Starting phenix.real_space_refine on Mon Aug 25 01:25:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4b_41026/08_2025/8t4b_41026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4b_41026/08_2025/8t4b_41026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4b_41026/08_2025/8t4b_41026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4b_41026/08_2025/8t4b_41026.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4b_41026/08_2025/8t4b_41026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4b_41026/08_2025/8t4b_41026.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 15429 2.51 5 N 4074 2.21 5 O 4875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24525 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 4 Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 942 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 8, 'TRANS': 116} Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 96} Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: E, F, J, K, M, N, G, I, O, P, Q, R, U, W, V, X Time building chain proxies: 4.80, per 1000 atoms: 0.20 Number of scatterers: 24525 At special positions: 0 Unit cell: (142.6, 151.8, 174.8, 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 147 16.00 O 4875 8.00 N 4074 7.00 C 15429 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=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " 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 ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG 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 X 2 " - " BMA X 3 " NAG-ASN " NAG A 601 " - " ASN A 289 " " NAG A 602 " - " ASN A 301 " " NAG A 603 " - " ASN A 88 " " NAG A 604 " - " ASN A 156 " " NAG A 605 " - " ASN A 160 " " NAG A 606 " - " ASN A 197 " " NAG A 607 " - " ASN A 234 " " NAG A 608 " - " ASN A 276 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 339 " " NAG A 611 " - " ASN A 386 " " NAG A 612 " - " ASN A 448 " " NAG A 613 " - " ASN A 241 " " NAG B 701 " - " ASN B 611 " " NAG E 601 " - " ASN E 289 " " NAG E 602 " - " ASN E 301 " " NAG E 603 " - " ASN E 88 " " NAG E 604 " - " ASN E 156 " " NAG E 605 " - " ASN E 160 " " NAG E 606 " - " ASN E 197 " " NAG E 607 " - " ASN E 234 " " NAG E 608 " - " ASN E 276 " " NAG E 609 " - " ASN E 295 " " NAG E 610 " - " ASN E 339 " " NAG E 611 " - " ASN E 386 " " NAG E 612 " - " ASN E 448 " " NAG E 613 " - " ASN E 241 " " NAG F 601 " - " ASN F 289 " " NAG F 602 " - " ASN F 301 " " NAG F 603 " - " ASN F 88 " " NAG F 604 " - " ASN F 156 " " NAG F 605 " - " ASN F 160 " " NAG F 606 " - " ASN F 197 " " NAG F 607 " - " ASN F 234 " " NAG F 608 " - " ASN F 276 " " NAG F 609 " - " ASN F 295 " " NAG F 610 " - " ASN F 339 " " NAG F 611 " - " ASN F 386 " " NAG F 612 " - " ASN F 448 " " NAG F 613 " - " ASN F 241 " " NAG G 701 " - " ASN G 611 " " NAG I 701 " - " ASN I 611 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN E 332 " " NAG V 1 " - " ASN E 262 " " NAG W 1 " - " ASN F 332 " " NAG X 1 " - " ASN F 262 " Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 960.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 48 sheets defined 19.6% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 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 194 through 199 removed outlier: 4.184A pdb=" N THR A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.681A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.531A pdb=" N PHE A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.157A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.080A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.058A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.423A 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 542 removed outlier: 3.665A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.582A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100F Processing helix chain 'L' and resid 79 through 83 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 194 through 199 removed outlier: 4.184A pdb=" N THR E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.681A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 removed outlier: 3.531A pdb=" N PHE E 391 " --> pdb=" O SER E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.157A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.080A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 4.057A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 528 removed outlier: 4.423A 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 542 removed outlier: 3.665A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 595 Processing helix chain 'G' and resid 618 through 625 Processing helix chain 'G' and resid 627 through 635 removed outlier: 3.582A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 661 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100B through 100F Processing helix chain 'Q' and resid 79 through 83 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 194 through 199 removed outlier: 4.184A pdb=" N THR F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.681A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 391 removed outlier: 3.531A pdb=" N PHE F 391 " --> pdb=" O SER F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.157A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 484 removed outlier: 4.080A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.057A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.423A 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 542 removed outlier: 3.665A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 595 Processing helix chain 'I' and resid 618 through 625 Processing helix chain 'I' and resid 627 through 635 removed outlier: 3.582A pdb=" N LYS I 633 " --> pdb=" O LEU I 629 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 661 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100B through 100F Processing helix chain 'R' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.185A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.813A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.725A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.381A 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: 7.077A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.310A 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 'C' and resid 3 through 6 removed outlier: 3.842A pdb=" N