Starting phenix.real_space_refine on Thu Sep 18 22:35:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mii_48291/09_2025/9mii_48291.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mii_48291/09_2025/9mii_48291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mii_48291/09_2025/9mii_48291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mii_48291/09_2025/9mii_48291.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mii_48291/09_2025/9mii_48291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mii_48291/09_2025/9mii_48291.map" } resolution = 3.3 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 137 5.16 5 C 13118 2.51 5 N 3534 2.21 5 O 4168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20957 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3428 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "B" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 973 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3393 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 4 Chain: "D" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "J" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3389 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 4 Chain: "F" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 973 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "M" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 937 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 717 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.32, per 1000 atoms: 0.21 Number of scatterers: 20957 At special positions: 0 Unit cell: (120.966, 123.034, 148.882, 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 137 16.00 O 4168 8.00 N 3534 7.00 C 13118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 188 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 210 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 220 " - pdb=" SG CYS E 231 " distance=2.02 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 323 " distance=2.02 Simple disulfide: pdb=" SG CYS E 370 " - pdb=" SG CYS E 437 " distance=2.02 Simple disulfide: pdb=" SG CYS E 377 " - pdb=" SG CYS E 410 " distance=2.03 Simple disulfide: pdb=" SG CYS E 493 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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 U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA V 3 " - " MAN V 5 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 339 " " NAG A 607 " - " ASN A 392 " " NAG A 608 " - " ASN A 156 " " NAG A 609 " - " ASN A 197 " " NAG A 610 " - " ASN A 276 " " NAG A 611 " - " ASN A 448 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 295 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 332 " " NAG C 609 " - " ASN C 339 " " NAG C 610 " - " ASN C 355 " " NAG C 611 " - " ASN C 363 " " NAG C 612 " - " ASN C 392 " " NAG C 613 " - " ASN C 197 " " NAG C 614 " - " ASN C 448 " " NAG C 615 " - " ASN C 386 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 152 " " NAG E 603 " - " ASN E 226 " " NAG E 604 " - " ASN E 268 " " NAG E 605 " - " ASN E 287 " " NAG E 606 " - " ASN E 293 " " NAG E 607 " - " ASN E 324 " " NAG E 608 " - " ASN E 355 " " NAG E 609 " - " ASN E 148 " " NAG E 610 " - " ASN E 189 " " NAG E 611 " - " ASN E 378 " " NAG E 612 " - " ASN E 440 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 618 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 332 " " NAG Q 1 " - " ASN A 363 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 386 " " NAG T 1 " - " ASN C 156 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN E 254 " Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 752.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4726 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 41 sheets defined 19.0% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.075A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.377A pdb=" N ASN A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.918A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.946A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.514A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.372A 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: 4.320A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 removed outlier: 3.530A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.621A pdb=" N SER G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.679A pdb=" N THR G 87 " --> pdb=" O ASP G 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.163A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.914A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.657A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.707A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.555A pdb=" N SER J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.572A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.179A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 346 removed outlier: 3.620A pdb=" N THR E 333 " --> pdb=" O THR E 329 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 334 " --> pdb=" O TRP E 330 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS E 343 " --> pdb=" O LYS E 339 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N HIS E 344 " --> pdb=" O GLN E 340 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE E 345 " --> pdb=" O LEU E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 365 Processing helix chain 'E' and resid 467 through 476 removed outlier: 3.627A pdb=" N TRP E 471 " --> pdb=" O MET E 467 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU E 474 " --> pdb=" O ASN E 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 538 through 543 removed outlier: 3.736A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 624 removed outlier: 3.532A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.693A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.712A pdb=" N LYS M 64 " --> pdb=" O ASP M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.557A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.805A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.174A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.068A 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: 