start: 0.8469 (mmmm) cc_final: 0.8237 (mmmm) outliers start: 45 outliers final: 23 residues processed: 330 average time/residue: 0.1696 time to fit residues: 83.1101 Evaluate side-chains 288 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 263 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 287 optimal weight: 0.0770 chunk 121 optimal weight: 4.9990 chunk 286 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 82BASN R 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.096799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.069457 restraints weight = 62309.999| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.14 r_work: 0.3122 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25575 Z= 0.133 Angle : 0.593 12.879 34893 Z= 0.300 Chirality : 0.045 0.254 4092 Planarity : 0.004 0.042 4281 Dihedral : 6.422 53.543 4953 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.28 % Allowed : 8.19 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.15), residues: 2991 helix: 2.54 (0.27), residues: 399 sheet: 1.33 (0.17), residues: 867 loop : -0.21 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 38 TYR 0.020 0.001 TYR P 90 PHE 0.010 0.001 PHE F 176 TRP 0.011 0.001 TRP A 479 HIS 0.006 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00303 (25449) covalent geometry : angle 0.57049 (34560) SS BOND : bond 0.00398 ( 45) SS BOND : angle 0.74624 ( 90) hydrogen bonds : bond 0.03848 ( 957) hydrogen bonds : angle 5.08187 ( 2727) link_ALPHA1-3 : bond 0.01216 ( 6) link_ALPHA1-3 : angle 2.76412 ( 18) link_BETA1-4 : bond 0.00423 ( 15) link_BETA1-4 : angle 1.95902 ( 45) link_NAG-ASN : bond 0.00337 ( 60) link_NAG-ASN : angle 1.92259 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8657 (ttt180) REVERT: D 79 GLN cc_start: 0.7014 (mp10) cc_final: 0.6798 (mp10) REVERT: H 55 ASP cc_start: 0.7908 (t0) cc_final: 0.7597 (t0) REVERT: H 64 LYS cc_start: 0.8130 (mtpp) cc_final: 0.7791 (mttm) REVERT: H 66 ARG cc_start: 0.8195 (mtp-110) cc_final: 0.7387 (ttm110) REVERT: H 82 MET cc_start: 0.6155 (ppp) cc_final: 0.4984 (ppp) REVERT: H 82 ASN cc_start: 0.8472 (t0) cc_final: 0.8169 (t0) REVERT: L 95 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8348 (mmmm) REVERT: M 42 LYS cc_start: 0.7702 (pttm) cc_final: 0.7491 (pttp) REVERT: M 79 GLN cc_start: 0.7026 (mp10) cc_final: 0.6594 (mp10) REVERT: O 57 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8168 (mtpp) REVERT: O 64 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7727 (mttm) REVERT: Q 95 LYS cc_start: 0.8534 (mmmm) cc_final: 0.8230 (mmmm) REVERT: F 111 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8856 (mt) REVERT: F 161 MET cc_start: 0.8721 (tpp) cc_final: 0.8513 (tpt) REVERT: K 75 LYS cc_start: 0.9275 (mtpp) cc_final: 0.9063 (mtmt) REVERT: P 71 LYS cc_start: 0.6876 (ttpt) cc_final: 0.6315 (pttm) REVERT: R 92 ASP cc_start: 0.7298 (t0) cc_final: 0.7091 (t70) REVERT: R 95 LYS cc_start: 0.8504 (mmmm) cc_final: 0.8130 (mmmm) outliers start: 34 outliers final: 20 residues processed: 311 average time/residue: 0.1695 time to fit residues: 78.8869 Evaluate side-chains 280 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 258 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 91 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 184 optimal weight: 0.9990 chunk 238 optimal weight: 3.9990 chunk 146 optimal weight: 0.0370 chunk 81 optimal weight: 0.2980 chunk 198 optimal weight: 0.9990 chunk 181 optimal weight: 0.2980 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 overall best weight: 0.