Starting phenix.real_space_refine on Wed Jun 18 05:21:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mii_48291/06_2025/9mii_48291.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mii_48291/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mii_48291/06_2025/9mii_48291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mii_48291/06_2025/9mii_48291.map" model { file = "/net/cci-nas-00/data/ceres_data/9mii_48291/06_2025/9mii_48291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mii_48291/06_2025/9mii_48291.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.97, per 1000 atoms: 0.62 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: 4.96 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.72 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: 7.43 Time building geometry restraints manager: 5.91 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 503 or resid 601 through 611)) selection = (chain 'C' and (resid 33 through 185 or resid 189 through 503 or resid 601 throu \ gh 611)) selection = (chain 'E' and (resid 33 through 449 or resid 455 through 495 or resid 601 throu \ gh 611)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 520 through 545 or resid 569 through 664 or resid 701)) selection = (chain 'F' and (resid 520 through 664 or resid 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: 6.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 47.960 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.500 ------------------------------------------------------------------------------- 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 : 2.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (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 TRP 0.027 0.003 TRP J 103 HIS 0.015 0.002 HIS E 366 PHE 0.031 0.003 PHE C 159 TYR 0.037 0.003 TYR H 96 ARG 0.029 0.002 ARG K 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00877 ( 51) link_NAG-ASN : angle 4.08428 ( 153) 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_ALPHA1-3 : bond 0.01703 ( 2) link_ALPHA1-3 : angle 1.49394 ( 6) hydrogen bonds : bond 0.13837 ( 584) hydrogen bonds : angle 6.51101 ( 1569) SS BOND : bond 0.00516 ( 41) SS BOND : angle 1.74132 ( 82) covalent geometry : bond 0.00634 (21375) covalent geometry : angle 1.13885 (28997) *********************** 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 : 2.152 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: 0.7182 (mt0) outliers start: 9 outliers final: 2 residues processed: 426 average time/residue: 0.3460 time to fit residues: 222.6766 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 : 2.144 ------------------------------------------------------------------------------- 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 211 optimal weight: 0.9980 chunk 190 optimal weight: 0.0470 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 overall best weight: 0.8078 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.157578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133037 restraints weight = 28462.748| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.40 r_work: 0.3516 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21481 Z= 0.142 Angle : 0.623 11.339 29274 Z= 0.312 Chirality : 0.044 0.258 3423 Planarity : 0.004 0.048 3618 Dihedral : 7.968 82.460 4145 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.89 % Allowed : 11.06 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2523 helix: 1.53 (0.28), residues: 383 sheet: 0.52 (0.18), residues: 838 loop : -0.35 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 103 HIS 0.005 0.001 HIS J 82A PHE 0.022 0.002 PHE J 67 TYR 0.016 0.001 TYR I 49 ARG 0.006 0.001 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 51) link_NAG-ASN : angle 3.01803 ( 153) link_ALPHA1-6 : bond 0.00150 ( 1) link_ALPHA1-6 : angle 1.90260 ( 3) link_BETA1-4 : bond 0.00448 ( 11) link_BETA1-4 : angle 2.01596 ( 33) link_ALPHA1-3 : bond 0.01240 ( 2) link_ALPHA1-3 : angle 1.47824 ( 6) hydrogen bonds : bond 0.04207 ( 584) hydrogen bonds : angle 5.10175 ( 1569) SS BOND : bond 0.00406 ( 41) SS BOND : angle 0.86767 ( 82) covalent geometry : bond 0.00320 (21375) covalent geometry : angle 0.58033 (28997) *********************** 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 429 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 387 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8538 (tpt) cc_final: 0.7674 (tpt) REVERT: A 211 GLU cc_start: 