3.791A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.139A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.805A 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 260 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 260 current: chain 'A' and resid 284 through 298 removed outlier: 5.991A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 331 through 334 current: chain 'A' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 393 through 395 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.202A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'G' and resid 34 through 39 removed outlier: 6.914A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100H through 103 Processing sheet with id=AB3, first strand: chain 'I' and resid 9 through 13 Processing sheet with id=AB4, first strand: chain 'I' and resid 20 through 24 Processing sheet with id=AB5, first strand: chain 'I' and resid 45 through 48 removed outlier: 5.659A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE I 97 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.095A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.760A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.639A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 90 through 94 removed outlier: 3.609A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC2, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.473A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 302 removed outlier: 6.970A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 329 through 334 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AC4, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.967A pdb=" N THR J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP J 72 " --> pdb=" O THR J 77 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AC7, first strand: chain 'K' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 9 through 13 current: chain 'K' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 45 through 49 current: chain 'K' and resid 96 through 98 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'K' and resid 20 through 24 Processing sheet with id=AC9, first strand: chain 'E' and resid 486 through 491 removed outlier: 5.214A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.735A pdb=" N ILE E 217 " --> pdb=" O VAL E 237 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD3, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AD4, first strand: chain 'E' and resid 161 through 169 Processing sheet with id=AD5, first strand: chain 'E' and resid 192 through 195 Processing sheet with id=AD6, first strand: chain 'E' and resid 251 through 253 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 251 through 253 current: chain 'E' and resid 276 through 304 removed outlier: 6.633A pdb=" N ASN E 293 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ILE E 315 " --> pdb=" O ASN E 293 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR E 295 " --> pdb=" O GLY E 313 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN E 307 " --> pdb=" O ILE E 301 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 307 through 315 current: chain 'E' and resid 373 through 377 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 373 through 377 current: chain 'E' and resid 457 through 462 Processing sheet with id=AD7, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100H through 103 Processing sheet with id=AD9, first strand: chain 'N' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 9 through 13 current: chain 'N' and resid 44 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 44 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.697A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 97 through 98 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'L' and resid 20 through 24 584 hydrogen bonds defined for protein. 1569 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: 3.20 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5230 1.33 - 1.45: 5090 1.45 - 1.58: 10862 1.58 - 1.70: 1 1.70 - 1.83: 192 Bond restraints: 21375 Sorted by residual: bond pdb=" N GLY H 98 " pdb=" CA GLY H 98 " ideal model delta sigma weight residual 1.444 1.476 -0.032 9.30e-03 1.16e+04 1.18e+01 bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.334 1.409 -0.075 2.34e-02 1.83e+03 1.02e+01 bond pdb=" N ALA F 662 " pdb=" CA ALA F 662 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.27e-02 6.20e+03 7.80e+00 bond pdb=" N ALA B 662 " pdb=" CA ALA B 662 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.32e-02 5.74e+03 7.44e+00 bond pdb=" CA ALA F 662 " pdb=" CB ALA F 662 " ideal model delta sigma weight residual 1.532 1.491 0.041 1.53e-02 4.27e+03 7.19e+00 ... (remaining 21370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.27: 28912 6.27 - 12.54: 81 12.54 - 18.81: 2 18.81 - 25.08: 1 25.08 - 31.34: 1 Bond angle restraints: 28997 Sorted by residual: angle pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " pdb=" C7 NAG P 1 " ideal model delta sigma weight residual 124.56 155.90 -31.34 3.00e+00 1.11e-01 1.09e+02 angle pdb=" C2 NAG A 610 " pdb=" N2 NAG A 610 " pdb=" C7 NAG A 610 " ideal model delta sigma weight residual 124.56 144.07 -19.51 3.00e+00 1.11e-01 4.23e+01 angle pdb=" N LEU F 663 " pdb=" CA LEU F 663 " pdb=" C LEU F 663 " ideal model delta sigma weight residual 110.80 97.08 13.72 2.13e+00 2.20e-01 4.15e+01 angle pdb=" CA GLN I 37 " pdb=" CB GLN I 37 " pdb=" CG GLN I 37 " ideal model delta sigma weight residual 114.10 123.99 -9.89 2.00e+00 2.50e-01 2.45e+01 angle pdb=" CA GLU L 83 " pdb=" CB GLU L 83 " pdb=" CG GLU L 83 " ideal model delta sigma weight residual 114.10 123.99 -9.89 2.00e+00 2.50e-01 2.45e+01 ... (remaining 28992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.13: 12715 21.13 - 42.25: 686 42.25 - 63.38: 161 63.38 - 84.50: 36 84.50 - 105.63: 16 Dihedral angle restraints: 13614 sinusoidal: 6239 harmonic: 7375 Sorted by residual: dihedral pdb=" CD ARG L 54 " pdb=" NE ARG L 54 " pdb=" CZ ARG L 54 " pdb=" NH1 ARG L 54 " ideal model delta sinusoidal sigma weight residual 0.00 -62.81 62.81 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 155.25 -62.25 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 143.57 -50.57 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 