GLY C 16 " --> pdb=" O SER C 82B" (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 34 through 39 removed outlier: 5.751A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 38 removed outlier: 6.468A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 48 current: chain 'D' and resid 95A through 98 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 33 through 39 removed outlier: 6.580A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.792A 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 102 through 103 Processing sheet with id=AB5, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.185A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.812A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.725A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 172 through 177 Processing sheet with id=AC4, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.382A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 7.077A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.310A 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=AC6, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.843A pdb=" N GLY J 16 " --> pdb=" O SER J 82B" (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 34 through 39 removed outlier: 5.750A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AC8, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC9, first strand: chain 'M' and resid 33 through 38 removed outlier: 6.469A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 95A through 98 Processing sheet with id=AD1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'O' and resid 33 through 39 removed outlier: 6.580A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.792A 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 102 through 103 Processing sheet with id=AD3, first strand: chain 'O' and resid 98 through 99 Processing sheet with id=AD4, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'Q' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 10 through 12 current: chain 'Q' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 53 through 54 current: chain 'Q' and resid 97 through 98 Processing sheet with id=AD6, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.186A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.813A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AD9, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.725A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 172 through 177 Processing sheet with id=AE2, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.382A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 312 removed outlier: 7.077A pdb=" N ASN F 301 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.310A 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=AE4, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.842A pdb=" N GLY K 16 " --> pdb=" O SER K 82B" (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 34 through 39 removed outlier: 5.751A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100H through 103 Processing sheet with id=AE6, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'N' and resid 33 through 38 removed outlier: 6.468A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 95A through 98 Processing sheet with id=AE8, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'P' and resid 33 through 39 removed outlier: 6.580A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.793A 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 102 through 103 Processing sheet with id=AF1, first strand: chain 'P' and resid 98 through 99 Processing sheet with id=AF2, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'R' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 10 through 12 current: chain 'R' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 53 through 54 current: chain 'R' and resid 97 through 98 699 hydrogen bonds defined for protein. 1728 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: 4.08 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7708 1.34 - 1.47: 6546 1.47 - 1.60: 10604 1.60 - 1.72: 0 1.72 - 1.85: 201 Bond restraints: 25059 Sorted by residual: bond pdb=" CG PRO Q 80 " pdb=" CD PRO Q 80 " ideal model delta sigma weight residual 1.503 1.303 0.200 3.40e-02 8.65e+02 3.47e+01 bond pdb=" CG PRO L 80 " pdb=" CD PRO L 80 " ideal model delta sigma weight residual 1.503 1.303 0.200 3.40e-02 8.65e+02 3.47e+01 bond pdb=" CG PRO R 80 " pdb=" CD PRO R 80 " ideal model delta sigma weight residual 1.503 1.303 0.200 3.40e-02 8.65e+02 3.46e+01 bond pdb=" CB CYS E 331 " pdb=" SG CYS E 331 " ideal model delta sigma weight residual 1.808 1.727 0.081 3.30e-02 9.18e+02 6.02e+00 bond pdb=" CB CYS F 331 " pdb=" SG CYS F 331 " ideal model delta sigma weight residual 1.808 1.727 0.081 3.30e-02 9.18e+02 6.00e+00 ... (remaining 25054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 33076 2.83 - 5.67: 867 5.67 - 8.50: 71 8.50 - 11.34: 9 11.34 - 14.17: 3 Bond angle restraints: 34026 Sorted by residual: angle pdb=" CA PRO Q 80 " pdb=" N PRO Q 80 " pdb=" CD PRO Q 80 " ideal model delta sigma weight residual 112.00 97.83 14.17 1.40e+00 5.10e-01 1.03e+02 angle pdb=" CA PRO R 80 " pdb=" N PRO R 80 " pdb=" CD PRO R 80 " ideal model delta sigma weight residual 112.00 97.83 14.17 1.40e+00 5.10e-01 1.03e+02 angle pdb=" CA PRO L 80 " pdb=" N PRO L 80 " pdb=" CD PRO L 80 " ideal model delta sigma weight residual 112.00 97.86 14.14 1.40e+00 5.10e-01 1.02e+02 angle pdb=" N PRO L 80 " pdb=" CD PRO L 80 " pdb=" CG PRO L 80 " ideal model delta sigma weight residual 103.20 92.65 10.55 1.50e+00 4.44e-01 4.94e+01 angle pdb=" N PRO R 80 " pdb=" CD PRO R 80 " pdb=" CG PRO R 80 " ideal model delta sigma weight residual 103.20 92.66 10.54 1.50e+00 4.44e-01 4.93e+01 ... (remaining 34021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.53: 15054 21.53 - 43.06: 522 43.06 - 64.59: 144 64.59 - 86.12: 45 86.12 - 107.64: 27 Dihedral angle restraints: 15792 sinusoidal: 7092 harmonic: 8700 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 42.86 50.14 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS O 22 " pdb=" SG CYS O 22 " pdb=" SG CYS O 92 " pdb=" CB CYS O 92 " ideal model delta sinusoidal sigma weight residual 93.00 42.88 50.12 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS P 22 " pdb=" SG CYS P 22 " pdb=" SG CYS P 92 " pdb=" CB CYS