0.7907 (pt0) cc_final: 0.7636 (pt0) REVERT: A 360 ARG cc_start: 0.7949 (mtt-85) cc_final: 0.7066 (mtp85) REVERT: G 97 MET cc_start: 0.8987 (ttp) cc_final: 0.8702 (ttt) REVERT: C 104 MET cc_start: 0.8709 (ttt) cc_final: 0.8463 (ttt) REVERT: C 160 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7781 (m110) REVERT: C 166 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.7937 (mtm-85) REVERT: C 168 LYS cc_start: 0.8497 (mmmt) cc_final: 0.7967 (mmtp) REVERT: C 199 SER cc_start: 0.9262 (p) cc_final: 0.8687 (t) REVERT: C 232 LYS cc_start: 0.8408 (pttm) cc_final: 0.7603 (tmtt) REVERT: K 95 GLN cc_start: 0.8504 (mp10) cc_final: 0.8208 (mm-40) REVERT: E 142 MET cc_start: 0.8268 (mtp) cc_final: 0.7778 (ttm) REVERT: F 632 ASP cc_start: 0.8804 (t70) cc_final: 0.8549 (t0) REVERT: M 49 SER cc_start: 0.8435 (t) cc_final: 0.8070 (m) REVERT: M 72 ASP cc_start: 0.8337 (t70) cc_final: 0.7868 (t0) REVERT: N 60 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7936 (t0) outliers start: 42 outliers final: 26 residues processed: 409 average time/residue: 0.3170 time to fit residues: 200.5277 Evaluate side-chains 385 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 357 time to evaluate : 2.099 ------------------------------------------------------------------------------- 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 I residue 58 VAL Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain K residue 12 SER 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 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 51 VAL Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 25 optimal weight: 6.9990 chunk 195 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 126 optimal weight: 0.0980 chunk 231 optimal weight: 0.9980 chunk 242 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 216 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN E 340 GLN F 543 ASN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.161677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136348 restraints weight = 29541.520| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.55 r_work: 0.3486 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21481 Z= 0.130 Angle : 0.574 11.248 29274 Z= 0.285 Chirality : 0.044 0.275 3423 Planarity : 0.003 0.037 3618 Dihedral : 6.720 68.910 4142 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.16 % Allowed : 11.96 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2523 helix: 1.85 (0.29), residues: 380 sheet: 0.50 (0.18), residues: 830 loop : -0.28 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.005 0.001 HIS E 366 PHE 0.020 0.001 PHE A 53 TYR 0.018 0.001 TYR E 165 ARG 0.006 0.000 ARG G 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 51) link_NAG-ASN : angle 2.75663 ( 153) link_ALPHA1-6 : bond 0.00496 ( 1) link_ALPHA1-6 : angle 1.73046 ( 3) link_BETA1-4 : bond 0.00479 ( 11) link_BETA1-4 : angle 1.80577 ( 33) link_ALPHA1-3 : bond 0.01477 ( 2) link_ALPHA1-3 : angle 1.14959 ( 6) hydrogen bonds : bond 0.03672 ( 584) hydrogen bonds : angle 4.71678 ( 1569) SS BOND : bond 0.00262 ( 41) SS BOND : angle 0.65051 ( 82) covalent geometry : bond 0.00299 (21375) covalent geometry : angle 0.53544 (28997) *********************** 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 415 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 367 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8525 (tpt) cc_final: 0.7830 (tpt) REVERT: A 360 ARG cc_start: 0.7738 (mtt-85) cc_final: 0.6972 (mtp85) REVERT: G 81 GLN cc_start: 0.7654 (tp40) cc_final: 0.7372 (mm-40) REVERT: C 104 MET cc_start: 0.8635 (ttt) cc_final: 0.8345 (ttt) REVERT: C 160 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7977 (m110) REVERT: C 166 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.7895 (mtm-85) REVERT: C 168 LYS cc_start: 0.8454 (mmmt) cc_final: 0.8009 (mmtp) REVERT: C 199 SER cc_start: 0.9247 (p) cc_final: 0.8663 (t) REVERT: C 232 LYS cc_start: 0.8433 (pttm) cc_final: 0.7682 (tmtt) REVERT: C 475 MET cc_start: 0.8285 (mmt) cc_final: 0.7982 (mmt) REVERT: D 621 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8223 (mt-10) REVERT: D 635 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7946 (tt) REVERT: J 81 GLN cc_start: 0.8681 (tm-30) cc_final: 0.7609 (tm-30) REVERT: K 95 GLN cc_start: 0.8333 (mp10) cc_final: 0.8126 (mm-40) REVERT: E 418 MET cc_start: 0.7862 (mtp) cc_final: 0.7581 (mmm) REVERT: M 27 TYR cc_start: 0.8527 (p90) cc_final: 