Starting phenix.real_space_refine on Mon Aug 25 02:41:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t49_41024/08_2025/8t49_41024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t49_41024/08_2025/8t49_41024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t49_41024/08_2025/8t49_41024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t49_41024/08_2025/8t49_41024.map" model { file = "/net/cci-nas-00/data/ceres_data/8t49_41024/08_2025/8t49_41024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t49_41024/08_2025/8t49_41024.cif" } resolution = 3.2 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 15642 2.51 5 N 4140 2.21 5 O 5013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 24939 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 4 Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} 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: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 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, O, P, Q, R, J, K, M, N, G, I, W, a, X, b, Y, c, Z, d Time building chain proxies: 3.84, per 1000 atoms: 0.15 Number of scatterers: 24939 At special positions: 0 Unit cell: (146.05, 149.5, 172.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 5013 8.00 N 4140 7.00 C 15642 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 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 E 54 " - pdb=" SG CYS E 74 " distance=2.05 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 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 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 ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN W 4 " - " MAN W 5 " " MAN a 4 " - " MAN a 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " " BMA c 3 " - " MAN c 4 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA W 3 " - " MAN W 6 " " BMA a 3 " - " MAN a 6 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG 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 a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 601 " - " ASN A 301 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 386 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 289 " " NAG A 612 " - " ASN A 241 " " NAG A 613 " - " ASN A 355 " " NAG 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 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 386 " " NAG E 610 " - " ASN E 448 " " NAG E 611 " - " ASN E 289 " " NAG E 612 " - " ASN E 241 " " NAG E 613 " - " ASN E 355 " " NAG E 614 " - " ASN E 392 " " NAG F 601 " - " ASN F 301 " " NAG F 602 " - " ASN F 88 " " NAG F 603 " - " ASN F 160 " " NAG F 604 " - " ASN F 197 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 276 " " NAG F 607 " - " ASN F 295 " " NAG F 608 " - " ASN F 339 " " NAG F 609 " - " ASN F 386 " " NAG F 610 " - " ASN F 448 " " NAG F 611 " - " ASN F 289 " " NAG F 612 " - " ASN F 241 " " NAG F 613 " - " ASN F 355 " " NAG 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 156 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN H 60 " " NAG W 1 " - " ASN E 332 " " NAG X 1 " - " ASN E 156 " " NAG Y 1 " - " ASN E 262 " " NAG Z 1 " - " ASN O 60 " " NAG a 1 " - " ASN F 332 " " NAG b 1 " - " ASN F 156 " " NAG c 1 " - " ASN F 262 " " NAG d 1 " - " ASN P 60 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 831.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 45 sheets defined 20.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.030A 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 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.247A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.227A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100F Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.652A pdb=" N GLU L 29 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 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: 4.085A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.441A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.585A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.667A 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 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.030A 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 387 through 391 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.247A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 removed outlier: 4.227A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100B through 100F Processing helix chain 'Q' and resid 26 through 30 removed outlier: 3.652A pdb=" N GLU Q 29 " --> pdb=" O ASP Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 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: 4.084A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 528 removed outlier: 4.441A pdb=" N GLY G 527 " --> pdb=" O GLY G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.585A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.668A 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 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 354 removed outlier: 4.030A 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 387 through 391 Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.247A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 484 removed outlier: 4.227A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 65 No H-bonds generated for 'chain 'P' and resid 63 through 65' Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100B through 100F Processing helix chain 'R' and resid 26 through 30 removed outlier: 3.652A pdb=" N GLU R 29 " --> pdb=" O ASP R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 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: 4.085A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.441A pdb=" N GLY I 527 " --> pdb=" O GLY I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 543 removed outlier: 3.585A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN I 543 " --> pdb=" O VAL I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 596 Processing helix chain 'I' and resid 618 through 626 removed outlier: 3.667A 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 sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.360A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.446A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 7.059A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 469 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.762A pdb=" N TRP H 35 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 97 through 98 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.807A