P 92 " ideal model delta sinusoidal sigma weight residual 93.00 42.88 50.12 1 1.00e+01 1.00e-02 3.44e+01 ... (remaining 15789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.171: 3939 0.171 - 0.343: 30 0.343 - 0.514: 0 0.514 - 0.685: 3 0.685 - 0.857: 3 Chirality restraints: 3975 Sorted by residual: chirality pdb=" C1 NAG F 607 " pdb=" ND2 ASN F 234 " pdb=" C2 NAG F 607 " pdb=" O5 NAG F 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.83e+01 chirality pdb=" C1 NAG E 607 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 607 " pdb=" O5 NAG E 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.83e+01 chirality pdb=" C1 NAG A 607 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 607 " pdb=" O5 NAG A 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.55 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 3972 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN R 79 " -0.099 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO R 80 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO R 80 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO R 80 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " -0.099 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO L 80 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN Q 79 " -0.099 5.00e-02 4.00e+02 1.38e-01 3.04e+01 pdb=" N PRO Q 80 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO Q 80 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO Q 80 " -0.075 5.00e-02 4.00e+02 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3395 2.76 - 3.30: 22450 3.30 - 3.83: 39817 3.83 - 4.37: 48129 4.37 - 4.90: 82373 Nonbonded interactions: 196164 Sorted by model distance: nonbonded pdb=" NH2 ARG E 500 " pdb=" OG SER J 98 " model vdw 2.227 3.120 nonbonded pdb=" NH2 ARG A 500 " pdb=" OG SER C 98 " model vdw 2.228 3.120 nonbonded pdb=" NH2 ARG F 500 " pdb=" OG SER K 98 " model vdw 2.228 3.120 nonbonded pdb=" NH1 ARG R 61 " pdb=" O SER R 77 " model vdw 2.265 3.120 nonbonded pdb=" NH1 ARG L 61 " pdb=" O SER L 77 " model vdw 2.265 3.120 ... (remaining 196159 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 '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 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'X' } 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 group one per residue 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: 5.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.860 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 0.200 25173 Z= 0.293 Angle : 1.120 18.831 34323 Z= 0.599 Chirality : 0.065 0.857 3975 Planarity : 0.007 0.138 4239 Dihedral : 13.170 107.645 10095 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.34 % Allowed : 5.30 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.88 (0.15), residues: 2973 helix: 0.56 (0.26), residues: 357 sheet: 0.80 (0.17), residues: 942 loop : 0.61 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 66 TYR 0.043 0.003 TYR H 50 PHE 0.054 0.004 PHE A 320 TRP 0.023 0.003 TRP O 34 HIS 0.010 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00694 (25059) covalent geometry : angle 1.08611 (34026) SS BOND : bond 0.00702 ( 45) SS BOND : angle 2.22366 ( 90) hydrogen bonds : bond 0.14335 ( 699) hydrogen bonds : angle 6.19108 ( 1728) link_ALPHA1-3 : bond 0.00305 ( 6) link_ALPHA1-3 : angle 2.54094 ( 18) link_ALPHA1-6 : bond 0.00471 ( 3) link_ALPHA1-6 : angle 1.13353 ( 9) link_BETA1-4 : bond 0.00487 ( 12) link_BETA1-4 : angle 2.15424 ( 36) link_NAG-ASN : bond 0.00452 ( 48) link_NAG-ASN : angle 3.90767 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 391 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ASN cc_start: 0.8449 (t0) cc_final: 0.8187 (t0) REVERT: D 42 LYS cc_start: 0.7750 (mmmm) cc_final: 0.7516 (mtpt) REVERT: B 657 GLU cc_start: 0.8495 (tp30) cc_final: 0.8236 (mt-10) REVERT: H 72 ASP cc_start: 0.6771 (t0) cc_final: 0.6138 (t0) REVERT: H 75 GLU cc_start: 0.7777 (mp0) cc_final: 0.7367 (mp0) REVERT: E 434 MET cc_start: 0.8182 (ttt) cc_final: 0.7743 (ttt) REVERT: J 28 THR cc_start: 0.8789 (p) cc_final: 0.8406 (p) REVERT: J 72 ASP cc_start: 0.7981 (t0) cc_final: 0.7687 (t0) REVERT: M 50 ASP cc_start: 0.8358 (t70) cc_final: 0.7673 (t0) REVERT: M 91 TYR cc_start: 0.9006 (t80) cc_final: 0.8756 (t80) REVERT: O 72 ASP cc_start: 0.7105 (t0) cc_final: 0.6419 (t0) REVERT: O 75 GLU cc_start: 0.8047 (mp0) cc_final: 0.7455 (mp0) REVERT: Q 73 LEU cc_start: 0.8236 (tp) cc_final: 0.8021 (tp) REVERT: F 434 MET cc_start: 0.8261 (ttt) cc_final: 0.7794 (ttt) REVERT: K 28 THR cc_start: 0.8820 (p) cc_final: 0.8486 (p) REVERT: K 52 ASP cc_start: 0.8683 (p0) cc_final: 0.8362 (p0) REVERT: K 72 ASP cc_start: 0.7777 (t0) cc_final: 0.7496 (t0) REVERT: N 50 ASP cc_start: 0.8040 (t70) cc_final: 0.7741 (t0) REVERT: I 607 ASN cc_start: 0.8067 (m-40) cc_final: 0.7857 (m-40) REVERT: I 647 GLU cc_start: 0.7595 (tt0) cc_final: 0.7163 (tt0) REVERT: P 72 ASP cc_start: 0.6894 (t0) cc_final: 0.6114 (t0) REVERT: P 75 GLU cc_start: 0.8020 (mp0) cc_final: 0.7507 (mp0) REVERT: R 69 THR cc_start: 0.7586 (p) cc_final: 0.6982 (p) outliers start: 9 outliers final: 5 residues processed: 397 average time/residue: 0.1643 time to fit residues: 100.2961 Evaluate side-chains 260 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 255 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain F residue 188 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN H 39 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN O 39 GLN Q 90 GLN F 183 GLN R 37 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.090387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.071764 restraints weight = 54536.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.074059 restraints weight = 30985.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.075548 restraints weight = 21405.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.076533 restraints weight = 16748.