0.8024 (p90) REVERT: M 72 ASP cc_start: 0.8316 (t70) cc_final: 0.7839 (t0) REVERT: N 85 ASP cc_start: 0.8083 (m-30) cc_final: 0.7829 (m-30) REVERT: L 62 PHE cc_start: 0.7214 (m-80) cc_final: 0.6901 (m-10) REVERT: L 86 TYR cc_start: 0.7648 (m-80) cc_final: 0.7424 (m-80) outliers start: 48 outliers final: 37 residues processed: 395 average time/residue: 0.3413 time to fit residues: 211.1086 Evaluate side-chains 388 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 349 time to evaluate : 2.148 ------------------------------------------------------------------------------- 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 20 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 320 THR 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 19 VAL 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 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 F residue 636 SER Chi-restraints excluded: chain F residue 660 LEU 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 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 L residue 11 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 87 optimal weight: 1.9990 chunk 232 optimal weight: 0.2980 chunk 245 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 0.0770 chunk 89 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 E 340 GLN F 543 ASN L 38 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.156508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.131580 restraints weight = 28781.267| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.45 r_work: 0.3509 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21481 Z= 0.110 Angle : 0.536 11.326 29274 Z= 0.266 Chirality : 0.043 0.273 3423 Planarity : 0.003 0.046 3618 Dihedral : 5.992 58.994 4142 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.05 % Favored : 96.91 % Rotamer: Outliers : 2.11 % Allowed : 12.63 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2523 helix: 1.99 (0.29), residues: 380 sheet: 0.51 (0.18), residues: 819 loop : -0.27 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.004 0.001 HIS E 366 PHE 0.018 0.001 PHE A 53 TYR 0.015 0.001 TYR L 91 ARG 0.006 0.000 ARG I 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 51) link_NAG-ASN : angle 2.61580 ( 153) link_ALPHA1-6 : bond 0.00470 ( 1) link_ALPHA1-6 : angle 1.56306 ( 3) link_BETA1-4 : bond 0.00433 ( 11) link_BETA1-4 : angle 1.68370 ( 33) link_ALPHA1-3 : bond 0.01421 ( 2) link_ALPHA1-3 : angle 1.23268 ( 6) hydrogen bonds : bond 0.03310 ( 584) hydrogen bonds : angle 4.49431 ( 1569) SS BOND : bond 0.00232 ( 41) SS BOND : angle 0.55562 ( 82) covalent geometry : bond 0.00246 (21375) covalent geometry : angle 0.49920 (28997) *********************** 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 409 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 362 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8515 (tpt) cc_final: 0.7916 (tpt) REVERT: A 360 ARG cc_start: 0.7934 (mtt-85) cc_final: 0.7128 (mtp85) REVERT: G 81 GLN cc_start: 0.7694 (tp40) cc_final: 0.7277 (mm-40) REVERT: C 104 MET cc_start: 0.8774 (ttt) cc_final: 0.8471 (ttt) REVERT: C 166 ARG cc_start: 0.8422 (mtm-85) cc_final: 0.7986 (mtm-85) REVERT: C 168 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8049 (mmtp) REVERT: C 199 SER cc_start: 0.9316 (p) cc_final: 0.8835 (t) REVERT: C 232 LYS cc_start: 0.8498 (pttm) cc_final: 0.7670 (tmtt) REVERT: D 635 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8021 (tt) REVERT: J 81 GLN cc_start: 0.8692 (tm-30) cc_final: 0.7612 (tm-30) REVERT: E 141 ASP cc_start: 0.6794 (p0) cc_final: 0.6573 (p0) REVERT: E 142 MET cc_start: 0.8259 (mtp) cc_final: 0.7738 (ttm) REVERT: E 418 MET cc_start: 0.7985 (mtp) cc_final: 0.7631 (mmm) REVERT: M 23 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7783 (ttm170) REVERT: M 27 TYR cc_start: 0.8724 (p90) cc_final: 0.8092 (p90) REVERT: M 72 ASP cc_start: 0.8416 (t0) cc_final: 0.7896 (t0) REVERT: N 85 ASP cc_start: 0.8130 (m-30) cc_final: 0.7755 (m-30) REVERT: H 87 THR cc_start: 0.8752 (t) cc_final: 0.8538 (t) REVERT: L 62 PHE cc_start: 0.7209 (m-80) cc_final: 0.6786 (m-10) REVERT: L 79 GLN cc_start: 0.7960 (tt0) cc_final: 0.7659 (tt0) outliers start: 47 outliers final: 40 residues processed: 390 average time/residue: 0.3088 time to fit residues: 187.4577 Evaluate side-chains 386 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 345 time to evaluate : 2.272 ------------------------------------------------------------------------------- 