pdb=" N GLY C 16 " --> pdb=" O SER C 82B" (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 34 through 39 removed outlier: 5.805A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100H through 103 Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'D' and resid 33 through 38 removed outlier: 6.268A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 48 current: chain 'D' and resid 95A through 98 Processing sheet with id=AB7, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.361A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'E' and resid 172 through 177 Processing sheet with id=AC3, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.446A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 7.059A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 469 Processing sheet with id=AC5, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'O' and resid 34 through 39 removed outlier: 6.762A pdb=" N TRP O 35 " --> pdb=" O ASN O 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN O 50 " --> pdb=" O TRP O 35 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100H through 103 Processing sheet with id=AC7, first strand: chain 'Q' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'Q' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 9 through 12 current: chain 'Q' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 45 through 48 current: chain 'Q' and resid 97 through 98 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.807A pdb=" N GLY J 16 " --> pdb=" O SER J 82B" (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 34 through 39 removed outlier: 5.804A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AD2, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'M' and resid 33 through 38 removed outlier: 6.268A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 95A through 98 Processing sheet with id=AD4, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.360A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'F' and resid 172 through 177 Processing sheet with id=AD9, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.446A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 312 removed outlier: 7.059A pdb=" N ASN F 301 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 315 through 323 current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 465 through 469 Processing sheet with id=AE2, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'P' and resid 34 through 39 removed outlier: 6.762A pdb=" N TRP P 35 " --> pdb=" O ASN P 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN P 50 " --> pdb=" O TRP P 35 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 100H through 103 Processing sheet with id=AE4, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'R' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 9 through 12 current: chain 'R' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 45 through 48 current: chain 'R' and resid 97 through 98 No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.808A pdb=" N GLY K 16 " --> pdb=" O SER K 82B" (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 34 through 39 removed outlier: 5.804A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100H through 103 Processing sheet with id=AE8, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'N' and resid 33 through 38 removed outlier: 6.268A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 95A through 98 720 hydrogen bonds defined for protein. 1782 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: 4.52 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7833 1.35 - 1.47: 6705 1.47 - 1.60: 10716 1.60 - 1.72: 0 1.72 - 1.85: 198 Bond restraints: 25452 Sorted by residual: bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.59e+00 bond pdb=" C5 MAN S 5 " pdb=" O5 MAN S 5 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" C5 MAN W 5 " pdb=" O5 MAN W 5 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" C1 NAG d 2 " pdb=" O5 NAG d 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.49e+00 ... (remaining 25447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 32477 2.23 - 4.47: 1773 4.47 - 6.70: 265 6.70 - 8.93: 27 8.93 - 11.16: 12 Bond angle restraints: 34554 Sorted by residual: angle pdb=" N LEU Q 97 " pdb=" CA LEU Q 97 " pdb=" C LEU Q 97 " ideal model delta sigma weight residual 107.93 96.77 11.16 1.65e+00 3.67e-01 4.58e+01 angle pdb=" N LEU L 97 " pdb=" CA LEU L 97 " pdb=" C LEU L 97 " ideal model delta sigma weight residual 107.93 96.78 11.15 1.65e+00 3.67e-01 4.57e+01 angle pdb=" N LEU R 97 " pdb=" CA LEU R 97 " pdb=" C LEU R 97 " ideal model delta sigma weight residual 107.93 96.79 11.14 1.65e+00 3.67e-01 4.56e+01 angle pdb=" CA TRP H 47 " pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 113.60 122.87 -9.27 1.90e+00 2.77e-01 2.38e+01 angle pdb=" CA TRP O 47 " pdb=" CB TRP O 47 " pdb=" CG TRP O 47 " ideal model delta sigma weight residual 113.60 122.87 -9.27 1.90e+00 2.77e-01 2.38e+01 ... (remaining 34549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 15536 21.50 - 42.99: 541 42.99 - 64.49: 141 64.49 - 85.99: 81 85.99 - 107.49: 39 Dihedral angle restraints: 16338 sinusoidal: 7644 harmonic: 8694 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.38 50.38 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS F 378 " pdb=" SG CYS F 378 " pdb=" SG CYS F 445 " pdb=" CB CYS F 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.37 50.37 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.36 50.36 1 1.00e+01 1.00e-02 3.48e+01 ... (remaining 16335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3889 0.122 - 0.245: 231 0.245 - 0.367: 14 0.367 - 0.489: 0 0.489 - 0.611: 3 Chirality restraints: 4137 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN O 60 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.35e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN H 60 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN P 60 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.28e+00 ... (remaining 4134 not shown) Planarity restraints: 4323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 476 " 0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C ARG A 476 " -0.069 2.00e-02 2.50e+03 pdb=" O ARG A 476 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP A 477 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 476 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C ARG E 476 " 0.069 2.00e-02 2.50e+03 pdb=" O ARG E 476 