13611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2967 0.100 - 0.201: 420 0.201 - 0.301: 29 0.301 - 0.402: 5 0.402 - 0.502: 2 Chirality restraints: 3423 Sorted by residual: chirality pdb=" CB ILE C 213 " pdb=" CA ILE C 213 " pdb=" CG1 ILE C 213 " pdb=" CG2 ILE C 213 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.30e+00 chirality pdb=" C1 NAG C 615 " pdb=" ND2 ASN C 386 " pdb=" C2 NAG C 615 " pdb=" O5 NAG C 615 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C1 NAG C 603 " pdb=" ND2 ASN C 160 " pdb=" C2 NAG C 603 " pdb=" O5 NAG C 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 3420 not shown) Planarity restraints: 3669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 54 " -0.976 9.50e-02 1.11e+02 4.38e-01 1.16e+02 pdb=" NE ARG L 54 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG L 54 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG L 54 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG L 54 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 1 " 0.077 2.00e-02 2.50e+03 8.78e-02 9.63e+01 pdb=" C7 NAG P 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG P 1 " -0.011 2.00e-02 2.50e+03 pdb=" N2 NAG P 1 " -0.159 2.00e-02 2.50e+03 pdb=" O7 NAG P 1 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 610 " 0.045 2.00e-02 2.50e+03 5.07e-02 3.21e+01 pdb=" C7 NAG A 610 " 0.049 2.00e-02 2.50e+03 pdb=" C8 NAG A 610 " -0.017 2.00e-02 2.50e+03 pdb=" N2 NAG A 610 " -0.089 2.00e-02 2.50e+03 pdb=" O7 NAG A 610 " 0.013 2.00e-02 2.50e+03 ... (remaining 3666 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 19 2.35 - 2.99: 10351 2.99 - 3.63: 28801 3.63 - 4.26: 47519 4.26 - 4.90: 80362 Nonbonded interactions: 167052 Sorted by model distance: nonbonded pdb=" ND2 ASN A 67 " pdb=" O TRP A 69 " model vdw 1.718 3.120 nonbonded pdb=" OG1 THR C 139 " pdb=" OD1 ASP C 141 " model vdw 2.257 3.040 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR B 606 " model vdw 2.261 3.040 nonbonded pdb=" O GLY G 96 " pdb=" OH TYR I 96 " model vdw 2.262 3.040 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.278 3.040 ... (remaining 167047 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 56 or resid 67 through 396 or resid 412 through \ 457 or resid 463 through 611)) selection = (chain 'C' and (resid 33 through 185 or resid 189 through 611)) selection = (chain 'E' and (resid 33 through 449 or resid 455 through 611)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 520 through 545 or resid 569 through 701)) selection = (chain 'F' and resid 520 through 701) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.920 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 21481 Z= 0.300 Angle : 1.183 31.345 29274 Z= 0.623 Chirality : 0.067 0.502 3423 Planarity : 0.013 0.438 3618 Dihedral : 13.953 105.631 8765 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 0.40 % Allowed : 11.06 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.16), residues: 2523 helix: 0.80 (0.27), residues: 376 sheet: 0.33 (0.18), residues: 786 loop : -0.57 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG K 54 TYR 0.037 0.003 TYR H 96 PHE 0.031 0.003 PHE C 159 TRP 0.027 0.003 TRP J 103 HIS 0.015 0.002 HIS E 366 Details of bonding type rmsd covalent geometry : bond 0.00634 (21375) covalent geometry : angle 1.13885 (28997) SS BOND : bond 0.00516 ( 41) SS BOND : angle 1.74132 ( 82) hydrogen bonds : bond 0.13837 ( 584) hydrogen bonds : angle 6.51101 ( 1569) link_ALPHA1-3 : bond 0.01703 ( 2) link_ALPHA1-3 : angle 1.49394 ( 6) link_ALPHA1-6 : bond 0.00572 ( 1) link_ALPHA1-6 : angle 2.17888 ( 3) link_BETA1-4 : bond 0.01283 ( 11) link_BETA1-4 : angle 3.96453 ( 33) link_NAG-ASN : bond 0.00877 ( 51) link_NAG-ASN : angle 4.08428 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 420 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7919 (tpt) cc_final: 0.7429 (tpt) REVERT: A 360 ARG cc_start: 0.7145 (mtt-85) cc_final: 0.6887 (mtp85) REVERT: C 160 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7152 (m110) REVERT: C 168 LYS cc_start: 0.8290 (mmmt) cc_final: 0.7974 (mmtp) REVERT: C 199 SER cc_start: 0.9128 (p) cc_final: 0.8818 (t) REVERT: C 232 LYS cc_start: 0.8235 (pttm) cc_final: 0.7826 (tmtt) REVERT: C 395 TRP cc_start: 0.7667 (m-10) cc_final: 0.7464 (m-10) REVERT: K 31 ASN cc_start: 0.7520 (t0) cc_final: 0.7283 (t0) REVERT: E 319 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7927 (mtm-85) REVERT: F 632 ASP cc_start: 0.8354 (t70) cc_final: 0.8076 (t0) REVERT: M 27 TYR cc_start: 0.8202 (p90) cc_final: 0.7759 (p90) REVERT: H 43 GLN cc_start: 0.7529 (mp10) cc_final: 0.7181 (mt0) outliers start: 9 outliers final: 2 residues processed: 426 average time/residue: 0.1545 time to fit residues: 99.4424 Evaluate side-chains 348 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 345 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain F residue 544 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 0.0040 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN J 82AHIS F 543 ASN N 39 HIS L 38 HIS L 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.151715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.126744 restraints weight = 28707.718| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.39 r_work: 0.3436 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 21481 Z= 0.242 Angle : 0.691 11.191 29274 Z= 0.347 Chirality : 0.047 0.335 3423 Planarity : 0.004 0.051 3618 Dihedral : 7.924 80.728 4145 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.52 % Allowed : 10.83 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.16), residues: 2523 helix: 1.17 (0.28), residues: 388 sheet: 0.44 (0.18), residues: 803 loop : -0.47 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 61 TYR 0.018 0.002 TYR K 49 PHE 0.020 0.002 PHE J 67 TRP 0.018 0.002 TRP E 45 HIS 0.007 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00569 (21375) covalent geometry : angle 0.65046 (28997) SS BOND : bond 0.00919 ( 41) SS BOND : angle 0.95872 ( 82) hydrogen bonds : bond 0.04568 ( 584) hydrogen bonds : angle 5.17221 ( 1569) link_ALPHA1-3 : bond 0.01190 ( 2) link_ALPHA1-3 : angle 1.58548 ( 6) link_ALPHA1-6 : bond 0.00281 ( 1) link_ALPHA1-6 : angle 1.83853 ( 3) link_BETA1-4 : bond 0.00465 ( 11) link_BETA1-4 : angle 2.19199 ( 33) link_NAG-ASN : bond 0.00417 ( 51) link_NAG-ASN : angle 3.08507 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 376 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8694 (tpt) cc_final: 0.7961 (tpt) REVERT: A 211 GLU cc_start: 0.7935 (pt0) cc_final: 0.7668 (pt0) REVERT: A 360 ARG cc_start: 0.7839 (mtt-85) cc_final: 0.7008 (mtp85) REVERT: A 475 MET cc_start: 0.8955 (tpp) cc_final: 0.8585 (tpp) REVERT: G 97 MET cc_start: 0.9026 (ttp) cc_final: 0.8755 (ttt) REVERT: C 104 MET cc_start: 0.8776 (ttt) cc_final: 0.8470 (ttt) REVERT: C 160 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7907 (m110) REVERT: C 166 ARG cc_start: 0.8466 (mtm-85) cc_final: 0.8067 (mtm-85) REVERT: C 168 LYS cc_start: 0.8482 (mmmt) cc_final: 0.7912 (mmtp) REVERT: C 199 SER cc_start: 0.9321 (p) cc_final: 0.8852 (t) REVERT: C 232 LYS cc_start: 0.8522 (pttm) cc_final: 0.7646 (tmtt) REVERT: J 38 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8234 (ttp80) REVERT: K 75 ILE cc_start: 0.7382 (pt) cc_final: 0.7098 (pt) REVERT: K 95 GLN cc_start: 0.8575 (mp10) cc_final: 0.8283 (mm-40) REVERT: E 123 THR cc_start: 0.8718 (m) cc_final: 0.8424 (p) REVERT: M 23 ARG cc_start: 0.8113 (ttm110) cc_final: 0.7815 (ttm170) REVERT: M 27 TYR cc_start: 0.8646 (p90) cc_final: 0.7931 (p90) REVERT: M 46 GLU cc_start: 0.8243 (tt0) cc_final: 0.7920 (tt0) REVERT: M 72 ASP cc_start: 0.8389 (t70) cc_final: 0.7908 (t0) REVERT: N 60 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7988 (t0) REVERT: H 86 ASP cc_start: 0.8301 (m-30) cc_final: 0.8076 (m-30) REVERT: L 91 TYR cc_start: 0.7404 (m-80) cc_final: 0.7136 (m-10) outliers start: 56 outliers final: 40 residues processed: 405 average time/residue: 0.1403 time to fit residues: 88.5300 Evaluate side-chains 386 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 343 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 100 GLN Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 183 optimal weight: 0.8980 chunk 126 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 7 optimal weight: 0.0670 chunk 225 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 247 optimal weight: 9.9990 chunk 230 optimal weight: 0.7980 chunk 245 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN E 340 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 38 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.159775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.134362 restraints weight = 29818.268| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.55 r_work: 0.3460 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21481 Z= 0.118 Angle : 0.574 11.378 29274 Z= 0.285 Chirality : 0.043 0.261 3423 Planarity : 0.003 0.038 3618 Dihedral : 6.839 69.782 4142 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.02 % Allowed : 12.40 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.17), residues: 2523 helix: 1.73 (0.29), residues: 382 sheet: 0.39 (0.18), residues: 824 loop : -0.36 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 61 TYR 0.017 0.001 TYR E 165 PHE 0.013 0.001 PHE J 67 TRP 0.013 0.001 TRP H 50 HIS 0.005 0.001 HIS E 366 Details of bonding type rmsd covalent geometry : bond 0.00264 (21375) covalent geometry : angle 0.53385 (28997) SS BOND : bond 0.00332 ( 41) SS BOND : angle 0.67450 ( 82) hydrogen bonds : bond 0.03696 ( 584) hydrogen bonds : angle 4.76611 ( 1569) link_ALPHA1-3 : bond 0.01380 ( 2) link_ALPHA1-3 : angle 1.12340 ( 6) link_ALPHA1-6 : bond 0.00444 ( 1) link_ALPHA1-6 : angle 1.78961 ( 3) link_BETA1-4 : bond 0.00463 ( 11) link_BETA1-4 : angle 1.73779 ( 33) link_NAG-ASN : bond 0.00445 ( 51) link_NAG-ASN : angle 2.82055 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 366 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8479 (tpt) cc_final: 0.7926 (tpt) REVERT: A 360 ARG cc_start: 0.7666 (mtt-85) cc_final: 0.6894 (mtp85) REVERT: G 81 GLN cc_start: 0.7666 (tp40) cc_final: 0.7177 (mm-40) REVERT: C 104 MET cc_start: 0.8660 (ttt) cc_final: 0.8376 (ttt) REVERT: C 166 ARG cc_start: 0.8394 (mtm-85) cc_final: 0.7979 (mtm-85) REVERT: C 168 LYS cc_start: 0.8393 (mmmt) cc_final: 0.7896 (mmtp) REVERT: C 199 SER cc_start: 0.9282 (p) cc_final: 0.8779 (t) REVERT: C 232 LYS cc_start: 0.8444 (pttm) cc_final: 0.7699 (tmtt) REVERT: C 475 MET cc_start: 0.8244 (mmt) cc_final: 0.7901 (mmt) REVERT: J 81 GLN cc_start: 0.8600 (tm-30) cc_final: 0.7515 (tm-30) REVERT: K 75 ILE cc_start: 0.7377 (pt) cc_final: 0.7143 (pt) REVERT: E 125 LEU cc_start: 0.8636 (tp) cc_final: 0.8434 (tp) REVERT: M 27 TYR cc_start: 0.8550 (p90) cc_final: 0.7992 (p90) REVERT: M 72 ASP cc_start: 0.8343 (t70) cc_final: 0.7849 (t0) REVERT: N 85 ASP cc_start: 0.7992 (m-30) cc_final: 0.7720 (m-30) REVERT: H 86 ASP cc_start: 0.8097 (m-30) cc_final: 0.7891 (m-30) REVERT: L 62 PHE cc_start: 0.7173 (m-80) cc_final: 0.6861 (m-10) outliers start: 45 outliers final: 32 residues processed: 393 average time/residue: 0.1404 time to fit residues: 85.9158 Evaluate side-chains 374 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 342 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 36 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.151623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126757 restraints weight = 28783.068| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.41 r_work: 0.3435 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21481 Z= 0.159 Angle : 0.576 11.524 29274 Z= 0.286 Chirality : 0.044 0.274 3423 Planarity : 0.004 0.052 3618 Dihedral : 6.151 56.318 4140 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 2.70 % Allowed : 11.87 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.17), residues: 2523 helix: 1.69 (0.28), residues: 387 sheet: 0.35 (0.18), residues: 777 loop : -0.44 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 61 TYR 0.016 0.001 TYR I 49 PHE 0.013 0.002 PHE J 100H TRP 0.014 0.001 TRP H 50 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00372 (21375) covalent geometry : angle 0.53942 (28997) SS BOND : bond 0.00313 ( 41) SS BOND : angle 0.67907 ( 82) hydrogen bonds : bond 0.03682 ( 584) hydrogen bonds : angle 4.63124 ( 1569) link_ALPHA1-3 : bond 0.01286 ( 2) link_ALPHA1-3 : angle 1.17469 ( 6) link_ALPHA1-6 : bond 0.00567 ( 1) link_ALPHA1-6 : angle 1.53103 ( 3) link_BETA1-4 : bond 0.00408 ( 11) link_BETA1-4 : angle 1.73838 ( 33) link_NAG-ASN : bond 0.00415 ( 51) link_NAG-ASN : angle 2.69955 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 355 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8498 (tm-30) cc_final: 0.7778 (tm-30) REVERT: A 161 MET cc_start: 0.8627 (tpt) cc_final: 0.8152 (tpt) REVERT: A 360 ARG cc_start: 0.7806 (mtt-85) cc_final: 0.6980 (mtp85) REVERT: A 475 MET cc_start: 0.8885 (tpp) cc_final: 0.8608 (tpp) REVERT: B 632 ASP cc_start: 0.9092 (t0) cc_final: 0.8887 (t0) REVERT: G 81 GLN cc_start: 0.7706 (tp40) cc_final: 0.7262 (mm-40) REVERT: C 104 MET cc_start: 0.8815 (ttt) cc_final: 0.8495 (ttt) REVERT: C 166 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8006 (mtm-85) REVERT: C 168 LYS cc_start: 0.8484 (mmmt) cc_final: 0.7902 (mmtp) REVERT: C 199 SER cc_start: 0.9320 (p) cc_final: 0.8805 (t) REVERT: C 232 LYS cc_start: 0.8537 (pttm) cc_final: 0.7629 (tmtt) REVERT: C 428 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8299 (mm110) REVERT: C 475 MET cc_start: 0.8356 (mmt) cc_final: 0.8154 (mmt) REVERT: D 621 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8507 (mt-10) REVERT: D 635 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8108 (tt) REVERT: J 81 GLN cc_start: 0.8592 (tm-30) cc_final: 0.7382 (tm-30) REVERT: J 83 ARG cc_start: 0.7503 (mtt-85) cc_final: 0.7257 (mtt-85) REVERT: K 75 ILE cc_start: 0.7481 (pt) cc_final: 0.7227 (pt) REVERT: E 125 LEU cc_start: 0.8880 (tp) cc_final: 0.8650 (tp) REVERT: M 23 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7812 (ttm170) REVERT: M 72 ASP cc_start: 0.8441 (t0) cc_final: 0.7936 (t0) REVERT: N 79 GLN cc_start: 0.8274 (mp10) cc_final: 0.7878 (mp10) REVERT: N 85 ASP cc_start: 0.8165 (m-30) cc_final: 0.7827 (m-30) REVERT: H 86 ASP cc_start: 0.8439 (m-30) cc_final: 0.8136 (m-30) outliers start: 60 outliers final: 51 residues processed: 393 average time/residue: 0.1354 time to fit residues: 82.9815 Evaluate side-chains 393 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 341 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 11 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 237 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 199 optimal weight: 0.0040 chunk 153 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN J 82AHIS L 38 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.151569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.126510 restraints weight = 28571.653| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.44 r_work: 0.3443 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21481 Z= 0.144 Angle : 0.558 11.450 29274 Z= 0.277 Chirality : 0.043 0.268 3423 Planarity : 0.003 0.038 3618 Dihedral : 5.800 56.243 4140 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 2.97 % Allowed : 12.31 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.17), residues: 2523 helix: 1.78 (0.28), residues: 381 sheet: 0.35 (0.18), residues: 766 loop : -0.43 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 61 TYR 0.019 0.001 TYR L 91 PHE 0.012 0.001 PHE M 102 TRP 0.014 0.001 TRP H 50 HIS 0.005 0.001 HIS J 82A Details of bonding type rmsd covalent geometry : bond 0.00335 (21375) covalent geometry : angle 0.52134 (28997) SS BOND : bond 0.00338 ( 41) SS BOND : angle 0.74928 ( 82) hydrogen bonds : bond 0.03500 ( 584) hydrogen bonds : angle 4.53630 ( 1569) link_ALPHA1-3 : bond 0.01336 ( 2) link_ALPHA1-3 : angle 1.16240 ( 6) link_ALPHA1-6 : bond 0.00539 ( 1) link_ALPHA1-6 : angle 1.49501 ( 3) link_BETA1-4 : bond 0.00427 ( 11) link_BETA1-4 : angle 1.67525 ( 33) link_NAG-ASN : bond 0.00457 ( 51) link_NAG-ASN : angle 2.64328 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 361 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7708 (tm-30) REVERT: A 161 MET cc_start: 0.8570 (tpt) cc_final: 0.7972 (tpt) REVERT: A 360 ARG cc_start: 0.7806 (mtt-85) cc_final: 0.6983 (mtp85) REVERT: G 81 GLN cc_start: 0.7658 (tp40) cc_final: 0.7233 (mm-40) REVERT: C 104 MET cc_start: 0.8848 (ttt) cc_final: 0.8526 (ttt) REVERT: C 168 LYS cc_start: 0.8530 (mmmt) cc_final: 0.7964 (mmtp) REVERT: C 199 SER cc_start: 0.9337 (p) cc_final: 0.8858 (t) REVERT: C 232 LYS cc_start: 0.8546 (pttm) cc_final: 0.7640 (tmtt) REVERT: C 428 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8297 (mm110) REVERT: D 621 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8583 (mt-10) REVERT: D 635 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8060 (tt) REVERT: J 81 GLN cc_start: 0.8572 (tm-30) cc_final: 0.7701 (tm-30) REVERT: J 83 ARG cc_start: 0.7471 (mtt-85) cc_final: 0.7213 (mtt-85) REVERT: K 75 ILE cc_start: 0.7448 (pt) cc_final: 0.7176 (pt) REVERT: E 125 LEU cc_start: 0.8858 (tp) cc_final: 0.8651 (tp) REVERT: M 23 ARG cc_start: 0.8036 (ttm110) cc_final: 0.7812 (ttm170) REVERT: M 72 ASP cc_start: 0.8419 (t0) cc_final: 0.7919 (t0) REVERT: N 79 GLN cc_start: 0.8253 (mp10) cc_final: 0.7863 (mp10) REVERT: N 85 ASP cc_start: 0.8176 (m-30) cc_final: 0.7837 (m-30) REVERT: H 86 ASP cc_start: 0.8438 (m-30) cc_final: 0.8170 (m-30) REVERT: L 62 PHE cc_start: 0.6978 (m-80) cc_final: 0.6740 (m-10) outliers start: 66 outliers final: 55 residues processed: 399 average time/residue: 0.1396 time to fit residues: 87.3105 Evaluate side-chains 405 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 349 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain M residue 84 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 187 optimal weight: 0.7980 chunk 196 optimal weight: 0.0000 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 3 optimal weight: 0.0040 chunk 164 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 247 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.150807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125925 restraints weight = 28479.230| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.41 r_work: 0.3436 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 21481 Z= 0.106 Angle : 0.523 11.269 29274 Z= 0.261 Chirality : 0.042 0.265 3423 Planarity : 0.003 0.050 3618 Dihedral : 5.581 58.951 4140 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.45 % Favored : 96.51 % Rotamer: Outliers : 2.97 % Allowed : 12.90 