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 I residue 58 VAL Chi-restraints excluded: chain C residue 364 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 19 VAL 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 315 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 660 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 68 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 235 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** C 133 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN F 543 ASN L 37 GLN L 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.152663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127747 restraints weight = 28560.209| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.41 r_work: 0.3452 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21481 Z= 0.150 Angle : 0.554 11.352 29274 Z= 0.276 Chirality : 0.044 0.280 3423 Planarity : 0.004 0.035 3618 Dihedral : 5.671 58.017 4140 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 2.74 % Allowed : 12.22 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2523 helix: 1.88 (0.28), residues: 381 sheet: 0.53 (0.18), residues: 766 loop : -0.33 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.004 0.001 HIS C 249 PHE 0.016 0.001 PHE A 53 TYR 0.021 0.001 TYR E 165 ARG 0.005 0.000 ARG I 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 51) link_NAG-ASN : angle 2.55990 ( 153) link_ALPHA1-6 : bond 0.00579 ( 1) link_ALPHA1-6 : angle 1.39119 ( 3) link_BETA1-4 : bond 0.00416 ( 11) link_BETA1-4 : angle 1.68849 ( 33) link_ALPHA1-3 : bond 0.01316 ( 2) link_ALPHA1-3 : angle 1.17144 ( 6) hydrogen bonds : bond 0.03523 ( 584) hydrogen bonds : angle 4.46683 ( 1569) SS BOND : bond 0.00284 ( 41) SS BOND : angle 0.66818 ( 82) covalent geometry : bond 0.00350 (21375) covalent geometry : angle 0.52022 (28997) *********************** 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 426 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 365 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8489 (tm-30) cc_final: 0.7751 (tm-30) REVERT: A 161 MET cc_start: 0.8621 (tpt) cc_final: 0.8094 (tpt) REVERT: A 360 ARG cc_start: 0.7873 (mtt-85) cc_final: 0.7042 (mtp85) REVERT: G 81 GLN cc_start: 0.7634 (tp40) cc_final: 0.7225 (mm-40) REVERT: C 104 MET cc_start: 0.8831 (ttt) cc_final: 0.8501 (ttt) REVERT: C 166 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.8006 (mtm-85) REVERT: C 168 LYS cc_start: 0.8510 (mmmt) cc_final: 0.7963 (mmtp) REVERT: C 199 SER cc_start: 0.9338 (p) cc_final: 0.8833 (t) REVERT: C 232 LYS cc_start: 0.8548 (pttm) cc_final: 0.7614 (tmtt) REVERT: C 475 MET cc_start: 0.8417 (mmt) cc_final: 0.8146 (mmt) REVERT: D 635 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8039 (tt) REVERT: J 81 GLN cc_start: 0.8630 (tm-30) cc_final: 0.7552 (tm-30) REVERT: J 83 ARG cc_start: 0.7549 (mtt-85) cc_final: 0.7349 (mtt-85) REVERT: E 142 MET cc_start: 0.8287 (mtp) cc_final: 0.7851 (ttm) REVERT: E 418 MET cc_start: 0.7855 (mtp) cc_final: 0.7588 (mmm) REVERT: F 626 MET cc_start: 0.8973 (ttm) cc_final: 0.8756 (mtp) REVERT: M 23 ARG cc_start: 0.8003 (ttm110) cc_final: 0.7783 (ttm170) REVERT: M 72 ASP cc_start: 0.8405 (t0) cc_final: 0.7886 (t0) REVERT: N 85 ASP cc_start: 0.8146 (m-30) cc_final: 0.7766 (m-30) REVERT: L 37 GLN cc_start: 0.8855 (tt0) cc_final: 0.8620 (tt0) outliers start: 61 outliers final: 52 residues processed: 397 average time/residue: 0.3140 time to fit residues: 194.5156 Evaluate side-chains 402 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 349 time to evaluate : 2.120 ------------------------------------------------------------------------------- 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 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 I residue 58 VAL Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 320 THR 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 19 VAL 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 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 660 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 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 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 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 221 optimal weight: 0.0020 chunk 57 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 146 optimal weight: 0.2980 chunk 227 optimal weight: 7.