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP E 477 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 476 " -0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C ARG F 476 " 0.069 2.00e-02 2.50e+03 pdb=" O ARG F 476 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP F 477 " -0.023 2.00e-02 2.50e+03 ... (remaining 4320 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1542 2.73 - 3.27: 23524 3.27 - 3.81: 40256 3.81 - 4.36: 50950 4.36 - 4.90: 84671 Nonbonded interactions: 200943 Sorted by model distance: nonbonded pdb=" OD1 ASP F 477 " pdb=" NH1 ARG F 480 " model vdw 2.187 3.120 nonbonded pdb=" OD1 ASP E 477 " pdb=" NH1 ARG E 480 " model vdw 2.187 3.120 nonbonded pdb=" OD1 ASP A 477 " pdb=" NH1 ARG A 480 " model vdw 2.187 3.120 nonbonded pdb=" O SER C 99 " pdb=" OG SER C 99 " model vdw 2.267 3.040 nonbonded pdb=" O SER J 99 " pdb=" OG SER J 99 " model vdw 2.267 3.040 ... (remaining 200938 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } 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 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'S' selection = chain 'W' selection = chain 'a' } ncs_group { reference = chain 'T' selection = chain 'X' selection = chain 'b' } ncs_group { reference = chain 'U' selection = chain 'Y' selection = chain 'c' } ncs_group { reference = chain 'V' selection = chain 'Z' selection = chain 'd' } 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: 6.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.330 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 0.073 25593 Z= 0.318 Angle : 1.196 11.163 34932 Z= 0.654 Chirality : 0.066 0.611 4137 Planarity : 0.007 0.074 4260 Dihedral : 14.060 107.487 10641 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.57 % Allowed : 5.25 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.03 (0.15), residues: 2979 helix: 0.71 (0.24), residues: 420 sheet: 1.18 (0.17), residues: 861 loop : 0.53 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG C 66 TYR 0.018 0.003 TYR D 36 PHE 0.023 0.003 PHE E 383 TRP 0.040 0.004 TRP P 47 HIS 0.006 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00714 (25452) covalent geometry : angle 1.16423 (34554) SS BOND : bond 0.00823 ( 45) SS BOND : angle 2.36853 ( 90) hydrogen bonds : bond 0.15447 ( 720) hydrogen bonds : angle 6.54430 ( 1782) link_ALPHA1-2 : bond 0.00599 ( 3) link_ALPHA1-2 : angle 5.93316 ( 9) link_ALPHA1-3 : bond 0.00195 ( 6) link_ALPHA1-3 : angle 2.75980 ( 18) link_ALPHA1-6 : bond 0.00746 ( 3) link_ALPHA1-6 : angle 0.79566 ( 9) link_BETA1-4 : bond 0.00576 ( 21) link_BETA1-4 : angle 2.89638 ( 63) link_NAG-ASN : bond 0.00777 ( 63) link_NAG-ASN : angle 2.94063 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 461 time to evaluate : 0.599 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 426 MET cc_start: 0.8906 (mtp) cc_final: 0.8621 (mtp) REVERT: L 21 MET cc_start: 0.5719 (mtm) cc_final: 0.5417 (mtm) REVERT: L 24 GLN cc_start: 0.7620 (tt0) cc_final: 0.7208 (tm-30) REVERT: L 58 ILE cc_start: 0.7348 (mm) cc_final: 0.6972 (pt) REVERT: L 75 ILE cc_start: 0.5727 (mt) cc_final: 0.5478 (tt) REVERT: L 86 TYR cc_start: 0.8223 (m-80) cc_final: 0.7373 (m-80) REVERT: C 86 ASP cc_start: 0.7786 (m-30) cc_final: 0.7484 (m-30) REVERT: C 94 THR cc_start: 0.8824 (m) cc_final: 0.8466 (p) REVERT: D 69 ASN cc_start: 0.8116 (m-40) cc_final: 0.7690 (m-40) REVERT: E 104 MET cc_start: 0.9467 (ttt) cc_final: 0.9246 (ttt) REVERT: E 426 MET cc_start: 0.8808 (mtp) cc_final: 0.8509 (mmm) REVERT: E 475 MET cc_start: 0.8550 (tpp) cc_final: 0.8341 (mmp) REVERT: Q 21 MET cc_start: 0.5762 (mtm) cc_final: 0.5492 (mtm) REVERT: Q 24 GLN cc_start: 0.7726 (tt0) cc_final: 0.7397 (tm-30) REVERT: Q 75 ILE cc_start: 0.5618 (mt) cc_final: 0.5171 (tt) REVERT: J 75 LYS cc_start: 0.9148 (mtpp) cc_final: 0.8942 (mtpt) REVERT: M 6 GLN cc_start: 0.7692 (mt0) cc_final: 0.7340 (mt0) REVERT: M 85 ASP cc_start: 0.8274 (m-30) cc_final: 0.7603 (m-30) REVERT: G 535 MET cc_start: 0.8778 (mtt) cc_final: 0.8404 (mtm) REVERT: G 632 ASP cc_start: 0.8589 (t0) cc_final: 0.8292 (t0) REVERT: F 150 MET cc_start: 0.9018 (mmm) cc_final: 0.8719 (mmt) REVERT: F 426 MET cc_start: 0.8916 (mtp) cc_final: 0.8680 (mtp) REVERT: F 475 MET cc_start: 0.8702 (tpp) cc_final: 0.8241 (mmt) REVERT: R 21 MET cc_start: 0.6214 (mtm) cc_final: 0.5993 (mtt) REVERT: R 24 GLN cc_start: 0.7621 (tt0) cc_final: 0.7332 (tm-30) REVERT: N 74 THR cc_start: 0.7821 (m) cc_final: 0.7429 (p) REVERT: N 85 ASP cc_start: 0.8264 (m-30) cc_final: 0.7834 (m-30) REVERT: I 535 MET cc_start: 0.8654 (mtt) cc_final: 0.8408 (mtp) REVERT: I 657 GLU cc_start: 0.8242 (tt0) cc_final: 0.8007 (tt0) outliers start: 15 outliers final: 3 residues processed: 470 average time/residue: 0.1773 time to fit residues: 123.8346 Evaluate side-chains 335 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 332 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN 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: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 195 ASN L 51 ASN L 52 ASN C 52 ASN D 95 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 GLN J 52 ASN F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 HIS N 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.110948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.081238 restraints weight = 47666.654| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.66 r_work: 0.3049 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25593 Z= 0.146 Angle : 0.657 9.018 34932 Z= 0.336 Chirality : 0.047 0.341 4137 Planarity : 0.004 0.033 4260 Dihedral : 10.363 86.210 5238 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.67 % Allowed : 6.93 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.97 (0.15), residues: 2979 helix: 1.74 (0.26), residues: 441 sheet: 1.12 (0.17), residues: 870 loop : 0.15 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 61 TYR 0.016 0.002 TYR J 100G PHE 0.012 0.002 PHE E 176 TRP 0.031 0.002 TRP O 47 HIS 0.011 0.001 HIS L 95B Details of bonding type rmsd covalent geometry : bond 0.00323 (25452) covalent geometry : angle 0.61790 (34554) SS BOND : bond 0.00317 ( 45) SS BOND : angle 0.92284 ( 90) hydrogen bonds : bond 0.05215 ( 720) hydrogen bonds : angle 5.06071 ( 1782) link_ALPHA1-2 : bond 0.00960 ( 3) link_ALPHA1-2 : angle 4.28322 ( 9) link_ALPHA1-3 : bond 0.00809 ( 6) link_ALPHA1-3 : angle 1.92048 ( 18) link_ALPHA1-6 : bond 0.00386 ( 3) link_ALPHA1-6 : angle 1.50681 ( 9) link_BETA1-4 : bond 0.00630 ( 21) link_BETA1-4 : angle 2.07022 ( 