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.076978 restraints weight = 14199.516| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25173 Z= 0.137 Angle : 0.643 12.909 34323 Z= 0.327 Chirality : 0.046 0.391 3975 Planarity : 0.004 0.049 4239 Dihedral : 9.480 81.749 4684 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.82 % Favored : 98.08 % Rotamer: Outliers : 1.14 % Allowed : 7.28 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.08 (0.15), residues: 2973 helix: 2.12 (0.28), residues: 372 sheet: 1.01 (0.17), residues: 969 loop : 0.29 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 94 TYR 0.027 0.001 TYR Q 49 PHE 0.024 0.002 PHE F 320 TRP 0.013 0.002 TRP P 34 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00310 (25059) covalent geometry : angle 0.60755 (34026) SS BOND : bond 0.00403 ( 45) SS BOND : angle 1.01967 ( 90) hydrogen bonds : bond 0.04181 ( 699) hydrogen bonds : angle 5.11309 ( 1728) link_ALPHA1-3 : bond 0.00595 ( 6) link_ALPHA1-3 : angle 2.09364 ( 18) link_ALPHA1-6 : bond 0.00342 ( 3) link_ALPHA1-6 : angle 1.84765 ( 9) link_BETA1-4 : bond 0.00488 ( 12) link_BETA1-4 : angle 1.99015 ( 36) link_NAG-ASN : bond 0.00434 ( 48) link_NAG-ASN : angle 2.98695 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 78 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8239 (mp) REVERT: H 72 ASP cc_start: 0.6877 (t0) cc_final: 0.6548 (t0) REVERT: H 75 GLU cc_start: 0.7942 (mp0) cc_final: 0.7598 (mp0) REVERT: L 78 LEU cc_start: 0.8255 (tt) cc_final: 0.7979 (tt) REVERT: J 28 THR cc_start: 0.8688 (p) cc_final: 0.8186 (p) REVERT: J 72 ASP cc_start: 0.8017 (t0) cc_final: 0.7782 (t0) REVERT: M 50 ASP cc_start: 0.8257 (t70) cc_final: 0.7635 (t0) REVERT: O 37 ILE cc_start: 0.9270 (mm) cc_final: 0.9060 (mt) REVERT: O 72 ASP cc_start: 0.7254 (t0) cc_final: 0.6714 (t0) REVERT: O 75 GLU cc_start: 0.7846 (mp0) cc_final: 0.7612 (mp0) REVERT: Q 78 LEU cc_start: 0.8280 (tt) cc_final: 0.7960 (tt) REVERT: F 161 MET cc_start: 0.8588 (tpp) cc_final: 0.8381 (tpp) REVERT: F 434 MET cc_start: 0.8626 (ttt) cc_final: 0.8139 (ttt) REVERT: K 28 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8367 (p) REVERT: K 72 ASP cc_start: 0.7921 (t0) cc_final: 0.7579 (t0) REVERT: N 50 ASP cc_start: 0.8145 (t70) cc_final: 0.7816 (t0) REVERT: P 72 ASP cc_start: 0.7045 (t0) cc_final: 0.6555 (t0) REVERT: P 75 GLU cc_start: 0.7942 (mp0) cc_final: 0.7610 (mp0) outliers start: 30 outliers final: 15 residues processed: 304 average time/residue: 0.1467 time to fit residues: 72.7492 Evaluate side-chains 254 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 237 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 108 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 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 = 0.3370 r_free = 0.3370 target = 0.083899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.064741 restraints weight = 55039.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066901 restraints weight = 32113.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.068322 restraints weight = 22594.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.069238 restraints weight = 17923.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.069849 restraints weight = 15373.109| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 25173 Z= 0.310 Angle : 0.729 13.714 34323 Z= 0.370 Chirality : 0.048 0.339 3975 Planarity : 0.004 0.050 4239 Dihedral : 8.835 81.835 4674 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.02 % Allowed : 8.28 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.50 (0.15), residues: 2973 helix: 1.88 (0.28), residues: 372 sheet: 0.61 (0.16), residues: 1008 loop : -0.16 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 38 TYR 0.023 0.002 TYR Q 49 PHE 0.039 0.003 PHE E 320 TRP 0.018 0.002 TRP F 45 HIS 0.007 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00740 (25059) covalent geometry : angle 0.69579 (34026) SS BOND : bond 0.00459 ( 45) SS BOND : angle 1.22740 ( 90) hydrogen bonds : bond 0.04732 ( 699) hydrogen bonds : angle 5.18714 ( 1728) link_ALPHA1-3 : bond 0.00773 ( 6) link_ALPHA1-3 : angle 1.65419 ( 18) link_ALPHA1-6 : bond 0.00164 ( 3) link_ALPHA1-6 : angle 1.91513 ( 9) link_BETA1-4 : bond 0.00410 ( 12) link_BETA1-4 : angle 2.04456 ( 36) link_NAG-ASN : bond 0.00626 ( 48) link_NAG-ASN : angle 3.11541 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 249 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8797 (p) cc_final: 0.8490 (p) REVERT: D 95 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8373 (p) REVERT: H 72 ASP cc_start: 0.6966 (t0) cc_final: 0.6647 (t0) REVERT: H 75 GLU cc_start: 0.7899 (mp0) cc_final: 0.7454 (mp0) REVERT: L 78 LEU cc_start: 0.8524 (tt) cc_final: 0.8208 (tt) REVERT: J 28 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8374 (p) REVERT: M 50 ASP cc_start: 0.8340 (t70) cc_final: 0.7859 (t0) REVERT: M 74 THR cc_start: 0.8110 (m) cc_final: 0.7416 (p) REVERT: O 72 ASP cc_start: 0.7322 (t0) cc_final: 0.6636 (t0) REVERT: O 75 GLU cc_start: 0.7880 (mp0) cc_final: 0.7444 (mp0) REVERT: Q 69 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7683 (m) REVERT: Q 78 LEU cc_start: 0.8467 (tt) cc_final: 0.8024 (tt) REVERT: F 125 LEU cc_start: 0.9084 (tp) cc_final: 0.8827 (tp) REVERT: F 426 MET cc_start: 0.8479 (mmm) cc_final: 0.8186 (mtp) REVERT: F 434 MET cc_start: 0.8721 (ttt) cc_final: 0.8302 (ttt) REVERT: K 28 THR cc_start: 0.8868 (p) cc_final: 0.8451 (p) REVERT: K 72 ASP cc_start: 0.8097 (t0) cc_final: 0.7741 (t0) REVERT: N 50 ASP cc_start: 0.8308 (t70) cc_final: 0.8035 (t0) REVERT: P 72 ASP cc_start: 0.7220 (t0) cc_final: 0.6713 (t0) REVERT: P 75 GLU cc_start: 0.7906 (mp0) cc_final: 0.7424 (mp0) REVERT: R 78 LEU cc_start: 0.8485 (tt) cc_final: 0.8181 (tt) outliers start: 53 outliers final: 34 residues processed: 284 average time/residue: 0.1477 time to fit residues: 68.7509 Evaluate side-chains 266 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 616 ASN Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 19 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 233 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.085948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.066937 restraints weight = 54554.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.069148 restraints weight = 31528.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.070592 restraints weight = 22034.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.071533 restraints weight = 17408.