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 F 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.152007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127290 restraints weight = 28581.075| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.40 r_work: 0.3450 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21481 Z= 0.106 Angle : 0.519 11.111 29274 Z= 0.259 Chirality : 0.043 0.302 3423 Planarity : 0.003 0.044 3618 Dihedral : 5.383 59.384 4140 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 2.70 % Allowed : 13.21 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2523 helix: 2.02 (0.29), residues: 381 sheet: 0.53 (0.18), residues: 773 loop : -0.29 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS E 366 PHE 0.018 0.001 PHE L 62 TYR 0.016 0.001 TYR E 165 ARG 0.004 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 51) link_NAG-ASN : angle 2.44838 ( 153) link_ALPHA1-6 : bond 0.00471 ( 1) link_ALPHA1-6 : angle 1.48806 ( 3) link_BETA1-4 : bond 0.00421 ( 11) link_BETA1-4 : angle 1.57783 ( 33) link_ALPHA1-3 : bond 0.01304 ( 2) link_ALPHA1-3 : angle 1.10123 ( 6) hydrogen bonds : bond 0.03196 ( 584) hydrogen bonds : angle 4.34834 ( 1569) SS BOND : bond 0.00216 ( 41) SS BOND : angle 0.55871 ( 82) covalent geometry : bond 0.00240 (21375) covalent geometry : angle 0.48553 (28997) *********************** 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 411 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 351 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 161 MET cc_start: 0.8541 (tpt) cc_final: 0.7897 (tpt) REVERT: A 360 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.7002 (mtp85) REVERT: B 620 SER cc_start: 0.9133 (t) cc_final: 0.8888 (t) REVERT: G 59 TYR cc_start: 0.8273 (m-80) cc_final: 0.8042 (m-10) REVERT: G 81 GLN cc_start: 0.7510 (tp40) cc_final: 0.7041 (mm-40) REVERT: I 53 GLN cc_start: 0.8536 (mp10) cc_final: 0.8316 (mp10) REVERT: C 104 MET cc_start: 0.8809 (ttt) cc_final: 0.8475 (ttt) REVERT: C 166 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.7970 (mtm-85) REVERT: C 168 LYS cc_start: 0.8458 (mmmt) cc_final: 0.7917 (mmtp) REVERT: C 199 SER cc_start: 0.9308 (p) cc_final: 0.8842 (t) REVERT: C 232 LYS cc_start: 0.8546 (pttm) cc_final: 0.7583 (tmtt) REVERT: C 475 MET cc_start: 0.8309 (mmt) cc_final: 0.8083 (mmt) REVERT: J 81 GLN cc_start: 0.8646 (tm-30) cc_final: 0.7604 (tm-30) REVERT: K 74 THR cc_start: 0.7783 (m) cc_final: 0.7518 (p) REVERT: E 142 MET cc_start: 0.8123 (mtp) cc_final: 0.7765 (ttm) REVERT: E 418 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7404 (mmm) REVERT: F 540 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8090 (mt0) REVERT: M 23 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7745 (ttm170) REVERT: M 27 TYR cc_start: 0.8823 (p90) cc_final: 0.8152 (p90) REVERT: M 72 ASP cc_start: 0.8383 (t0) cc_final: 0.7873 (t0) REVERT: N 85 ASP cc_start: 0.8015 (m-30) cc_final: 0.7649 (m-30) REVERT: H 87 THR cc_start: 0.8640 (t) cc_final: 0.8358 (t) outliers start: 60 outliers final: 47 residues processed: 388 average time/residue: 0.3131 time to fit residues: 190.0034 Evaluate side-chains 392 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 343 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 544 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 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 364 SER Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 19 VAL 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 315 ILE Chi-restraints excluded: chain E residue 418 MET Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 540 GLN 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 221 optimal weight: 0.0040 chunk 0 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- 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 133 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN K 37 GLN E 85 HIS E 322 HIS F 543 ASN H 64 GLN L 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.123595 restraints weight = 28707.495| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.38 r_work: 0.3390 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21481 Z= 0.183 Angle : 0.566 11.392 29274 Z= 0.284 Chirality : 0.044 0.283 3423 Planarity : 0.004 0.039 3618 Dihedral : 5.363 59.660 4140 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer: Outliers : 3.06 % Allowed : 12.94 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2523 helix: 1.74 (0.28), residues: 387 sheet: 0.43 (0.18), residues: 