63) link_NAG-ASN : bond 0.00554 ( 63) link_NAG-ASN : angle 2.62301 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 370 time to evaluate : 0.883 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: H 59 TYR cc_start: 0.6757 (m-10) cc_final: 0.6483 (m-10) REVERT: L 24 GLN cc_start: 0.7494 (tt0) cc_final: 0.7293 (tt0) REVERT: C 86 ASP cc_start: 0.7802 (m-30) cc_final: 0.7460 (m-30) REVERT: D 79 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: B 621 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8232 (mt-10) REVERT: O 3 GLN cc_start: 0.5847 (mp10) cc_final: 0.5582 (mp10) REVERT: O 66 ARG cc_start: 0.5096 (ptt90) cc_final: 0.4804 (ptt90) REVERT: O 100 ASP cc_start: 0.8004 (t0) cc_final: 0.7783 (t0) REVERT: Q 24 GLN cc_start: 0.7547 (tt0) cc_final: 0.7231 (tm-30) REVERT: Q 86 TYR cc_start: 0.8005 (m-80) cc_final: 0.7501 (m-10) REVERT: M 79 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7259 (mp10) REVERT: M 85 ASP cc_start: 0.8064 (m-30) cc_final: 0.7712 (m-30) REVERT: F 150 MET cc_start: 0.9165 (mmm) cc_final: 0.8914 (mmt) REVERT: F 426 MET cc_start: 0.8781 (mtp) cc_final: 0.8426 (mmm) REVERT: P 100 ASP cc_start: 0.7834 (t0) cc_final: 0.7596 (t0) REVERT: R 24 GLN cc_start: 0.7494 (tt0) cc_final: 0.7196 (tm-30) REVERT: R 58 ILE cc_start: 0.7232 (mm) cc_final: 0.6972 (mm) REVERT: R 61 ARG cc_start: 0.8658 (mtm-85) cc_final: 0.8422 (ttm110) REVERT: R 86 TYR cc_start: 0.8129 (m-80) cc_final: 0.7601 (m-10) REVERT: K 13 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7444 (mm110) REVERT: N 79 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.6940 (mp10) REVERT: N 85 ASP cc_start: 0.8192 (m-30) cc_final: 0.7985 (m-30) outliers start: 44 outliers final: 26 residues processed: 398 average time/residue: 0.1914 time to fit residues: 115.5119 Evaluate side-chains 348 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 319 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 39 optimal weight: 5.9990 chunk 171 optimal weight: 0.0870 chunk 292 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 195 ASN A 374 HIS L 17 HIS C 52 ASN D 95 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 374 HIS Q 17 HIS Q 51 ASN Q 89 ASN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 103 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 ASN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.105191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.073597 restraints weight = 47836.841| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.61 r_work: 0.2907 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 25593 Z= 0.296 Angle : 0.739 9.471 34932 Z= 0.373 Chirality : 0.050 0.275 4137 Planarity : 0.005 0.043 4260 Dihedral : 9.182 86.981 5232 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.36 % Allowed : 7.42 % Favored : 90.22 % 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: 0.39 (0.15), residues: 2979 helix: 1.35 (0.26), residues: 423 sheet: 0.65 (0.17), residues: 870 loop : -0.19 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 503 TYR 0.022 0.002 TYR J 27 PHE 0.024 0.003 PHE K 29 TRP 0.023 0.002 TRP P 47 HIS 0.008 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00714 (25452) covalent geometry : angle 0.70399 (34554) SS BOND : bond 0.00735 ( 45) SS BOND : angle 1.17388 ( 90) hydrogen bonds : bond 0.05782 ( 720) hydrogen bonds : angle 4.88406 ( 1782) link_ALPHA1-2 : bond 0.00679 ( 3) link_ALPHA1-2 : angle 3.99173 ( 9) link_ALPHA1-3 : bond 0.00597 ( 6) link_ALPHA1-3 : angle 1.55823 ( 18) link_ALPHA1-6 : bond 0.00109 ( 3) link_ALPHA1-6 : angle 1.75797 ( 9) link_BETA1-4 : bond 0.00614 ( 21) link_BETA1-4 : angle 2.10576 ( 63) link_NAG-ASN : bond 0.00646 ( 63) link_NAG-ASN : angle 2.64782 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 328 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 59 TYR cc_start: 0.7079 (m-10) cc_final: 0.6848 (m-10) REVERT: H 100 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7613 (mtpt) REVERT: L 24 GLN cc_start: 0.7709 (tt0) cc_final: 0.7446 (tt0) REVERT: C 43 LYS cc_start: 0.7214 (mppt) cc_final: 0.6996 (mttp) REVERT: C 86 ASP cc_start: 0.7801 (m-30) cc_final: 0.7438 (m-30) REVERT: D 94 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7789 (mtt180) REVERT: O 77 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: O 101 ASP cc_start: 0.7716 (t0) cc_final: 0.7441 (t70) REVERT: Q 24 GLN cc_start: 0.7562 (tt0) cc_final: 0.7190 (tm-30) REVERT: Q 51 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8797 (t0) REVERT: Q 61 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8189 (ttm110) REVERT: Q 86 TYR cc_start: 0.8042 (m-80) cc_final: 0.7621 (m-80) REVERT: F 95 MET cc_start: 0.9296 (ptt) cc_final: 0.9050 (ptt) REVERT: F 241 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.7241 (m-40) REVERT: R 24 GLN cc_start: 0.7581 (tt0) cc_final: 0.7113 (tm-30) REVERT: R 61 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.8379 (ttm110) REVERT: K 13 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7404 (mm110) outliers start: 62 outliers final: 36 residues processed: 359 average time/residue: 0.2052 time to fit residues: 111.1915 Evaluate side-chains 334 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 293 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 LYS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain O residue 77 GLN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 51 ASN Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 11 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 27 optimal weight: 0.7980 chunk 253 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 235 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 chunk 184 optimal weight: 7.9990 chunk 229 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN H 77 GLN D 17 GLN D 95 GLN J 13 GLN F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.107508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.077499 restraints weight = 47412.024| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.73 r_work: 0.2959 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25593 Z= 0.130 Angle : 0.591 9.440 34932 Z= 0.299 Chirality : 0.045 0.283 4137 Planarity : 0.004 0.051 4260 Dihedral : 8.237 82.538 5232 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.28 % Allowed : 7.91 % Favored : 89.80 % 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: 0.49 (0.15), residues: 2979 helix: 1.96 (0.27), residues: 405 sheet: 0.65 (0.17), residues: 891 loop : -0.22 