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.17), residues: 2523 helix: 1.93 (0.29), residues: 381 sheet: 0.32 (0.18), residues: 786 loop : -0.38 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 61 TYR 0.015 0.001 TYR L 91 PHE 0.010 0.001 PHE G 29 TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS E 366 Details of bonding type rmsd covalent geometry : bond 0.00239 (21375) covalent geometry : angle 0.48732 (28997) SS BOND : bond 0.00239 ( 41) SS BOND : angle 0.88175 ( 82) hydrogen bonds : bond 0.03186 ( 584) hydrogen bonds : angle 4.37930 ( 1569) link_ALPHA1-3 : bond 0.01340 ( 2) link_ALPHA1-3 : angle 1.10244 ( 6) link_ALPHA1-6 : bond 0.00515 ( 1) link_ALPHA1-6 : angle 1.46003 ( 3) link_BETA1-4 : bond 0.00420 ( 11) link_BETA1-4 : angle 1.55895 ( 33) link_NAG-ASN : bond 0.00430 ( 51) link_NAG-ASN : angle 2.51815 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 366 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8502 (tpt) cc_final: 0.7963 (tpt) REVERT: A 330 HIS cc_start: 0.8737 (p90) cc_final: 0.8276 (p90) REVERT: A 360 ARG cc_start: 0.7787 (mtt-85) cc_final: 0.6919 (mtp85) REVERT: G 81 GLN cc_start: 0.7563 (tp40) cc_final: 0.7075 (mm-40) REVERT: C 104 MET cc_start: 0.8832 (ttt) cc_final: 0.8457 (ttt) REVERT: C 166 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.8059 (mtm-85) REVERT: C 168 LYS cc_start: 0.8487 (mmmt) cc_final: 0.7927 (mmtp) REVERT: C 199 SER cc_start: 0.9354 (p) cc_final: 0.8845 (t) REVERT: C 232 LYS cc_start: 0.8532 (pttm) cc_final: 0.7602 (tmtt) REVERT: C 428 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8274 (mm110) REVERT: D 635 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8040 (tt) REVERT: J 81 GLN cc_start: 0.8570 (tm-30) cc_final: 0.7914 (tm-30) REVERT: K 74 THR cc_start: 0.7803 (m) cc_final: 0.7563 (p) REVERT: K 75 ILE cc_start: 0.7446 (pt) cc_final: 0.7153 (pt) REVERT: E 125 LEU cc_start: 0.8852 (tp) cc_final: 0.8639 (tp) REVERT: E 139 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7805 (p) REVERT: E 143 ARG cc_start: 0.8096 (ttt-90) cc_final: 0.7334 (ttp-110) REVERT: F 540 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: M 23 ARG cc_start: 0.7996 (ttm110) cc_final: 0.7768 (ttm170) REVERT: M 27 TYR cc_start: 0.8834 (p90) cc_final: 0.8199 (p90) REVERT: M 72 ASP cc_start: 0.8393 (t0) cc_final: 0.7921 (t0) REVERT: N 85 ASP cc_start: 0.8143 (m-30) cc_final: 0.7790 (m-30) REVERT: H 86 ASP cc_start: 0.8405 (m-30) cc_final: 0.8119 (m-30) REVERT: H 87 THR cc_start: 0.8651 (t) cc_final: 0.8384 (t) REVERT: L 78 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6439 (tt) outliers start: 66 outliers final: 55 residues processed: 406 average time/residue: 0.1433 time to fit residues: 91.0821 Evaluate side-chains 404 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 345 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 482 LYS Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 229 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 chunk 218 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN J 82AHIS E 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.150084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125285 restraints weight = 28820.953| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.39 r_work: 0.3415 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21481 Z= 0.133 Angle : 0.538 11.361 29274 Z= 0.268 Chirality : 0.043 0.274 3423 Planarity : 0.003 0.044 3618 Dihedral : 5.384 58.345 4140 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 3.33 % Allowed : 13.17 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.27 (0.17), residues: 2523 helix: 1.91 (0.28), residues: 381 sheet: 0.33 (0.18), residues: 794 loop : -0.38 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 103 TYR 0.015 0.001 TYR I 49 PHE 0.011 0.001 PHE L 62 TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00311 (21375) covalent geometry : angle 0.50271 (28997) SS BOND : bond 0.00282 ( 41) SS BOND : angle 0.84161 ( 82) hydrogen bonds : bond 0.03288 ( 584) hydrogen bonds : angle 4.37557 ( 1569) link_ALPHA1-3 : bond 0.01250 ( 2) link_ALPHA1-3 : angle 1.15015 ( 6) link_ALPHA1-6 : bond 0.00507 ( 1) link_ALPHA1-6 : angle 1.53567 ( 3) link_BETA1-4 : bond 0.00390 ( 11) link_BETA1-4 : angle 1.56574 ( 33) link_NAG-ASN : bond 0.00478 ( 51) link_NAG-ASN : angle 2.54699 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 353 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8575 (tpt) cc_final: 0.8040 (tpt) REVERT: A 330 HIS cc_start: 0.8803 (p90) cc_final: 0.8349 (p90) REVERT: A 360 ARG cc_start: 0.7755 (mtt-85) cc_final: 0.6931 (mtp85) REVERT: B 620 SER cc_start: 0.9192 (t) cc_final: 0.8960 (t) REVERT: G 81 GLN cc_start: 0.7542 (tp40) cc_final: 0.7043 (mm-40) REVERT: C 104 MET cc_start: 0.8864 (ttt) cc_final: 0.8486 (ttt) REVERT: C 166 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.8031 (mtm-85) REVERT: C 199 SER cc_start: 0.9373 (p) cc_final: 0.8898 (t) REVERT: C 232 LYS cc_start: 0.8536 (pttm) cc_final: 0.7706 (tmtt) REVERT: C 428 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8322 (mm110) REVERT: D 530 MET cc_start: 0.9096 (mtm) cc_final: 0.8655 (ptp) REVERT: D 635 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8094 (tt) REVERT: J 81 GLN cc_start: 0.8651 (tm-30) cc_final: 0.7486 (tm-30) REVERT: K 74 THR cc_start: 0.7821 (m) cc_final: 0.7567 (p) REVERT: K 75 ILE cc_start: 0.7436 (pt) cc_final: 0.7156 (pt) REVERT: E 125 LEU cc_start: 0.8849 (tp) cc_final: 0.8609 (tp) REVERT: E 139 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7753 (p) REVERT: E 143 ARG cc_start: 0.8152 (ttt-90) cc_final: 0.7411 (ttp-110) REVERT: E 203 GLU cc_start: 0.7851 (tp30) cc_final: 0.7539 (tp30) REVERT: F 540 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8062 (mt0) REVERT: M 27 TYR cc_start: 0.8845 (p90) cc_final: 0.8186 (p90) REVERT: M 72 ASP cc_start: 0.8406 (t0) cc_final: 0.8050 (t0) REVERT: N 85 ASP cc_start: 0.8132 (m-30) cc_final: 0.7835 (m-30) REVERT: H 86 ASP cc_start: 0.8441 (m-30) cc_final: 0.8134 (m-30) REVERT: L 78 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6478 (tt) outliers start: 74 outliers final: 61 residues processed: 400 average time/residue: 0.1360 time to fit residues: 84.9726 Evaluate