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 37 GLN N 17 GLN P 82BASN R 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.096528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.068881 restraints weight = 61727.193| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.95 r_work: 0.3140 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25575 Z= 0.113 Angle : 0.572 11.121 34893 Z= 0.289 Chirality : 0.045 0.372 4092 Planarity : 0.004 0.051 4281 Dihedral : 6.015 53.266 4953 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.36 % Allowed : 8.68 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.15), residues: 2991 helix: 2.64 (0.27), residues: 399 sheet: 1.40 (0.17), residues: 846 loop : -0.25 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 66 TYR 0.020 0.001 TYR K 27 PHE 0.009 0.001 PHE F 176 TRP 0.010 0.001 TRP A 479 HIS 0.006 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00252 (25449) covalent geometry : angle 0.55083 (34560) SS BOND : bond 0.00315 ( 45) SS BOND : angle 0.70490 ( 90) hydrogen bonds : bond 0.03569 ( 957) hydrogen bonds : angle 4.96466 ( 2727) link_ALPHA1-3 : bond 0.01197 ( 6) link_ALPHA1-3 : angle 2.65033 ( 18) link_BETA1-4 : bond 0.00443 ( 15) link_BETA1-4 : angle 1.87767 ( 45) link_NAG-ASN : bond 0.00324 ( 60) link_NAG-ASN : angle 1.84068 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8685 (ttt180) REVERT: A 328 MET cc_start: 0.8673 (tpp) cc_final: 0.8432 (ttt) REVERT: D 27 ASP cc_start: 0.8307 (p0) cc_final: 0.8096 (p0) REVERT: D 79 GLN cc_start: 0.7023 (mp10) cc_final: 0.6811 (mp10) REVERT: H 55 ASP cc_start: 0.7744 (t0) cc_final: 0.7387 (t0) REVERT: H 64 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7817 (mttm) REVERT: H 66 ARG cc_start: 0.8316 (mtp-110) cc_final: 0.7541 (ttm110) REVERT: H 82 MET cc_start: 0.6674 (ppp) cc_final: 0.6353 (ppp) REVERT: L 54 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7075 (mmm-85) REVERT: L 95 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8205 (mmmm) REVERT: M 42 LYS cc_start: 0.7688 (pttm) cc_final: 0.7465 (pttp) REVERT: M 79 GLN cc_start: 0.6993 (mp10) cc_final: 0.6601 (mp10) REVERT: O 57 LYS cc_start: 0.8441 (mtpp) cc_final: 0.8065 (mtpp) REVERT: O 64 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7585 (mttm) REVERT: Q 95 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8231 (mmmt) REVERT: F 111 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8827 (mt) REVERT: N 17 GLN cc_start: 0.8047 (mm110) cc_final: 0.7397 (pt0) REVERT: P 71 LYS cc_start: 0.6874 (ttpt) cc_final: 0.6325 (pttm) REVERT: P 82 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8378 (t0) REVERT: R 95 LYS cc_start: 0.8537 (mmmm) cc_final: 0.8168 (mmmm) outliers start: 36 outliers final: 21 residues processed: 310 average time/residue: 0.1663 time to fit residues: 77.7695 Evaluate side-chains 279 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 255 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 82 ASN Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 28 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 18 optimal weight: 0.6980 chunk 194 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 294 optimal weight: 0.0870 chunk 97 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.097110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.069886 restraints weight = 62340.291| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.16 r_work: 0.3130 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25575 Z= 0.122 Angle : 0.582 11.190 34893 Z= 0.293 Chirality : 0.045 0.301 4092 Planarity : 0.004 0.046 4281 Dihedral : 5.845 53.483 4953 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.17 % Allowed : 9.29 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.15), residues: 2991 helix: 2.64 (0.27), residues: 399 sheet: 1.39 (0.17), residues: 846 loop : -0.26 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 66 TYR 0.015 0.001 TYR H 100K PHE 0.020 0.001 PHE L 62 TRP 0.011 0.001 TRP E 69 HIS 0.005 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00276 (25449) covalent geometry : angle 0.56199 (34560) SS BOND : bond 0.00344 ( 45) SS BOND : angle 0.70546 ( 90) hydrogen bonds : bond 0.03545 ( 957) hydrogen bonds : angle 4.90884 ( 2727) link_ALPHA1-3 : bond 0.01131 ( 6) link_ALPHA1-3 : angle 2.51407 ( 18) link_BETA1-4 : bond 0.00434 ( 15) link_BETA1-4 : angle 1.87157 ( 45) link_NAG-ASN : bond 0.00355 ( 60) link_NAG-ASN : angle 1.82577 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8716 (ttt180) REVERT: A 328 MET cc_start: 0.8690 (tpp) cc_final: 0.8435 (ttt) REVERT: C 75 LYS cc_start: 0.9169 (mtpt) cc_final: 0.8915 (mttp) REVERT: D 79 GLN cc_start: 0.6999 (mp10) cc_final: 0.6776 (mp10) REVERT: H 55 ASP cc_start: 0.7755 (t0) cc_final: 0.7381 (t0) REVERT: H 64 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7830 (mttm) REVERT: L 54 ARG cc_start: 0.7623 (ttm110) cc_final: 0.7129 (mmm-85) REVERT: M 42 LYS cc_start: 0.7729 (pttm) cc_final: 0.7524 (pttp) REVERT: M 47 MET cc_start: 0.8983 (mmm) cc_final: 0.8534 (mmm) REVERT: M 79 GLN cc_start: 0.7010 (mp10) cc_final: 0.6631 (mp10) REVERT: O 57 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8259 (mtpp) REVERT: O 64 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7648 (mttm) REVERT: Q 2 TYR cc_start: 0.4790 (t80) cc_final: 0.4467 (t80) REVERT: Q 20 ARG cc_start: 0.8140 (mmt90) cc_final: 0.7919 (mmt90) REVERT: Q 54 ARG cc_start: 0.7297 (ttm110) cc_final: 0.6748 (mmm-85) REVERT: Q 95 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8192 (mmmt) REVERT: P 43 LYS cc_start: 0.7422 (ptmm) cc_final: 0.7148 (ptmm) REVERT: P 66 ARG cc_start: 0.8048 (mtp-110) cc_final: 0.7393 (mtp85) REVERT: P 71 LYS cc_start: 0.6860 (ttpt) cc_final: 0.6313 (pttm) REVERT: R 54 ARG cc_start: 0.7314 (ttm110) cc_final: 0.6693 (mmm-85) outliers start: 31 outliers final: 26 residues processed: 293 average time/residue: 0.1674 time to fit residues: 73.2166 Evaluate side-chains 282 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 85 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 19 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 265 optimal weight: 0.0670 chunk 113 optimal weight: 2.9990 chunk 81 optimal weight: 0.0470 chunk 82 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82BASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.095594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.068142 restraints weight = 62421.707| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.16 r_work: 0.3092 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25575 Z= 0.168 Angle : 0.611 9.751 34893 Z= 0.307 Chirality : 0.045 0.270 4092 Planarity : 0.004 0.045 4281 Dihedral : 5.904 54.790 4953 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.32 % Allowed : 9.21 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.15), residues: 2991 helix: 2.61 (0.27), residues: 393 sheet: 1.35 (0.17), residues: 852 loop : -0.34 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 66 TYR 0.021 0.002 TYR R 95B PHE 0.012 0.001 PHE J 29 TRP 0.012 0.001 TRP A 479 HIS 0.005 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00393 (25449) covalent geometry : angle 0.59100 (34560) SS BOND : bond 0.00391 ( 45) SS BOND : angle 0.76976 ( 90) hydrogen bonds : bond 0.03896 ( 957) hydrogen bonds : angle 4.98060 ( 2727) link_ALPHA1-3 : bond 0.01079 ( 6) link_ALPHA1-3 : angle 2.36247 ( 18) link_BETA1-4 : bond 0.00412 ( 15) link_BETA1-4 : angle 1.96702 ( 45) link_NAG-ASN : bond 0.00342 ( 60) link_NAG-ASN : angle 1.88222 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8764 (ttt180) REVERT: C 75 LYS cc_start: 0.9159 (mtpt) cc_final: 0.8895 (ptpp) REVERT: C 82 MET cc_start: 0.8391 (mtm) cc_final: 0.8036 (mtm) REVERT: D 79 GLN cc_start: 0.7105 (mp10) cc_final: 0.6859 (mp10) REVERT: H 55 ASP cc_start: 0.7841 (t0) cc_final: 0.7532 (t0) REVERT: H 64 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7836 (mttm) REVERT: M 47 MET cc_start: 0.8989 (mmm) cc_final: 0.8604 (mmm) REVERT: M 79 GLN cc_start: 0.7176 (mp10) cc_final: 0.6794 (mp10) REVERT: O 57 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8126 (mtpp) REVERT: O 64 LYS cc_start: 0.7906 (mtpp) cc_final: 0.7615 (mttm) REVERT: O 66 ARG cc_start: 0.8067 (mtp-110) cc_final: 0.7464 (ttm110) REVERT: O 90 TYR cc_start: 0.6640 (m-10) cc_final: 0.6427 (m-10) REVERT: Q 20 ARG cc_start: 