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 39 TYR 0.015 0.001 TYR J 100G PHE 0.012 0.001 PHE F 53 TRP 0.024 0.001 TRP Q 91 HIS 0.004 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00292 (25452) covalent geometry : angle 0.55488 (34554) SS BOND : bond 0.00310 ( 45) SS BOND : angle 0.74921 ( 90) hydrogen bonds : bond 0.04388 ( 720) hydrogen bonds : angle 4.59141 ( 1782) link_ALPHA1-2 : bond 0.00755 ( 3) link_ALPHA1-2 : angle 3.41128 ( 9) link_ALPHA1-3 : bond 0.00838 ( 6) link_ALPHA1-3 : angle 1.67325 ( 18) link_ALPHA1-6 : bond 0.00062 ( 3) link_ALPHA1-6 : angle 1.61450 ( 9) link_BETA1-4 : bond 0.00555 ( 21) link_BETA1-4 : angle 1.77274 ( 63) link_NAG-ASN : bond 0.00505 ( 63) link_NAG-ASN : angle 2.45004 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 318 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7439 (OUTLIER) cc_final: 0.7037 (t) REVERT: L 24 GLN cc_start: 0.7561 (tt0) cc_final: 0.7360 (tt0) REVERT: C 43 LYS cc_start: 0.7125 (mppt) cc_final: 0.6882 (mttp) REVERT: C 86 ASP cc_start: 0.7844 (m-30) cc_final: 0.7430 (m-30) REVERT: D 79 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.6962 (mp10) REVERT: D 83 GLU cc_start: 0.7653 (pm20) cc_final: 0.7427 (mp0) REVERT: O 101 ASP cc_start: 0.7468 (t0) cc_final: 0.7240 (t70) REVERT: Q 24 GLN cc_start: 0.7443 (tt0) cc_final: 0.7083 (tm-30) REVERT: Q 79 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7570 (mm110) REVERT: J 97 MET cc_start: 0.8659 (ttp) cc_final: 0.8429 (ttp) REVERT: G 648 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8684 (mt-10) REVERT: P 5 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8107 (mm-40) REVERT: P 105 ARG cc_start: 0.6288 (mmm160) cc_final: 0.6066 (mmm160) REVERT: R 24 GLN cc_start: 0.7522 (tt0) cc_final: 0.7175 (tm-30) REVERT: R 61 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8379 (ttm110) REVERT: R 98 PHE cc_start: 0.6137 (OUTLIER) cc_final: 0.3901 (t80) REVERT: K 13 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7291 (mm110) REVERT: I 624 ASP cc_start: 0.8982 (m-30) cc_final: 0.8628 (m-30) outliers start: 60 outliers final: 35 residues processed: 349 average time/residue: 0.2013 time to fit residues: 106.6967 Evaluate side-chains 334 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 296 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 27 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 236 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 246 optimal weight: 0.0980 chunk 96 optimal weight: 1.9990 chunk 271 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 195 ASN D 17 GLN D 95 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 ASN J 13 GLN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 ASN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.075824 restraints weight = 47373.017| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.78 r_work: 0.2886 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25593 Z= 0.212 Angle : 0.629 9.175 34932 Z= 0.316 Chirality : 0.046 0.269 4137 Planarity : 0.004 0.040 4260 Dihedral : 8.010 82.667 5232 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.63 % Allowed : 8.14 % Favored : 89.23 % 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: 0.32 (0.15), residues: 2979 helix: 1.82 (0.27), residues: 405 sheet: 0.54 (0.17), residues: 897 loop : -0.33 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 54 TYR 0.013 0.002 TYR O 91 PHE 0.016 0.002 PHE K 29 TRP 0.016 0.001 TRP F 479 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00511 (25452) covalent geometry : angle 0.59474 (34554) SS BOND : bond 0.00441 ( 45) SS BOND : angle 0.99439 ( 90) hydrogen bonds : bond 0.04844 ( 720) hydrogen bonds : angle 4.56928 ( 1782) link_ALPHA1-2 : bond 0.00619 ( 3) link_ALPHA1-2 : angle 3.43791 ( 9) link_ALPHA1-3 : bond 0.00658 ( 6) link_ALPHA1-3 : angle 1.48225 ( 18) link_ALPHA1-6 : bond 0.00106 ( 3) link_ALPHA1-6 : angle 1.77968 ( 9) link_BETA1-4 : bond 0.00550 ( 21) link_BETA1-4 : angle 1.85341 ( 63) link_NAG-ASN : bond 0.00568 ( 63) link_NAG-ASN : angle 2.44765 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 316 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7799 (mm-40) REVERT: H 24 VAL cc_start: 0.7668 (OUTLIER) cc_final: 0.7268 (t) REVERT: L 24 GLN cc_start: 0.7605 (tt0) cc_final: 0.7380 (tt0) REVERT: C 43 LYS cc_start: 0.7521 (mppt) cc_final: 0.7313 (mttp) REVERT: D 79 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7090 (mp10) REVERT: D 83 GLU cc_start: 0.7691 (pm20) cc_final: 0.7449 (pm20) REVERT: O 100 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.6773 (ttpp) REVERT: O 101 ASP cc_start: 0.7594 (t0) cc_final: 0.6972 (t0) REVERT: Q 24 GLN cc_start: 0.7700 (tt0) cc_final: 0.7332 (tm-30) REVERT: Q 79 GLN cc_start: 0.7868 (mm-40) cc_final: 0.6549 (pm20) REVERT: J 97 MET cc_start: 0.8691 (ttp) cc_final: 0.8474 (ttp) REVERT: G 648 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8804 (mt-10) REVERT: P 105 ARG cc_start: 0.6421 (mmm160) cc_final: 0.5789 (mmp80) REVERT: R 24 GLN cc_start: 0.7583 (tt0) cc_final: 0.7208 (tm-30) REVERT: R 61 ARG cc_start: 0.8684 (mtm-85) cc_final: 0.8407 (ttm110) REVERT: R 98 PHE cc_start: 0.6422 (OUTLIER) cc_final: 0.3863 (t80) REVERT: K 13 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7394 (mm110) REVERT: K 23 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8389 (tpp-160) REVERT: I 624 ASP cc_start: 0.8992 (m-30) cc_final: 0.8566 (m-30) outliers start: 69 outliers final: 47 residues processed: 347 average time/residue: 0.1821 time to fit residues: 96.6077 Evaluate side-chains 347 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 296 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 100 LYS Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 296 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 203 optimal weight: 0.3980 chunk 205 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 195 ASN H 77 GLN L 79 GLN D 17 GLN D 95 GLN O 39 GLN Q 38 GLN J 13 GLN F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.106835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.077775 restraints weight = 47244.981| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.81 r_work: 0.2933 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25593 Z= 0.123 Angle : 0.563 9.277 34932 Z= 0.284 Chirality : 0.044 0.268 4137 Planarity : 0.004 0.054 4260 Dihedral : 7.576 79.120 5232 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.32 % Allowed : 8.94 % Favored : 88.74 % 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: 