side-chains 407 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 342 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 482 LYS Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 75 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 198 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN D 540 GLN J 82AHIS L 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.151099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126317 restraints weight = 28665.064| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.40 r_work: 0.3433 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21481 Z= 0.113 Angle : 0.526 11.190 29274 Z= 0.263 Chirality : 0.043 0.270 3423 Planarity : 0.003 0.047 3618 Dihedral : 5.106 57.470 4140 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % Rotamer: Outliers : 3.06 % Allowed : 13.39 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.17), residues: 2523 helix: 2.00 (0.28), residues: 381 sheet: 0.37 (0.18), residues: 806 loop : -0.35 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 83 TYR 0.014 0.001 TYR E 476 PHE 0.009 0.001 PHE J 100H TRP 0.014 0.001 TRP H 50 HIS 0.006 0.001 HIS J 82A Details of bonding type rmsd covalent geometry : bond 0.00260 (21375) covalent geometry : angle 0.49268 (28997) SS BOND : bond 0.00248 ( 41) SS BOND : angle 0.79190 ( 82) hydrogen bonds : bond 0.03153 ( 584) hydrogen bonds : angle 4.31428 ( 1569) link_ALPHA1-3 : bond 0.01137 ( 2) link_ALPHA1-3 : angle 1.23012 ( 6) link_ALPHA1-6 : bond 0.00538 ( 1) link_ALPHA1-6 : angle 1.56878 ( 3) link_BETA1-4 : bond 0.00399 ( 11) link_BETA1-4 : angle 1.46012 ( 33) link_NAG-ASN : bond 0.00463 ( 51) link_NAG-ASN : angle 2.47133 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 345 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8507 (tpt) cc_final: 0.8018 (tpt) REVERT: A 330 HIS cc_start: 0.8760 (p90) cc_final: 0.8322 (p90) REVERT: A 360 ARG cc_start: 0.7756 (mtt-85) cc_final: 0.6927 (mtp85) REVERT: B 620 SER cc_start: 0.9180 (t) cc_final: 0.8948 (t) REVERT: G 81 GLN cc_start: 0.7451 (tp40) cc_final: 0.6981 (mm-40) REVERT: C 104 MET cc_start: 0.8869 (ttt) cc_final: 0.8475 (ttt) REVERT: C 199 SER cc_start: 0.9377 (p) cc_final: 0.8860 (t) REVERT: C 232 LYS cc_start: 0.8529 (pttm) cc_final: 0.7703 (tmtt) REVERT: C 428 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8270 (mm110) REVERT: D 635 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8084 (tt) REVERT: J 81 GLN cc_start: 0.8572 (tm-30) cc_final: 0.7830 (tm-30) REVERT: K 74 THR cc_start: 0.7830 (m) cc_final: 0.7572 (p) REVERT: K 75 ILE cc_start: 0.7453 (pt) cc_final: 0.7175 (pt) REVERT: E 125 LEU cc_start: 0.8826 (tp) cc_final: 0.8595 (tp) REVERT: E 139 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7732 (p) REVERT: E 143 ARG cc_start: 0.8126 (ttt-90) cc_final: 0.7406 (ttp-110) REVERT: E 203 GLU cc_start: 0.7788 (tp30) cc_final: 0.7503 (tp30) REVERT: F 540 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: M 27 TYR cc_start: 0.8849 (p90) cc_final: 0.8193 (p90) REVERT: M 70 SER cc_start: 0.8412 (p) cc_final: 0.7928 (m) REVERT: M 72 ASP cc_start: 0.8413 (t0) cc_final: 0.8050 (t0) REVERT: N 85 ASP cc_start: 0.8241 (m-30) cc_final: 0.7855 (m-30) REVERT: H 28 THR cc_start: 0.8567 (p) cc_final: 0.8322 (p) REVERT: H 43 GLN cc_start: 0.7793 (mp10) cc_final: 0.7189 (mt0) REVERT: H 86 ASP cc_start: 0.8439 (m-30) cc_final: 0.8117 (m-30) REVERT: H 87 THR cc_start: 0.8636 (t) cc_final: 0.8353 (t) REVERT: L 78 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6384 (tt) REVERT: L 86 TYR cc_start: 0.8007 (m-80) cc_final: 0.7588 (m-80) outliers start: 68 outliers final: 59 residues processed: 390 average time/residue: 0.1403 time to fit residues: 85.7803 Evaluate side-chains 394 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 331 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 482 LYS Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 99 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 0.0010 chunk 39 optimal weight: 8.9990 chunk 238 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 137 optimal weight: 0.0040 chunk 38 optimal weight: 0.6980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 540 GLN K 53 GLN H 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.150771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125739 restraints weight = 28842.492| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.42 r_work: 0.3421 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21481 Z= 0.121 Angle : 0.533 11.219 29274 Z= 0.264 Chirality : 0.043 0.276 3423 Planarity : 0.003 0.039 3618 Dihedral : 4.983 56.904 4140 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 3.10 % Allowed : 13.57 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.17), residues: 2523 helix: 2.02 (0.28), residues: 381 sheet: 0.35 (0.18), residues: 806 loop : -0.33 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 83 TYR 0.014 0.001 TYR I 49 PHE 0.009 0.001 PHE G 29 TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00282 (21375) covalent geometry : angle 0.50033 (28997) SS BOND : bond 0.00271 ( 41) SS BOND : angle 0.80931 ( 82) hydrogen bonds : bond 0.03187 ( 584) hydrogen bonds : angle 4.28690 ( 1569) link_ALPHA1-3 : bond 0.01225 ( 2) link_ALPHA1-3 : angle 1.34464 ( 6) link_ALPHA1-6 : bond 0.00566 ( 1) link_ALPHA1-6 : angle 1.55791 ( 3) link_BETA1-4 : bond 0.00409 ( 11) link_BETA1-4 : angle 1.44394 ( 33) link_NAG-ASN : bond 0.00455 ( 51) link_NAG-ASN : angle 2.44341 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 337 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8537 (tpt) cc_final: 0.8043 (tpt) REVERT: A 330 HIS cc_start: 0.8795 (p90) cc_final: 0.8353 (p90) REVERT: A 360 ARG cc_start: 0.7753 (mtt-85) cc_final: 0.6919 (mtp85) REVERT: B 620 SER cc_start: 0.9198 (t) cc_final: 0.8967 (t) REVERT: G 81 GLN cc_start: 0.7342 (tp40) cc_final: 0.6888 (mm-40) REVERT: G 82 MET cc_start: 0.8293 (mtm) cc_final: 0.7912 (mtm) REVERT: C 104 MET cc_start: 0.8872 (ttt) cc_final: 0.8474 (ttt) REVERT: C 166 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.8053 (mtm-85) REVERT: C 232 LYS cc_start: 0.8526 (pttm) cc_final: 0.7699 (tmtt) REVERT: D 635 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8133 (tt) REVERT: J 81 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7855 (tm-30) REVERT: K 74 THR cc_start: 0.7919 (m) cc_final: 0.7682 (p) REVERT: K 75 ILE cc_start: 0.7549 (pt) cc_final: 0.7270 (pt) REVERT: E 125 LEU cc_start: 0.8831 (tp) cc_final: 0.8594 (tp) REVERT: E 139 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7789 (p) REVERT: E 143 ARG cc_start: 0.8126 (ttt-90) cc_final: 0.7413 (ttp-110) REVERT: F 540 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7981 (mt0) REVERT: M 27 TYR cc_start: 0.8844 (p90) cc_final: 0.8187 (p90) REVERT: M 70 SER cc_start: 0.8429 (p) cc_final: 0.7941 (m) REVERT: M 72 ASP cc_start: 0.8414 (t0) cc_final: 0.8055 (t0) REVERT: H 28 THR cc_start: 0.8486 (p) cc_final: 0.8237 (p) REVERT: H 86 ASP cc_start: 0.8433 (m-30) cc_final: 0.8112 (m-30) outliers start: 69 outliers final: 60 residues processed: 383 average time/residue: 0.1347 time to fit residues: 81.3373 Evaluate side-chains 393 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 330 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 482 LYS Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 93 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 242 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 37 optimal weight: 0.0170 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN D 540 GLN J 13 GLN E 432 GLN L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125979 restraints weight = 29243.478| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.50 r_work: 0.3395 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21481 Z= 0.161 Angle : 0.569 11.335 29274 Z= 0.280 Chirality : 0.044 0.281 3423 Planarity : 0.003 0.046 3618 Dihedral : 5.026 55.231 4140 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.96 % Rotamer: Outliers : 3.01 % Allowed : 13.53 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.17), residues: 2523 helix: 1.95 (0.28), residues: 381 sheet: 0.26 (0.18), residues: 822 loop : -0.36 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 83 TYR 0.017 0.001 TYR I 49 PHE 0.010 0.001 PHE J 100H TRP 0.013 0.001 TRP L 35 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00382 (21375) covalent geometry : angle 0.53614 (28997) SS BOND : bond 0.00294 ( 41) SS BOND : angle 0.87627 ( 82) hydrogen bonds : bond 0.03429 ( 584) hydrogen bonds : angle 4.39050 ( 1569) link_ALPHA1-3 : bond 0.01046 ( 2) link_ALPHA1-3 : angle 1.29750 ( 6) link_ALPHA1-6 : bond 0.00604 ( 1) link_ALPHA1-6 : angle 1.56503 ( 3) link_BETA1-4 : bond 0.00363 ( 11) link_BETA1-4 : angle 1.45963 ( 33) link_NAG-ASN : bond 0.00460 ( 51) link_NAG-ASN : angle 2.53196 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 338 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8647 (tpt) cc_final: 0.8130 (tpt) REVERT: A 330 HIS cc_start: 0.8838 (p90) cc_final: 0.8532 (p90) REVERT: A 360 ARG cc_start: 0.7759 (mtt-85) cc_final: 0.6969 (mtp85) REVERT: B 620 SER cc_start: 0.9225 (t) cc_final: 0.8996 (t) REVERT: G 81 GLN cc_start: 0.7350 (tp40) cc_final: 0.6854 (mm-40) REVERT: C 104 MET cc_start: 0.8917 (ttt) cc_final: 0.8512 (ttt) REVERT: C 166 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8086 (mtm-85) REVERT: C 232 LYS cc_start: 0.8570 (pttm) cc_final: 0.7778 (tmtt) REVERT: D 635 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8128 (tt) REVERT: J 81 GLN cc_start: 0.8610 (tm-30) cc_final: 0.7678 (tm-30) REVERT: J 82 HIS cc_start: 0.8191 (m-70) cc_final: 0.7833 (m-70) REVERT: K 74 THR cc_start: 0.7969 (m) cc_final: 0.7716 (p) REVERT: K 75 ILE cc_start: 0.7697 (pt) cc_final: 0.7467 (pt) REVERT: E 125 LEU cc_start: 0.8882 (tp) cc_final: 0.8663 (tp) REVERT: E 139 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7789 (p) REVERT: E 143 ARG cc_start: 0.8224 (ttt-90) cc_final: 0.7537 (ttp-110) REVERT: E 263 MET cc_start: 0.8460 (mmm) cc_final: 0.8163 (mmm) REVERT: F 540 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8083 (mt0) REVERT: M 27 TYR cc_start: 0.8853 (p90) cc_final: 0.8163 (p90) REVERT: M 72 ASP cc_start: 0.8443 (t0) cc_final: 0.8095 (t0) REVERT: H 28 THR cc_start: 0.8609 (p) cc_final: 0.8371 (p) REVERT: H 43 GLN cc_start: 0.7779 (mp10) cc_final: 0.7181 (mt0) REVERT: H 86 ASP cc_start: 0.8455 (m-30) cc_final: 0.8123 (m-30) outliers start: 67 outliers final: 60 residues processed: 384 average time/residue: 0.1402 time to fit residues: 83.7954 Evaluate side-chains 395 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 332 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 482 LYS Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 9 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 236 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 167 optimal weight: 0.0470 chunk 146 optimal weight: 0.0000 chunk 126 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** D 540 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 = 0.3860 r_free = 0.3860 target = 0.150802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125864 restraints weight = 28722.417| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.44 r_work: 0.3429 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21481 Z= 0.107 Angle : 0.534 11.078 29274 Z= 0.264 Chirality : 0.042 0.272 3423 Planarity : 0.003 0.038 3618 Dihedral : 4.861 56.359 4140 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 2.65 % Allowed : 14.07 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.17), residues: 2523 helix: 2.06 (0.28), residues: 383 sheet: 0.31 (0.18), residues: 810 loop : -0.32 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 83 TYR 0.012 0.001 TYR I 49 PHE 0.012 0.001 PHE G 29 TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00246 (21375) covalent geometry : angle 0.50218 (28997) SS BOND : bond 0.00231 ( 41) SS BOND : angle 0.78457 ( 82) hydrogen bonds : bond 0.03108 ( 584) hydrogen bonds : angle 4.26918 ( 1569) link_ALPHA1-3 : bond 0.00991 ( 2) link_ALPHA1-3 : angle 1.29577 ( 6) link_ALPHA1-6 : bond 0.00609 ( 1) link_ALPHA1-6 : angle 1.59238 ( 3) link_BETA1-4 : bond 0.00373 ( 11) link_BETA1-4 : angle 1.37406 ( 33) link_NAG-ASN : bond 0.00451 ( 51) link_NAG-ASN : angle 2.41885 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5005.11 seconds wall clock time: 86 minutes 30.78 seconds (5190.78 seconds total)