0.8175 (mmt90) cc_final: 0.7956 (mmt90) REVERT: Q 85 ASP cc_start: 0.7638 (m-30) cc_final: 0.7294 (m-30) REVERT: Q 95 LYS cc_start: 0.8428 (mmmm) cc_final: 0.8208 (mmmt) REVERT: N 17 GLN cc_start: 0.8002 (mp10) cc_final: 0.7290 (pt0) REVERT: R 54 ARG cc_start: 0.7197 (ttm110) cc_final: 0.6595 (mmm-85) outliers start: 35 outliers final: 28 residues processed: 293 average time/residue: 0.1617 time to fit residues: 70.7047 Evaluate side-chains 279 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 83 ASP Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 28 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 248 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82BASN M 17 GLN O 82BASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.095208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.067869 restraints weight = 61849.849| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.13 r_work: 0.3097 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25575 Z= 0.145 Angle : 0.602 9.723 34893 Z= 0.303 Chirality : 0.044 0.278 4092 Planarity : 0.004 0.053 4281 Dihedral : 5.801 54.584 4953 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.28 % Allowed : 9.32 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.15), residues: 2991 helix: 2.55 (0.27), residues: 399 sheet: 1.36 (0.18), residues: 855 loop : -0.39 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 66 TYR 0.019 0.001 TYR R 95B PHE 0.009 0.001 PHE L 62 TRP 0.020 0.001 TRP E 69 HIS 0.005 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00337 (25449) covalent geometry : angle 0.58225 (34560) SS BOND : bond 0.00394 ( 45) SS BOND : angle 0.75686 ( 90) hydrogen bonds : bond 0.03692 ( 957) hydrogen bonds : angle 4.96275 ( 2727) link_ALPHA1-3 : bond 0.01017 ( 6) link_ALPHA1-3 : angle 2.28975 ( 18) link_BETA1-4 : bond 0.00401 ( 15) link_BETA1-4 : angle 1.94134 ( 45) link_NAG-ASN : bond 0.00327 ( 60) link_NAG-ASN : angle 1.86248 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 256 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8726 (ttt180) REVERT: C 75 LYS cc_start: 0.9158 (mtpt) cc_final: 0.8909 (ptpp) REVERT: C 82 MET cc_start: 0.8380 (mtm) cc_final: 0.8075 (mtm) REVERT: D 27 ASP cc_start: 0.8265 (p0) cc_final: 0.7986 (p0) REVERT: D 79 GLN cc_start: 0.7093 (mp10) cc_final: 0.6812 (mp10) REVERT: H 55 ASP cc_start: 0.7907 (t0) cc_final: 0.7625 (t0) REVERT: H 64 LYS cc_start: 0.8218 (mtpp) cc_final: 0.8001 (mttp) REVERT: H 82 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8104 (t0) REVERT: M 47 MET cc_start: 0.8955 (mmm) cc_final: 0.8621 (mmm) REVERT: M 79 GLN cc_start: 0.7175 (mp10) cc_final: 0.6791 (mp10) REVERT: O 57 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8312 (mtpp) REVERT: O 64 LYS cc_start: 0.7907 (mtpp) cc_final: 0.7612 (mttm) REVERT: O 82 MET cc_start: 0.6754 (tmm) cc_final: 0.6289 (tmm) REVERT: Q 20 ARG cc_start: 0.8116 (mmt90) cc_final: 0.7898 (mmt90) REVERT: Q 95 LYS cc_start: 0.8444 (mmmm) cc_final: 0.8219 (mmmt) REVERT: N 17 GLN cc_start: 0.8117 (mp10) cc_final: 0.7478 (pt0) REVERT: P 66 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7317 (mtp85) REVERT: R 54 ARG cc_start: 0.7279 (ttm110) cc_final: 0.6824 (mmm-85) outliers start: 34 outliers final: 24 residues processed: 280 average time/residue: 0.1627 time to fit residues: 68.6453 Evaluate side-chains 272 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 285 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 272 optimal weight: 0.9990 chunk 106 optimal weight: 0.0980 chunk 62 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 6 GLN ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.095064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.068371 restraints weight = 63002.064| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.26 r_work: 0.3075 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25575 Z= 0.190 Angle : 0.638 9.851 34893 Z= 0.320 Chirality : 0.045 0.261 4092 Planarity : 0.004 