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.072121 restraints weight = 14882.130| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25173 Z= 0.129 Angle : 0.593 14.334 34323 Z= 0.297 Chirality : 0.044 0.308 3975 Planarity : 0.004 0.036 4239 Dihedral : 8.192 78.263 4674 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.30 % Allowed : 9.61 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.58 (0.15), residues: 2973 helix: 2.34 (0.29), residues: 372 sheet: 0.73 (0.17), residues: 924 loop : -0.23 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 139 TYR 0.023 0.001 TYR Q 49 PHE 0.025 0.002 PHE A 320 TRP 0.012 0.001 TRP P 47 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00298 (25059) covalent geometry : angle 0.55512 (34026) SS BOND : bond 0.00455 ( 45) SS BOND : angle 1.18021 ( 90) hydrogen bonds : bond 0.03610 ( 699) hydrogen bonds : angle 4.73733 ( 1728) link_ALPHA1-3 : bond 0.00855 ( 6) link_ALPHA1-3 : angle 1.91088 ( 18) link_ALPHA1-6 : bond 0.00397 ( 3) link_ALPHA1-6 : angle 1.92031 ( 9) link_BETA1-4 : bond 0.00322 ( 12) link_BETA1-4 : angle 1.80654 ( 36) link_NAG-ASN : bond 0.00445 ( 48) link_NAG-ASN : angle 2.95278 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8781 (p) cc_final: 0.8415 (p) REVERT: D 95 THR cc_start: 0.8593 (p) cc_final: 0.8314 (p) REVERT: H 72 ASP cc_start: 0.6977 (t0) cc_final: 0.6762 (t0) REVERT: H 75 GLU cc_start: 0.7929 (mp0) cc_final: 0.7528 (mp0) REVERT: L 21 ILE cc_start: 0.8297 (mm) cc_final: 0.8073 (tp) REVERT: L 49 TYR cc_start: 0.8082 (p90) cc_final: 0.7847 (p90) REVERT: L 78 LEU cc_start: 0.8485 (tt) cc_final: 0.8205 (tt) REVERT: J 28 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8391 (p) REVERT: J 72 ASP cc_start: 0.8067 (t0) cc_final: 0.7814 (t0) REVERT: J 82 MET cc_start: 0.7343 (mtm) cc_final: 0.7020 (ptp) REVERT: M 50 ASP cc_start: 0.8302 (t70) cc_final: 0.7825 (t0) REVERT: M 74 THR cc_start: 0.8066 (m) cc_final: 0.7359 (p) REVERT: O 72 ASP cc_start: 0.7286 (t0) cc_final: 0.6666 (t0) REVERT: O 75 GLU cc_start: 0.7835 (mp0) cc_final: 0.7529 (mp0) REVERT: Q 71 TYR cc_start: 0.8205 (m-80) cc_final: 0.7786 (m-10) REVERT: F 125 LEU cc_start: 0.9119 (tp) cc_final: 0.8855 (tp) REVERT: F 426 MET cc_start: 0.8376 (mmm) cc_final: 0.8056 (mtp) REVERT: F 434 MET cc_start: 0.8673 (ttt) cc_final: 0.8206 (ttt) REVERT: K 28 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8374 (p) REVERT: K 72 ASP cc_start: 0.8005 (t0) cc_final: 0.7665 (t0) REVERT: N 50 ASP cc_start: 0.8264 (t70) cc_final: 0.8008 (t0) REVERT: P 72 ASP cc_start: 0.7185 (t0) cc_final: 0.6885 (t0) REVERT: P 75 GLU cc_start: 0.7862 (mp0) cc_final: 0.7348 (mp0) outliers start: 34 outliers final: 19 residues processed: 290 average time/residue: 0.1362 time to fit residues: 64.7798 Evaluate side-chains 257 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain P residue 24 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 126 optimal weight: 0.0570 chunk 107 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 285 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 130 optimal weight: 0.0060 chunk 171 optimal weight: 0.8980 overall best weight: 0.4714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.086829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.067903 restraints weight = 54182.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.070109 restraints weight = 31221.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.071562 restraints weight = 21827.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072498 restraints weight = 17206.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.073096 restraints weight = 14715.393| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25173 Z= 0.111 Angle : 0.572 14.585 34323 Z= 0.286 Chirality : 0.044 0.298 3975 Planarity : 0.003 0.035 4239 Dihedral : 7.769 76.227 4674 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.03 % Allowed : 10.18 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.69 (0.16), residues: 2973 helix: 2.56 (0.29), residues: 372 sheet: 0.75 (0.17), residues: 900 loop : -0.15 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 500 TYR 0.023 0.001 TYR Q 49 PHE 0.022 0.001 PHE A 320 TRP 0.009 0.001 TRP P 34 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00255 (25059) covalent geometry : angle 0.53437 (34026) SS BOND : bond 0.00661 ( 45) SS BOND : angle 1.36466 ( 90) hydrogen bonds : bond 0.03248 ( 699) hydrogen bonds : angle 4.55759 ( 1728) link_ALPHA1-3 : bond 0.00865 ( 6) link_ALPHA1-3 : angle 1.73455 ( 18) link_ALPHA1-6 : bond 0.00443 ( 3) link_ALPHA1-6 : angle 1.87673 ( 9) link_BETA1-4 : bond 0.00360 ( 12) link_BETA1-4 : angle 1.74095 ( 36) link_NAG-ASN : bond 0.00475 ( 48) link_NAG-ASN : angle 2.83712 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 262 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8738 (p) cc_final: 0.8355 (p) REVERT: D 62 PHE cc_start: 0.7222 (m-80) cc_final: 0.6828 (m-80) REVERT: D 95 THR cc_start: 0.8606 (p) cc_final: 0.8346 (p) REVERT: H 75 GLU cc_start: 0.7903 (mp0) cc_final: 0.7533 (mp0) REVERT: J 28 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8487 (p) REVERT: J 72 ASP cc_start: 0.8019 (t0) cc_final: 0.7754 (t0) REVERT: J 82 MET cc_start: 0.7338 (mtm) cc_final: 0.7059 (ptp) REVERT: M 50 ASP cc_start: 0.8304 (t70) cc_final: 0.7827 (t0) REVERT: M 74 THR cc_start: 0.8082 (m) cc_final: 0.7372 (p) REVERT: O 3 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7410 (tm-30) REVERT: O 72 ASP cc_start: 0.7232 (t0) cc_final: 0.6706 (t0) REVERT: O 75 GLU cc_start: 0.7918 (mp0) cc_final: 0.7707 (mp0) REVERT: Q 71 TYR cc_start: 0.8163 (m-80) cc_final: 0.7781 (m-10) REVERT: Q 78 LEU cc_start: 0.8040 (tp) cc_final: 0.7835 (tt) REVERT: F 426 MET cc_start: 0.8344 (mmm) cc_final: 0.8047 (mtp) REVERT: F 434 MET cc_start: 0.8690 (ttt) cc_final: 0.8206 (ttt) REVERT: K 28 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8356 (p) REVERT: K 72 ASP cc_start: 0.7978 (t0) cc_final: 0.7680 (t0) REVERT: K 97 MET cc_start: 0.8341 (ttm) cc_final: 0.8131 (ttm) REVERT: N 50 ASP cc_start: 0.8249 (t70) cc_final: 0.7999 (t0) REVERT: P 72 ASP cc_start: 0.7130 (t0) cc_final: 0.6862 (t0) REVERT: P 75 GLU cc_start: 0.7938 (mp0) cc_final: 0.7551 (mp0) REVERT: R 78 LEU cc_start: 0.8282 (tt) cc_final: 0.8032 (tt) outliers start: 27 outliers final: 15 residues processed: 280 average time/residue: 0.1327 time to fit residues: 61.3566 Evaluate side-chains 267 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain P residue 24 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 134 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 256 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 84 optimal weight: 0.1980 chunk 135 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.067085 restraints weight = 54653.