0.42 (0.15), residues: 2979 helix: 2.05 (0.27), residues: 405 sheet: 0.54 (0.17), residues: 933 loop : -0.29 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 61 TYR 0.017 0.001 TYR O 91 PHE 0.020 0.001 PHE O 78 TRP 0.016 0.001 TRP Q 91 HIS 0.004 0.001 HIS Q 95B Details of bonding type rmsd covalent geometry : bond 0.00281 (25452) covalent geometry : angle 0.52971 (34554) SS BOND : bond 0.00328 ( 45) SS BOND : angle 0.71277 ( 90) hydrogen bonds : bond 0.04050 ( 720) hydrogen bonds : angle 4.38079 ( 1782) link_ALPHA1-2 : bond 0.00678 ( 3) link_ALPHA1-2 : angle 2.98813 ( 9) link_ALPHA1-3 : bond 0.00727 ( 6) link_ALPHA1-3 : angle 1.43647 ( 18) link_ALPHA1-6 : bond 0.00108 ( 3) link_ALPHA1-6 : angle 1.65951 ( 9) link_BETA1-4 : bond 0.00535 ( 21) link_BETA1-4 : angle 1.66256 ( 63) link_NAG-ASN : bond 0.00504 ( 63) link_NAG-ASN : angle 2.31003 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 321 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7611 (OUTLIER) cc_final: 0.7241 (t) REVERT: L 61 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7942 (ttm110) REVERT: L 79 GLN cc_start: 0.7850 (mm-40) cc_final: 0.6833 (pm20) REVERT: C 83 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7702 (ttp-110) REVERT: C 86 ASP cc_start: 0.7669 (m-30) cc_final: 0.7260 (m-30) REVERT: D 79 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: O 100 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.6744 (ttpp) REVERT: O 101 ASP cc_start: 0.7517 (t0) cc_final: 0.6910 (t0) REVERT: Q 24 GLN cc_start: 0.7685 (tt0) cc_final: 0.7275 (tm-30) REVERT: Q 32 TYR cc_start: 0.8763 (m-80) cc_final: 0.8038 (m-80) REVERT: Q 79 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7662 (mm110) REVERT: G 648 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8722 (mt-10) REVERT: P 5 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8104 (mm-40) REVERT: P 24 VAL cc_start: 0.7360 (OUTLIER) cc_final: 0.7055 (t) REVERT: P 105 ARG cc_start: 0.6344 (mmm160) cc_final: 0.5771 (mmp80) REVERT: R 24 GLN cc_start: 0.7558 (tt0) cc_final: 0.7110 (tm-30) REVERT: R 61 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8395 (ttm110) REVERT: R 98 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.4057 (t80) REVERT: K 13 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7403 (mm110) REVERT: I 624 ASP cc_start: 0.8950 (m-30) cc_final: 0.8541 (m-30) outliers start: 61 outliers final: 41 residues processed: 348 average time/residue: 0.1961 time to fit residues: 103.7186 Evaluate side-chains 355 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 309 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 100 LYS Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 94 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 282 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 210 optimal weight: 0.0270 chunk 34 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 195 ASN F 33 ASN ** F 195 ASN ** 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 = 0.3637 r_free = 0.3637 target = 0.107390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.078321 restraints weight = 47144.692| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.81 r_work: 0.2959 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25593 Z= 0.111 Angle : 0.546 9.063 34932 Z= 0.275 Chirality : 0.043 0.273 4137 Planarity : 0.004 0.056 4260 Dihedral : 7.284 76.961 5232 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.05 % Allowed : 9.59 % Favored : 88.36 % 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: 0.47 (0.15), residues: 2979 helix: 2.14 (0.27), residues: 405 sheet: 0.61 (0.17), residues: 933 loop : -0.29 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 54 TYR 0.014 0.001 TYR K 100G PHE 0.020 0.001 PHE O 78 TRP 0.016 0.001 TRP O 36 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00253 (25452) covalent geometry : angle 0.51306 (34554) SS BOND : bond 0.00265 ( 45) SS BOND : angle 0.72882 ( 90) hydrogen bonds : bond 0.03788 ( 720) hydrogen bonds : angle 4.26342 ( 1782) link_ALPHA1-2 : bond 0.00648 ( 3) link_ALPHA1-2 : angle 2.84462 ( 9) link_ALPHA1-3 : bond 0.00693 ( 6) link_ALPHA1-3 : angle 1.39236 ( 18) link_ALPHA1-6 : bond 0.00106 ( 3) link_ALPHA1-6 : angle 1.66053 ( 9) link_BETA1-4 : bond 0.00503 ( 21) link_BETA1-4 : angle 1.65600 ( 63) link_NAG-ASN : bond 0.00483 ( 63) link_NAG-ASN : angle 2.23985 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 320 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ASP cc_start: 0.6570 (OUTLIER) cc_final: 0.6317 (m-30) REVERT: H 91 TYR cc_start: 0.5537 (m-80) cc_final: 0.4985 (m-80) REVERT: L 24 GLN cc_start: 0.7942 (tt0) cc_final: 0.7698 (tm-30) REVERT: L 61 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.7912 (ttm110) REVERT: L 79 GLN cc_start: 0.7844 (mm-40) cc_final: 0.6846 (pm20) REVERT: C 86 ASP cc_start: 0.7578 (m-30) cc_final: 0.7154 (m-30) REVERT: D 79 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: O 27 ASP cc_start: 0.6627 (OUTLIER) cc_final: 0.6296 (m-30) REVERT: O 100 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.6763 (ttpp) REVERT: O 101 ASP cc_start: 0.7519 (t0) cc_final: 0.7041 (t0) REVERT: Q 11 LEU cc_start: 0.7311 (tp) cc_final: 0.6935 (mt) REVERT: Q 24 GLN cc_start: 0.7725 (tt0) cc_final: 0.7278 (tm-30) REVERT: Q 32 TYR cc_start: 0.8733 (m-80) cc_final: 0.8161 (m-80) REVERT: Q 79 GLN cc_start: 0.7925 (mm-40) cc_final: 0.6841 (pm20) REVERT: G 648 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8705 (mt-10) REVERT: P 5 GLN cc_start: 0.8315 (mm-40) cc_final: 0.8113 (mm-40) REVERT: P 24 VAL cc_start: 0.7353 (OUTLIER) cc_final: 0.7076 (t) REVERT: P 105 ARG cc_start: 0.6405 (mmm160) cc_final: 0.5799 (mmp80) REVERT: R 24 GLN cc_start: 0.7577 (tt0) cc_final: 0.7081 (tm-30) REVERT: R 61 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.8308 (ttm110) REVERT: R 98 PHE cc_start: 0.6601 (OUTLIER) cc_final: 0.4050 (t80) REVERT: K 13 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7349 (mm110) REVERT: K 23 ARG cc_start: 0.8582 (mmm-85) cc_final: 0.8367 (ttm-80) REVERT: I 624 ASP cc_start: 0.8920 (m-30) cc_final: 0.8506 (m-30) outliers start: 54 outliers final: 36 residues processed: 341 average time/residue: 0.1990 time to fit residues: 103.2777 Evaluate side-chains 347 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 305 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 100 LYS Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 129 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 