801 loop : -0.42 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.004 0.001 HIS C 249 PHE 0.015 0.002 PHE A 53 TYR 0.018 0.002 TYR I 49 ARG 0.009 0.001 ARG I 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 51) link_NAG-ASN : angle 2.53194 ( 153) link_ALPHA1-6 : bond 0.00488 ( 1) link_ALPHA1-6 : angle 1.51101 ( 3) link_BETA1-4 : bond 0.00387 ( 11) link_BETA1-4 : angle 1.60851 ( 33) link_ALPHA1-3 : bond 0.01221 ( 2) link_ALPHA1-3 : angle 1.23308 ( 6) hydrogen bonds : bond 0.03676 ( 584) hydrogen bonds : angle 4.50335 ( 1569) SS BOND : bond 0.00326 ( 41) SS BOND : angle 0.70125 ( 82) covalent geometry : bond 0.00433 (21375) covalent geometry : angle 0.53381 (28997) *********************** 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: 68 poor density : 359 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 161 MET cc_start: 0.8679 (tpt) cc_final: 0.8062 (tpt) REVERT: A 330 HIS cc_start: 0.8844 (p90) cc_final: 0.8487 (p90) REVERT: A 360 ARG cc_start: 0.7773 (mtt-85) cc_final: 0.6954 (mtp85) REVERT: B 620 SER cc_start: 0.9189 (t) cc_final: 0.8952 (t) REVERT: G 81 GLN cc_start: 0.7469 (tp40) cc_final: 0.6989 (mm-40) REVERT: C 104 MET cc_start: 0.8865 (ttt) cc_final: 0.8525 (ttt) REVERT: C 168 LYS cc_start: 0.8452 (mmmt) cc_final: 0.7905 (mmtp) REVERT: C 217 TYR cc_start: 0.9021 (m-80) cc_final: 0.8623 (m-80) REVERT: C 232 LYS cc_start: 0.8547 (pttm) cc_final: 0.7626 (tmtt) REVERT: C 475 MET cc_start: 0.8402 (mmt) cc_final: 0.8191 (mmt) REVERT: J 38 ARG cc_start: 0.8930 (ptp90) cc_final: 0.8573 (ptp90) REVERT: J 81 GLN cc_start: 0.8670 (tm-30) cc_final: 0.7616 (tm-30) REVERT: E 142 MET cc_start: 0.8143 (mtp) cc_final: 0.7909 (ttm) REVERT: F 626 MET cc_start: 0.8886 (ttm) cc_final: 0.8672 (mtp) REVERT: M 23 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7819 (ttm170) REVERT: M 27 TYR cc_start: 0.8846 (p90) cc_final: 0.8198 (p90) REVERT: M 72 ASP cc_start: 0.8432 (t0) cc_final: 0.8105 (t0) REVERT: N 85 ASP cc_start: 0.8064 (m-30) cc_final: 0.7656 (m-30) REVERT: L 61 ARG cc_start: 0.7479 (mtm180) cc_final: 0.6957 (ptt180) outliers start: 68 outliers final: 62 residues processed: 401 average time/residue: 0.3299 time to fit residues: 204.3884 Evaluate side-chains 408 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 346 time to evaluate : 2.097 ------------------------------------------------------------------------------- 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 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 20 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 58 VAL 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 546 SER Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 19 VAL 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 193 ILE Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 322 HIS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 599 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 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 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 97 VAL 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 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 232 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 K 53 GLN F 540 GLN F 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124025 restraints weight = 28848.187| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.39 r_work: 0.3392 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 21481 Z= 0.156 Angle : 0.557 11.203 29274 Z= 0.279 Chirality : 0.043 0.274 3423 Planarity : 0.004 0.042 3618 Dihedral : 5.282 57.390 4140 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.35 % Rotamer: Outliers : 3.28 % Allowed : 13.12 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2523 helix: 1.85 (0.28), residues: 381 sheet: 0.38 (0.18), residues: 801 loop : -0.42 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 571 HIS 0.013 0.001 HIS E 322 PHE 0.012 0.001 PHE M 102 TYR 0.016 0.001 TYR I 49 ARG 0.009 0.000 ARG J 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 51) link_NAG-ASN : angle 2.49658 ( 153) link_ALPHA1-6 : bond 0.00535 ( 1) link_ALPHA1-6 : angle 1.55723 ( 3) link_BETA1-4 : bond 0.00384 ( 11) link_BETA1-4 : angle 1.49839 ( 33) link_ALPHA1-3 : bond 0.01133 ( 2) link_ALPHA1-3 : angle 1.22375 ( 6) hydrogen bonds : bond 0.03522 ( 584) hydrogen bonds : angle 4.47023 ( 1569) SS BOND : bond 0.00350 ( 41) SS BOND : angle 0.98894 ( 82) covalent geometry : bond 