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.069270 restraints weight = 31526.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.070714 restraints weight = 22065.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.071653 restraints weight = 17402.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.072255 restraints weight = 14891.472| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25173 Z= 0.139 Angle : 0.578 13.374 34323 Z= 0.289 Chirality : 0.044 0.297 3975 Planarity : 0.003 0.035 4239 Dihedral : 7.622 75.721 4674 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.07 % Allowed : 10.41 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.59 (0.15), residues: 2973 helix: 2.57 (0.29), residues: 372 sheet: 0.64 (0.17), residues: 900 loop : -0.20 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 500 TYR 0.025 0.001 TYR Q 49 PHE 0.023 0.002 PHE A 320 TRP 0.009 0.001 TRP F 479 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00331 (25059) covalent geometry : angle 0.54161 (34026) SS BOND : bond 0.00599 ( 45) SS BOND : angle 1.34036 ( 90) hydrogen bonds : bond 0.03374 ( 699) hydrogen bonds : angle 4.53348 ( 1728) link_ALPHA1-3 : bond 0.00840 ( 6) link_ALPHA1-3 : angle 1.66367 ( 18) link_ALPHA1-6 : bond 0.00383 ( 3) link_ALPHA1-6 : angle 1.86915 ( 9) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 1.78498 ( 36) link_NAG-ASN : bond 0.00458 ( 48) link_NAG-ASN : angle 2.78275 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8745 (p) cc_final: 0.8345 (p) REVERT: C 52 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8828 (p0) REVERT: D 62 PHE cc_start: 0.7289 (m-80) cc_final: 0.6906 (m-80) REVERT: D 95 THR cc_start: 0.8655 (p) cc_final: 0.8374 (p) REVERT: J 28 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8299 (p) REVERT: M 50 ASP cc_start: 0.8169 (t70) cc_final: 0.7673 (t0) REVERT: M 74 THR cc_start: 0.8129 (m) cc_final: 0.7443 (p) REVERT: O 72 ASP cc_start: 0.7263 (t0) cc_final: 0.6759 (t0) REVERT: O 75 GLU cc_start: 0.7944 (mp0) cc_final: 0.7735 (mp0) REVERT: Q 78 LEU cc_start: 0.8102 (tp) cc_final: 0.7853 (tt) REVERT: F 434 MET cc_start: 0.8692 (ttt) cc_final: 0.8175 (ttt) REVERT: K 28 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8334 (p) REVERT: K 72 ASP cc_start: 0.8005 (t0) cc_final: 0.7713 (t0) REVERT: K 97 MET cc_start: 0.8419 (ttm) cc_final: 0.8198 (ttm) REVERT: N 50 ASP cc_start: 0.8296 (t70) cc_final: 0.8041 (t0) REVERT: P 72 ASP cc_start: 0.7149 (t0) cc_final: 0.6826 (t0) REVERT: P 75 GLU cc_start: 0.7908 (mp0) cc_final: 0.7557 (mp0) REVERT: R 78 LEU cc_start: 0.8236 (tt) cc_final: 0.7985 (tt) outliers start: 28 outliers final: 20 residues processed: 280 average time/residue: 0.1380 time to fit residues: 63.5059 Evaluate side-chains 274 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 103 LYS Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 621 GLU Chi-restraints excluded: chain P residue 24 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 290 optimal weight: 2.9990 chunk 189 optimal weight: 0.0470 chunk 8 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 174 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.067142 restraints weight = 54655.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.069333 restraints weight = 31522.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.070768 restraints weight = 22067.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.071692 restraints weight = 17430.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.072305 restraints weight = 14921.266| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25173 Z= 0.132 Angle : 0.579 12.869 34323 Z= 0.290 Chirality : 0.044 0.291 3975 Planarity : 0.003 0.036 4239 Dihedral : 7.515 74.761 4674 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.11 % Allowed : 11.06 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.51 (0.15), residues: 2973 helix: 2.27 (0.29), residues: 393 sheet: 0.64 (0.18), residues: 885 loop : -0.25 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 500 TYR 0.025 0.001 TYR L 49 PHE 0.022 0.002 PHE A 320 TRP 0.010 0.001 TRP P 34 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00313 (25059) covalent geometry : angle 0.54435 (34026) SS BOND : bond 0.00591 ( 45) SS BOND : angle 1.29508 ( 90) hydrogen bonds : bond 0.03276 ( 699) hydrogen bonds : angle 4.50520 ( 1728) link_ALPHA1-3 : bond 0.00842 ( 6) link_ALPHA1-3 : angle 1.64096 ( 18) link_ALPHA1-6 : bond 0.00401 ( 3) link_ALPHA1-6 : angle 1.86746 ( 9) link_BETA1-4 : bond 0.00342 ( 12) link_BETA1-4 : angle 1.76097 ( 36) link_NAG-ASN : bond 0.00468 ( 48) link_NAG-ASN : angle 2.75378 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8726 (p) cc_final: 0.8317 (p) REVERT: C 52 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8801 (p0) REVERT: D 95 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8410 (p) REVERT: H 75 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: J 28 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8268 (p) REVERT: M 50 ASP cc_start: 0.8151 (t70) cc_final: 0.7664 (t0) REVERT: M 74 THR cc_start: 0.8175 (m) cc_final: 0.7511 (p) REVERT: O 72 ASP cc_start: 0.7276 (t0) cc_final: 0.6766 (t0) REVERT: O 75 GLU cc_start: 0.7940 (mp0) cc_final: 0.7722 (mp0) REVERT: O 86 ASP cc_start: 0.8691 (m-30) cc_final: 0.8225 (m-30) REVERT: F 426 MET cc_start: 0.8274 (mmm) cc_final: 0.8050 (mtp) REVERT: F 434 MET cc_start: 0.8691 (ttt) cc_final: 0.8202 (ttt) REVERT: K 28 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8334 (p) REVERT: K 72 ASP cc_start: 0.8011 (t0) cc_final: 0.7735 (t0) REVERT: K 97 MET cc_start: 0.8410 (ttm) cc_final: 0.8190 (ttm) REVERT: N 50 ASP cc_start: 0.8295 (t70) cc_final: 0.8040 (t0) REVERT: P 72 ASP cc_start: 0.7165 (t0) cc_final: 0.6807 (t0) REVERT: P 75 GLU cc_start: 0.7955 (mp0) cc_final: 0.7581 (mp0) REVERT: R 3 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7553 (mm-40) REVERT: R 78 LEU cc_start: 0.8259 (tt) cc_final: 0.8011 (tt) outliers start: 29 outliers final: 21 residues processed: 278 average time/residue: 0.1437 time to fit residues: 65.3350 Evaluate side-chains 274 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 103 LYS Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 621 GLU Chi-restraints excluded: chain P residue 24 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 191 optimal weight: 7.9990 chunk 114 optimal weight: 0.5980 chunk 111 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 189 optimal weight: 0.0470 chunk 118 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 295 optimal weight: 8.9990 overall best weight: 1.1238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 585 HIS F 170 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** P 3 GLN ** 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 = 0.3397 r_free = 0.3397 target = 0.085403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.066334 restraints weight = 54864.