226 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 265 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 195 ASN H 77 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.104917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.075636 restraints weight = 47373.992| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.74 r_work: 0.2895 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 25593 Z= 0.231 Angle : 0.641 9.194 34932 Z= 0.321 Chirality : 0.046 0.258 4137 Planarity : 0.004 0.066 4260 Dihedral : 7.573 78.449 5232 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.44 % Allowed : 9.89 % Favored : 87.67 % 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: 0.25 (0.15), residues: 2979 helix: 1.85 (0.27), residues: 405 sheet: 0.44 (0.17), residues: 945 loop : -0.40 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 61 TYR 0.020 0.002 TYR O 91 PHE 0.019 0.002 PHE O 78 TRP 0.016 0.001 TRP F 479 HIS 0.006 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00556 (25452) covalent geometry : angle 0.60911 (34554) SS BOND : bond 0.00399 ( 45) SS BOND : angle 1.05441 ( 90) hydrogen bonds : bond 0.04858 ( 720) hydrogen bonds : angle 4.45850 ( 1782) link_ALPHA1-2 : bond 0.00511 ( 3) link_ALPHA1-2 : angle 2.95176 ( 9) link_ALPHA1-3 : bond 0.00559 ( 6) link_ALPHA1-3 : angle 1.38638 ( 18) link_ALPHA1-6 : bond 0.00192 ( 3) link_ALPHA1-6 : angle 1.85554 ( 9) link_BETA1-4 : bond 0.00509 ( 21) link_BETA1-4 : angle 1.79800 ( 63) link_NAG-ASN : bond 0.00553 ( 63) link_NAG-ASN : angle 2.37220 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 300 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7415 (OUTLIER) cc_final: 0.7130 (t) REVERT: H 27 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6483 (m-30) REVERT: H 77 GLN cc_start: 0.8470 (tt0) cc_final: 0.7829 (mm-40) REVERT: L 24 GLN cc_start: 0.8011 (tt0) cc_final: 0.7696 (tm-30) REVERT: L 79 GLN cc_start: 0.7904 (mm-40) cc_final: 0.6900 (pm20) REVERT: C 86 ASP cc_start: 0.7667 (m-30) cc_final: 0.7378 (m-30) REVERT: D 79 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7109 (mp10) REVERT: D 103 ARG cc_start: 0.8682 (tpp80) cc_final: 0.8426 (tpp80) REVERT: O 24 VAL cc_start: 0.7620 (OUTLIER) cc_final: 0.7410 (t) REVERT: O 27 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: O 100 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.6786 (ttpp) REVERT: O 101 ASP cc_start: 0.7735 (t0) cc_final: 0.7152 (t0) REVERT: O 105 ARG cc_start: 0.7214 (tpp80) cc_final: 0.6924 (mmp80) REVERT: Q 4 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7292 (tp) REVERT: Q 24 GLN cc_start: 0.7774 (tt0) cc_final: 0.7355 (tm-30) REVERT: Q 32 TYR cc_start: 0.8771 (m-80) cc_final: 0.7996 (m-80) REVERT: Q 61 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8148 (ttp-110) REVERT: Q 79 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7691 (mm110) REVERT: G 648 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8800 (mt-10) REVERT: P 24 VAL cc_start: 0.7301 (OUTLIER) cc_final: 0.7096 (t) REVERT: P 66 ARG cc_start: 0.5260 (ptt90) cc_final: 0.4822 (ptt90) REVERT: P 105 ARG cc_start: 0.6512 (mmm160) cc_final: 0.5839 (mmp80) REVERT: R 61 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8267 (ttm110) REVERT: K 13 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7375 (mm110) REVERT: I 624 ASP cc_start: 0.9017 (m-30) cc_final: 0.8601 (m-30) outliers start: 64 outliers final: 44 residues processed: 332 average time/residue: 0.1989 time to fit residues: 100.9490 Evaluate side-chains 341 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 289 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 100 LYS Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 152 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 186 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 165 optimal weight: 20.0000 chunk 228 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 82 optimal weight: 0.0030 chunk 288 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.106138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.076841 restraints weight = 47586.920| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.79 r_work: 0.2930 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25593 Z= 0.161 Angle : 0.593 9.144 34932 Z= 0.299 Chirality : 0.045 0.264 4137 Planarity : 0.004 0.049 4260 Dihedral : 7.450 76.579 5232 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.17 % Allowed : 10.01 % Favored : 87.82 % 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: 0.28 (0.15), residues: 2979 helix: 1.95 (0.27), residues: 405 sheet: 0.43 (0.17), residues: 939 loop : -0.37 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 54 TYR 0.018 0.001 TYR O 91 PHE 0.022 0.001 PHE O 78 TRP 0.015 0.001 TRP Q 91 HIS 0.004 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00383 (25452) covalent geometry : angle 0.56053 (34554) SS BOND : bond 0.00392 ( 45) SS BOND : angle 1.06885 ( 90) hydrogen bonds : bond 0.04349 ( 720) hydrogen bonds : angle 4.40781 ( 1782) link_ALPHA1-2 : bond 0.00555 ( 3) link_ALPHA1-2 : angle 2.74289 ( 9) link_ALPHA1-3 : bond 0.00574 ( 6) link_ALPHA1-3 : angle 1.39130 ( 18) link_ALPHA1-6 : bond 0.00039 ( 3) link_ALPHA1-6 : angle 1.80452 ( 9) link_BETA1-4 : bond 0.00483 ( 21) link_BETA1-4 : angle 1.66965 ( 63) link_NAG-ASN : bond 0.00486 ( 63) link_NAG-ASN : angle 2.31570 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 301 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7442 (OUTLIER) cc_final: 0.7184 (t) REVERT: H 27 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6467 (m-30) REVERT: H 77 GLN cc_start: 0.8435 (tt0) cc_final: 0.7818 (mm-40) REVERT: L 79 GLN cc_start: 0.7937 (mm-40) cc_final: 0.6923 (pm20) REVERT: C 86 ASP cc_start: 0.7641 (m-30) cc_final: 0.7357 (m-30) REVERT: D 79 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7108 (mp10) REVERT: D 103 ARG cc_start: 0.8643 (tpp80) cc_final: 0.8357 (tpp80) REVERT: O 24 VAL cc_start: 0.7666 (OUTLIER) cc_final: 0.7456 (t) REVERT: O 27 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6563 (m-30) REVERT: O 100 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.6833 (ttpp) REVERT: O 101 ASP cc_start: 0.7727 (t0) cc_final: 0.7158 (t0) REVERT: Q 24 GLN cc_start: 0.7746 (tt0) cc_final: 0.7336 (tm-30) REVERT: Q 32 TYR cc_start: 0.8723 (m-80) cc_final: 0.7948 (m-80) REVERT: Q 61 ARG cc_start: 0.8590 (ttm110) cc_final: 0.8240 (ttp-110) REVERT: Q 79 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7695 (mm110) REVERT: G 