0.00366 (21375) covalent geometry : angle 0.52411 (28997) *********************** 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 426 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 353 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8428 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 161 MET cc_start: 0.8622 (tpt) cc_final: 0.8079 (tpt) REVERT: A 330 HIS cc_start: 0.8836 (p90) cc_final: 0.8480 (p90) REVERT: A 360 ARG cc_start: 0.7779 (mtt-85) cc_final: 0.6961 (mtp85) REVERT: B 620 SER cc_start: 0.9188 (t) cc_final: 0.8951 (t) REVERT: G 81 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6961 (mm-40) REVERT: C 104 MET cc_start: 0.8866 (ttt) cc_final: 0.8463 (ttt) REVERT: C 166 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.8125 (mtm-85) REVERT: C 199 SER cc_start: 0.9303 (p) cc_final: 0.8908 (t) REVERT: C 217 TYR cc_start: 0.9036 (m-80) cc_final: 0.8691 (m-80) REVERT: C 232 LYS cc_start: 0.8530 (pttm) cc_final: 0.7727 (tmtt) REVERT: J 38 ARG cc_start: 0.8871 (ptp90) cc_final: 0.8578 (ptp90) REVERT: J 81 GLN cc_start: 0.8686 (tm-30) cc_final: 0.7647 (tm-30) REVERT: K 95 GLN cc_start: 0.8508 (mp10) cc_final: 0.8279 (mm-40) REVERT: E 142 MET cc_start: 0.8128 (mtp) cc_final: 0.7873 (ttm) REVERT: E 143 ARG cc_start: 0.8117 (ttt-90) cc_final: 0.7419 (ttp-110) REVERT: F 626 MET cc_start: 0.8896 (ttm) cc_final: 0.8692 (mtp) REVERT: M 23 ARG cc_start: 0.8046 (ttm110) cc_final: 0.7812 (ttm170) REVERT: M 27 TYR cc_start: 0.8837 (p90) cc_final: 0.8204 (p90) REVERT: M 72 ASP cc_start: 0.8459 (t0) cc_final: 0.7884 (t0) REVERT: M 75 LYS cc_start: 0.9171 (mmmt) cc_final: 0.8942 (mmmt) REVERT: N 85 ASP cc_start: 0.8044 (m-30) cc_final: 0.7770 (m-30) outliers start: 73 outliers final: 64 residues processed: 397 average time/residue: 0.3289 time to fit residues: 202.8433 Evaluate side-chains 410 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 345 time to evaluate : 2.200 ------------------------------------------------------------------------------- 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 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 81 GLN 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 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 334 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 19 VAL 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 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 46 GLU 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 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 100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 86 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 92 optimal weight: 0.0000 chunk 216 optimal weight: 2.9990 chunk 96 optimal weight: 0.0870 chunk 117 optimal weight: 0.1980 chunk 176 optimal weight: 0.7980 chunk 188 optimal weight: 0.0470 chunk 214 optimal weight: 0.0980 overall best weight: 0.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 280 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN F 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.154054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129595 restraints weight = 28602.904| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.40 r_work: 0.3476 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21481 Z= 0.088 Angle : 0.511 10.852 29274 Z= 0.256 Chirality : 0.042 0.264 3423 Planarity : 0.003 0.041 3618 Dihedral : 4.806 59.191 4140 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.29 % Favored : 96.63 % Rotamer: Outliers : 2.02 % Allowed : 14.61 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.17), residues: 2523 helix: 2.12 (0.29), residues: 383 sheet: 0.42 (0.18), residues: 810 loop : -0.30 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 571 HIS 0.003 0.000 HIS E 366 PHE 0.011 0.001 PHE A 53 TYR 0.014 0.001 TYR E 165 ARG 0.011 0.000 ARG J 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 51) link_NAG-ASN : angle 2.32208 ( 153) link_ALPHA1-6 : bond 0.00241 ( 1) link_ALPHA1-6 : angle 1.50778 ( 3) link_BETA1-4 : bond 0.00453 ( 11) link_BETA1-4 : angle 1.37924 ( 33) link_ALPHA1-3 : bond 0.01264 ( 2) link_ALPHA1-3 : angle 1.35772 ( 6) hydrogen bonds : bond 0.02876 ( 584) hydrogen bonds : angle 4.19655 ( 1569) SS BOND : bond 0.00189 ( 41) SS BOND : angle 0.85864 ( 82) covalent geometry : bond 0.00188 (21375) covalent geometry : angle 0.48042 (28997) *********************** 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 