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.068503 restraints weight = 31833.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.069935 restraints weight = 22349.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.070855 restraints weight = 17693.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.071459 restraints weight = 15179.120| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25173 Z= 0.162 Angle : 0.595 12.921 34323 Z= 0.298 Chirality : 0.044 0.292 3975 Planarity : 0.004 0.036 4239 Dihedral : 7.502 74.437 4674 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.07 % Allowed : 11.40 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.41 (0.15), residues: 2973 helix: 2.20 (0.29), residues: 393 sheet: 0.57 (0.18), residues: 885 loop : -0.32 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.024 0.001 TYR L 49 PHE 0.024 0.002 PHE A 320 TRP 0.010 0.001 TRP E 479 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00388 (25059) covalent geometry : angle 0.56084 (34026) SS BOND : bond 0.00606 ( 45) SS BOND : angle 1.32583 ( 90) hydrogen bonds : bond 0.03466 ( 699) hydrogen bonds : angle 4.56193 ( 1728) link_ALPHA1-3 : bond 0.00785 ( 6) link_ALPHA1-3 : angle 1.58832 ( 18) link_ALPHA1-6 : bond 0.00351 ( 3) link_ALPHA1-6 : angle 1.85722 ( 9) link_BETA1-4 : bond 0.00325 ( 12) link_BETA1-4 : angle 1.79812 ( 36) link_NAG-ASN : bond 0.00471 ( 48) link_NAG-ASN : angle 2.75829 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8707 (p) cc_final: 0.8262 (p) REVERT: C 52 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8789 (p0) REVERT: D 95 THR cc_start: 0.8696 (p) cc_final: 0.8426 (p) REVERT: H 75 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: J 28 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8261 (p) REVERT: M 50 ASP cc_start: 0.8109 (t70) cc_final: 0.7623 (t0) REVERT: M 74 THR cc_start: 0.8204 (m) cc_final: 0.7546 (p) REVERT: O 72 ASP cc_start: 0.7330 (t0) cc_final: 0.6798 (t0) REVERT: O 75 GLU cc_start: 0.7975 (mp0) cc_final: 0.7746 (mp0) REVERT: F 426 MET cc_start: 0.8307 (mmm) cc_final: 0.8069 (mtp) REVERT: F 434 MET cc_start: 0.8668 (ttt) cc_final: 0.8208 (ttt) REVERT: K 28 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8359 (p) REVERT: K 72 ASP cc_start: 0.8084 (t0) cc_final: 0.7799 (t0) REVERT: K 97 MET cc_start: 0.8507 (ttm) cc_final: 0.8269 (ttm) REVERT: N 50 ASP cc_start: 0.8313 (t70) cc_final: 0.8069 (t0) REVERT: P 72 ASP cc_start: 0.7173 (t0) cc_final: 0.6854 (t0) REVERT: P 75 GLU cc_start: 0.7986 (mp0) cc_final: 0.7622 (mp0) REVERT: R 78 LEU cc_start: 0.8283 (tt) cc_final: 0.8015 (tt) outliers start: 28 outliers final: 22 residues processed: 275 average time/residue: 0.1388 time to fit residues: 62.7151 Evaluate side-chains 269 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 621 GLU Chi-restraints excluded: chain P residue 24 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 126 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 296 optimal weight: 0.0060 chunk 284 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 585 HIS O 3 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** P 3 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 = 0.3388 r_free = 0.3388 target = 0.084870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.065838 restraints weight = 55156.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.068000 restraints weight = 31954.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.069422 restraints weight = 22449.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.070339 restraints weight = 17766.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.070936 restraints weight = 15241.354| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25173 Z= 0.181 Angle : 0.615 12.968 34323 Z= 0.307 Chirality : 0.045 0.288 3975 Planarity : 0.004 0.035 4239 Dihedral : 7.524 74.174 4674 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.99 % Allowed : 11.78 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.30 (0.15), residues: 2973 helix: 2.12 (0.29), residues: 393 sheet: 0.48 (0.18), residues: 885 loop : -0.39 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.024 0.001 TYR D 91 PHE 0.025 0.002 PHE A 320 TRP 0.011 0.001 TRP E 479 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00436 (25059) covalent geometry : angle 0.58158 (34026) SS BOND : bond 0.00661 ( 45) SS BOND : angle 1.32463 ( 90) hydrogen bonds : bond 0.03579 ( 699) hydrogen bonds : angle 4.60784 ( 1728) link_ALPHA1-3 : bond 0.00746 ( 6) link_ALPHA1-3 : angle 1.57874 ( 18) link_ALPHA1-6 : bond 0.00318 ( 3) link_ALPHA1-6 : angle 1.87209 ( 9) link_BETA1-4 : bond 0.00297 ( 12) link_BETA1-4 : angle 1.81127 ( 36) link_NAG-ASN : bond 0.00484 ( 48) link_NAG-ASN : angle 2.78018 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8650 (p) cc_final: 0.8194 (p) REVERT: C 52 ASP cc_start: 0.9111 (OUTLIER) cc_final: 0.8806 (p0) REVERT: D 95 THR cc_start: 0.8711 (p) cc_final: 0.8444 (p) REVERT: J 28 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8263 (p) REVERT: M 50 ASP cc_start: 0.8140 (t70) cc_final: 0.7669 (t0) REVERT: M 74 THR cc_start: 0.8216 (m) cc_final: 0.7561 (p) REVERT: O 72 ASP cc_start: 0.7341 (t0) cc_final: 0.6821 (t0) REVERT: O 75 GLU cc_start: 0.7992 (mp0) cc_final: 0.7742 (mp0) REVERT: Q 71 TYR cc_start: 0.8100 (m-80) cc_final: 0.7682 (m-10) REVERT: F 95 MET cc_start: 0.8817 (ptm) cc_final: 0.8588 (ttp) REVERT: F 426 MET cc_start: 0.8372 (mmm) cc_final: 0.8115 (mtp) REVERT: F 434 MET cc_start: 0.8678 (ttt) cc_final: 0.8258 (ttt) REVERT: K 28 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8362 (p) REVERT: K 72 ASP cc_start: 0.8097 (t0) cc_final: 0.7807 (t0) REVERT: K 97 MET cc_start: 0.8528 (ttm) cc_final: 0.8308 (ttm) REVERT: N 50 ASP cc_start: 0.8310 (t70) cc_final: 0.8079 (t0) REVERT: P 72 ASP cc_start: 0.7208 (t0) cc_final: 0.6878 (t0) REVERT: P 75 GLU cc_start: 0.8019 (mp0) cc_final: 0.7587 (mp0) REVERT: R 3 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7560 (mm-40) REVERT: R 78 LEU cc_start: 0.8317 (tt) cc_final: 0.8052 (tt) outliers start: 26 outliers final: 21 residues processed: 263 average time/residue: 0.1394 time to fit residues: 59.7806 Evaluate side-chains 269 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 621 GLU Chi-restraints excluded: chain P residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 97 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 117 optimal weight: 0.0980 chunk 60 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 279 optimal weight: 0.6980 chunk 226 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 585 HIS ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** P 3 GLN ** 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 = 0.3404 r_free = 0.3404 target = 0.085790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066887 restraints weight = 54357.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.069057 restraints weight = 31464.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.070481 restraints weight = 22045.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.071405 restraints weight = 17453.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.071997 restraints weight = 14942.938| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25173 Z= 0.125 Angle : 0.586 12.552 34323 Z= 0.291 Chirality : 0.044 0.284 3975 Planarity : 0.003 0.035 4239 Dihedral : 7.334 72.388 4674 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.11 % Allowed : 11.86 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.36 (0.16), residues: 2973 helix: 2.28 (0.29), residues: 393 sheet: 0.48 (0.18), residues: 885 loop : -0.36 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 500 TYR 0.024 0.001 TYR L 49 PHE 0.021 0.001 PHE A 320 TRP 0.010 0.001 TRP E 479 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00298 (25059) covalent geometry : angle 0.55215 (34026) SS BOND : bond 0.00592 ( 45) SS BOND : angle 1.23925 ( 90) hydrogen bonds : bond 0.03261 ( 699) hydrogen bonds : angle 4.47159 ( 1728) link_ALPHA1-3 : bond 0.00737 ( 6) link_ALPHA1-3 : angle 1.56023 ( 18) link_ALPHA1-6 : bond 0.00429 ( 3) link_ALPHA1-6 : angle 1.82541 ( 9) link_BETA1-4 : bond 0.00305 ( 12) link_BETA1-4 : angle 1.72332 ( 36) link_NAG-ASN : bond 0.00482 ( 48) link_NAG-ASN : angle 2.73498 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 258 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8633 (p) cc_final: 0.8165 (p) REVERT: C 52 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8741 (p0) REVERT: D 50 ASP cc_start: 0.8169 (t0) cc_final: 0.7888 (m-30) REVERT: D 95 THR cc_start: 0.8641 (p) cc_final: 0.8361 (p) REVERT: H 64 LYS cc_start: 0.8556 (mmtm) cc_final: 0.8309 (ptpp) REVERT: J 28 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8201 (p) REVERT: M 50 ASP cc_start: 0.8118 (t70) cc_final: 0.7640 (t0) REVERT: M 74 THR cc_start: 0.8221 (m) cc_final: 0.7563 (p) REVERT: O 72 ASP cc_start: 0.7334 (t0) cc_final: 0.6804 (t0) REVERT: O 75 GLU cc_start: 0.7959 (mp0) cc_final: 0.7724 (mp0) REVERT: Q 71 TYR cc_start: 0.8071 (m-80) cc_final: 0.7666 (m-10) REVERT: F 95 MET cc_start: 0.8766 (ptm) cc_final: 0.8537 (ttp) REVERT: F 426 MET cc_start: 0.8304 (mmm) cc_final: 0.8046 (mtp) REVERT: F 434 MET cc_start: 0.8637 (ttt) cc_final: 0.8156 (ttt) REVERT: K 28 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8214 (p) REVERT: K 72 ASP cc_start: 0.8018 (t0) cc_final: 0.7740 (t0) REVERT: N 50 ASP cc_start: 0.8283 (t70) cc_final: 0.8040 (t0) REVERT: P 72 ASP cc_start: 0.7198 (t0) cc_final: 0.6862 (t0) REVERT: P 75 GLU cc_start: 0.7991 (mp0) cc_final: 0.7567 (mp0) REVERT: R 3 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7703 (mm-40) REVERT: R 78 LEU cc_start: 0.8317 (tt) cc_final: 0.8050 (tt) outliers start: 29 outliers final: 21 residues processed: 275 average time/residue: 0.1422 time to fit residues: 63.3504 Evaluate side-chains 271 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 621 GLU Chi-restraints excluded: chain P residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 167 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 287 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 152 optimal weight: 0.0980 chunk 296 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** P 3 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 = 0.3403 r_free = 0.3403 target = 0.085668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.066712 restraints weight = 54929.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.068885 restraints weight = 31760.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.070313 restraints weight = 22233.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.071233 restraints weight = 17587.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.071825 restraints weight = 15091.651| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25173 Z= 0.134 Angle : 0.593 12.457 34323 Z= 0.295 Chirality : 0.044 0.285 3975 Planarity : 0.003 0.035 4239 Dihedral : 7.252 71.672 4674 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.03 % Allowed : 11.94 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.37 (0.16), residues: 2973 helix: 2.28 (0.29), residues: 393 sheet: 0.44 (0.18), residues: 921 loop : -0.33 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.024 0.001 TYR L 49 PHE 0.021 0.002 PHE A 320 TRP 0.010 0.001 TRP E 479 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00319 (25059) covalent geometry : angle 0.55969 (34026) SS BOND : bond 0.00584 ( 45) SS BOND : angle 1.29266 ( 90) hydrogen bonds : bond 0.03267 ( 699) hydrogen bonds : angle 4.44451 ( 1728) link_ALPHA1-3 : bond 0.00748 ( 6) link_ALPHA1-3 : angle 1.53627 ( 18) link_ALPHA1-6 : bond 0.00423 ( 3) link_ALPHA1-6 : angle 1.80044 ( 9) link_BETA1-4 : bond 0.00316 ( 12) link_BETA1-4 : angle 1.71812 ( 36) link_NAG-ASN : bond 0.00481 ( 48) link_NAG-ASN : angle 2.72038 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3586.85 seconds wall clock time: 63 minutes 5.35 seconds (3785.35 seconds total)