648 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8697 (mt-10) REVERT: P 5 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8069 (mm-40) REVERT: P 24 VAL cc_start: 0.7329 (OUTLIER) cc_final: 0.7125 (t) REVERT: P 27 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6665 (m-30) REVERT: P 105 ARG cc_start: 0.6495 (mmm160) cc_final: 0.5795 (mmp80) REVERT: R 24 GLN cc_start: 0.7640 (tt0) cc_final: 0.7364 (tm-30) REVERT: R 61 ARG cc_start: 0.8626 (mtm-85) cc_final: 0.8279 (ttm110) REVERT: R 98 PHE cc_start: 0.6510 (OUTLIER) cc_final: 0.5431 (m-80) REVERT: K 13 GLN cc_start: 0.7571 (mm-40) cc_final: 0.7334 (mm110) REVERT: I 601 LYS cc_start: 0.9189 (mttm) cc_final: 0.8906 (mtpt) REVERT: I 624 ASP cc_start: 0.8998 (m-30) cc_final: 0.8563 (m-30) outliers start: 57 outliers final: 43 residues processed: 325 average time/residue: 0.1755 time to fit residues: 86.7356 Evaluate side-chains 347 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 295 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 100 LYS Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 288 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.105424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.073597 restraints weight = 47629.834| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.62 r_work: 0.2911 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25593 Z= 0.205 Angle : 0.624 9.069 34932 Z= 0.314 Chirality : 0.046 0.260 4137 Planarity : 0.004 0.050 4260 Dihedral : 7.502 76.357 5232 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.17 % Allowed : 10.35 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.07 % 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: 0.17 (0.15), residues: 2979 helix: 1.84 (0.27), residues: 405 sheet: 0.30 (0.17), residues: 954 loop : -0.41 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 54 TYR 0.019 0.002 TYR O 91 PHE 0.022 0.002 PHE O 78 TRP 0.015 0.001 TRP F 479 HIS 0.005 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00494 (25452) covalent geometry : angle 0.59078 (34554) SS BOND : bond 0.00445 ( 45) SS BOND : angle 1.40609 ( 90) hydrogen bonds : bond 0.04580 ( 720) hydrogen bonds : angle 4.45838 ( 1782) link_ALPHA1-2 : bond 0.00502 ( 3) link_ALPHA1-2 : angle 2.75780 ( 9) link_ALPHA1-3 : bond 0.00533 ( 6) link_ALPHA1-3 : angle 1.36163 ( 18) link_ALPHA1-6 : bond 0.00226 ( 3) link_ALPHA1-6 : angle 1.79619 ( 9) link_BETA1-4 : bond 0.00480 ( 21) link_BETA1-4 : angle 1.72921 ( 63) link_NAG-ASN : bond 0.00528 ( 63) link_NAG-ASN : angle 2.34860 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 293 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.7285 (t) REVERT: H 27 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6310 (m-30) REVERT: H 77 GLN cc_start: 0.8469 (tt0) cc_final: 0.7799 (mm-40) REVERT: L 79 GLN cc_start: 0.7907 (mm-40) cc_final: 0.6905 (pm20) REVERT: C 86 ASP cc_start: 0.7578 (m-30) cc_final: 0.7285 (m-30) REVERT: D 79 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6982 (mp10) REVERT: D 103 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8388 (tpp80) REVERT: O 27 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6459 (m-30) REVERT: O 100 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.6703 (ttpp) REVERT: O 101 ASP cc_start: 0.7747 (t0) cc_final: 0.7198 (t0) REVERT: Q 11 LEU cc_start: 0.7534 (tp) cc_final: 0.7272 (mt) REVERT: Q 24 GLN cc_start: 0.7748 (tt0) cc_final: 0.7276 (tt0) REVERT: Q 32 TYR cc_start: 0.8751 (m-80) cc_final: 0.7898 (m-80) REVERT: Q 61 ARG cc_start: 0.8510 (ttm110) cc_final: 0.8160 (ttp-110) REVERT: Q 79 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7695 (mm110) REVERT: G 648 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8604 (mt-10) REVERT: P 5 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8156 (mm-40) REVERT: P 24 VAL cc_start: 0.7396 (OUTLIER) cc_final: 0.7190 (t) REVERT: P 27 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6660 (m-30) REVERT: P 105 ARG cc_start: 0.6333 (mmm160) cc_final: 0.5725 (mmp80) REVERT: R 61 ARG cc_start: 0.8642 (mtm-85) cc_final: 0.8246 (ttm110) REVERT: R 98 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.5425 (m-80) REVERT: K 13 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7249 (mm-40) REVERT: I 601 LYS cc_start: 0.9228 (mttm) cc_final: 0.8894 (mtpt) REVERT: I 624 ASP cc_start: 0.9107 (m-30) cc_final: 0.8663 (m-30) outliers start: 57 outliers final: 44 residues processed: 320 average time/residue: 0.1959 time to fit residues: 95.7127 Evaluate side-chains 339 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 287 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 100 LYS Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 36 optimal weight: 0.8980 chunk 263 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 280 optimal weight: 0.9990 chunk 246 optimal weight: 10.0000 chunk 269 optimal weight: 0.0670 chunk 233 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.105466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.073728 restraints weight = 47607.529| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.56 r_work: 0.2918 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.280 25593 Z= 0.233 Angle : 0.746 59.199 34932 Z= 0.401 Chirality : 0.046 0.738 4137 Planarity : 0.004 0.049 4260 Dihedral : 7.500 76.345 5232 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.02 % Allowed : 10.46 % Favored : 87.52 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.07 % 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: 0.17 (0.15), residues: 2979 helix: 1.85 (0.27), residues: 405 sheet: 0.30 (0.17), residues: 954 loop : -0.41 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 54 TYR 0.018 0.001 TYR O 91 PHE 0.021 0.002 PHE O 78 TRP 0.015 0.001 TRP F 479 HIS 0.005 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00538 (25452) covalent geometry : angle 0.71985 (34554) SS BOND : bond 0.00354 ( 45) SS BOND : angle 1.32814 ( 90) hydrogen bonds : bond 0.04524 ( 720) hydrogen bonds : angle 4.45744 ( 1782) link_ALPHA1-2 : bond 0.00494 ( 3) link_ALPHA1-2 : angle 2.75444 ( 9) link_ALPHA1-3 : bond 0.00544 ( 6) link_ALPHA1-3 : angle 1.39283 ( 18) link_ALPHA1-6 : bond 0.00152 ( 3) link_ALPHA1-6 : angle 1.85277 ( 9) link_BETA1-4 : bond 0.00478 ( 21) link_BETA1-4 : angle 1.72498 ( 63) link_NAG-ASN : bond 0.00513 ( 63) link_NAG-ASN : angle 2.35392 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7108.51 seconds wall clock time: 122 minutes 33.74 seconds (7353.74 seconds total)