0.074 4281 Dihedral : 5.925 55.130 4953 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.17 % Allowed : 9.51 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.15), residues: 2991 helix: 2.52 (0.27), residues: 393 sheet: 1.31 (0.18), residues: 855 loop : -0.46 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 66 TYR 0.020 0.002 TYR K 27 PHE 0.013 0.001 PHE J 29 TRP 0.017 0.001 TRP E 69 HIS 0.005 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00449 (25449) covalent geometry : angle 0.61765 (34560) SS BOND : bond 0.00437 ( 45) SS BOND : angle 0.83840 ( 90) hydrogen bonds : bond 0.03992 ( 957) hydrogen bonds : angle 5.00997 ( 2727) link_ALPHA1-3 : bond 0.00965 ( 6) link_ALPHA1-3 : angle 2.24576 ( 18) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 2.03158 ( 45) link_NAG-ASN : bond 0.00497 ( 60) link_NAG-ASN : angle 1.96543 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8693 (ttt180) REVERT: C 75 LYS cc_start: 0.9099 (mtpt) cc_final: 0.8854 (ptpp) REVERT: C 82 MET cc_start: 0.8396 (mtm) cc_final: 0.8123 (mtm) REVERT: D 27 ASP cc_start: 0.8235 (p0) cc_final: 0.7987 (p0) REVERT: D 42 LYS cc_start: 0.7405 (pttm) cc_final: 0.6810 (tptp) REVERT: D 79 GLN cc_start: 0.6992 (mp10) cc_final: 0.6737 (mp10) REVERT: H 55 ASP cc_start: 0.7973 (t0) cc_final: 0.7687 (t0) REVERT: H 64 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7998 (mttp) REVERT: J 82 MET cc_start: 0.8445 (mtt) cc_final: 0.8113 (mmt) REVERT: M 47 MET cc_start: 0.8895 (mmm) cc_final: 0.8636 (mmm) REVERT: M 79 GLN cc_start: 0.7159 (mp10) cc_final: 0.6769 (mp10) REVERT: O 57 LYS cc_start: 0.8528 (mtpp) cc_final: 0.8266 (mtpp) REVERT: O 64 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7656 (mttm) REVERT: O 90 TYR cc_start: 0.6668 (m-10) cc_final: 0.5902 (m-10) REVERT: Q 20 ARG cc_start: 0.8095 (mmt90) cc_final: 0.7884 (mmt90) REVERT: Q 54 ARG cc_start: 0.7068 (ttm110) cc_final: 0.6744 (tpp80) REVERT: N 17 GLN cc_start: 0.8182 (mp10) cc_final: 0.7455 (pt0) REVERT: N 47 MET cc_start: 0.8794 (mmm) cc_final: 0.8339 (mmm) REVERT: P 34 MET cc_start: 0.7997 (mtm) cc_final: 0.7609 (mtm) REVERT: R 54 ARG cc_start: 0.7249 (ttm110) cc_final: 0.6793 (mmm-85) outliers start: 31 outliers final: 26 residues processed: 277 average time/residue: 0.1666 time to fit residues: 69.5658 Evaluate side-chains 273 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 54 ASN Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 174 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 220 optimal weight: 0.5980 chunk 196 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN H 82BASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.095508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.069225 restraints weight = 62491.050| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.17 r_work: 0.3087 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25575 Z= 0.151 Angle : 0.621 10.903 34893 Z= 0.311 Chirality : 0.045 0.268 4092 Planarity : 0.004 0.053 4281 Dihedral : 5.843 54.966 4953 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.13 % Allowed : 9.44 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.15), residues: 2991 helix: 2.60 (0.27), residues: 393 sheet: 1.28 (0.18), residues: 861 loop : -0.48 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 66 TYR 0.015 0.001 TYR R 95B PHE 0.010 0.001 PHE D 98 TRP 0.015 0.001 TRP E 69 HIS 0.005 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00353 (25449) covalent geometry : angle 0.60022 (34560) SS BOND : bond 0.00402 ( 45) SS BOND : angle 0.78714 ( 90) hydrogen bonds : bond 0.03782 ( 957) hydrogen bonds : angle 4.98319 ( 2727) link_ALPHA1-3 : bond 0.00936 ( 6) link_ALPHA1-3 : angle 2.23659 ( 18) link_BETA1-4 : bond 0.00371 ( 15) link_BETA1-4 : angle 1.98226 ( 45) link_NAG-ASN : bond 0.00374 ( 60) link_NAG-ASN : angle 1.96221 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5158.63 seconds wall clock time: 89 minutes 19.21 seconds (5359.21 seconds total)