414 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 369 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8445 (tpt) cc_final: 0.7963 (tpt) REVERT: A 360 ARG cc_start: 0.7790 (mtt-85) cc_final: 0.6935 (mtp85) REVERT: B 620 SER cc_start: 0.9124 (t) cc_final: 0.8889 (t) REVERT: G 81 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.6881 (mm-40) REVERT: G 82 MET cc_start: 0.8121 (mtm) cc_final: 0.7838 (mtt) REVERT: C 104 MET cc_start: 0.8853 (ttt) cc_final: 0.8448 (ttt) REVERT: C 166 ARG cc_start: 0.8363 (mtm-85) cc_final: 0.8139 (mtm-85) REVERT: C 168 LYS cc_start: 0.8305 (mmmt) cc_final: 0.7654 (mmtp) REVERT: C 232 LYS cc_start: 0.8514 (pttm) cc_final: 0.7676 (tmtt) REVERT: C 426 MET cc_start: 0.8335 (tpt) cc_final: 0.7675 (tpt) REVERT: D 635 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7962 (tt) REVERT: J 81 GLN cc_start: 0.8614 (tm-30) cc_final: 0.7943 (tm-30) REVERT: K 95 GLN cc_start: 0.8453 (mp10) cc_final: 0.8222 (mm-40) REVERT: E 121 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8220 (mmtt) REVERT: E 157 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8254 (mt) REVERT: E 476 TYR cc_start: 0.8547 (p90) cc_final: 0.8321 (p90) REVERT: M 23 ARG cc_start: 0.8006 (ttm110) cc_final: 0.7782 (ttm170) REVERT: M 27 TYR cc_start: 0.8788 (p90) cc_final: 0.8230 (p90) REVERT: M 70 SER cc_start: 0.8446 (p) cc_final: 0.7952 (m) REVERT: M 72 ASP cc_start: 0.8381 (t0) cc_final: 0.7847 (t0) REVERT: M 75 LYS cc_start: 0.9177 (mmmt) cc_final: 0.8970 (mmmt) REVERT: N 85 ASP cc_start: 0.8027 (m-30) cc_final: 0.7638 (m-30) REVERT: H 43 GLN cc_start: 0.7658 (mp10) cc_final: 0.7118 (mt0) REVERT: H 53 LYS cc_start: 0.8485 (tptt) cc_final: 0.7790 (ttpp) REVERT: H 87 THR cc_start: 0.8494 (t) cc_final: 0.8142 (t) outliers start: 45 outliers final: 36 residues processed: 395 average time/residue: 0.3293 time to fit residues: 201.5242 Evaluate side-chains 386 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 347 time to evaluate : 2.130 ------------------------------------------------------------------------------- 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 150 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain K residue 24 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 157 LEU 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 544 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain M residue 82 LEU 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 21 SER 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 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 223 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN I 79 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.150268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125256 restraints weight = 29212.590| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.40 r_work: 0.3364 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 21481 Z= 0.231 Angle : 0.617 11.441 29274 Z= 0.308 Chirality : 0.046 0.295 3423 Planarity : 0.004 0.042 3618 Dihedral : 5.173 57.306 4140 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.20 % Favored : 95.72 % Rotamer: Outliers : 1.98 % Allowed : 15.24 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2523 helix: 1.80 (0.28), residues: 381 sheet: 0.38 (0.18), residues: 803 loop : -0.49 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 571 HIS 0.005 0.001 HIS C 249 PHE 0.017 0.002 PHE M 102 TYR 0.019 0.002 TYR I 49 ARG 0.009 0.001 ARG I 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 51) link_NAG-ASN : angle 2.58708 ( 153) link_ALPHA1-6 : bond 0.00524 ( 1) link_ALPHA1-6 : angle 1.52321 ( 3) link_BETA1-4 : bond 0.00375 ( 11) link_BETA1-4 : angle 1.54645 ( 33) link_ALPHA1-3 : bond 0.01039 ( 2) link_ALPHA1-3 : angle 1.37029 ( 6) hydrogen bonds : bond 0.03877 ( 584) hydrogen bonds : angle 4.52658 ( 1569) SS BOND : bond 0.00401 ( 41) SS BOND : angle 1.03432 ( 82) covalent geometry : bond 0.00549 (21375) covalent geometry : angle 0.58561 (28997) ********************** 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 399 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 355 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8518 (tm-30) cc_final: 0.7886 (tm-30) REVERT: A 330 HIS cc_start: 0.8881 (p90) cc_final: 0.8625 (p90) REVERT: A 360 ARG cc_start: 0.7777 (mtt-85) cc_final: 0.6921 (mtp85) REVERT: B 620 SER cc_start: 0.9231 (t) cc_final: 0.9000 (t) REVERT: G 81 GLN cc_start: 0.7362 (tp40) cc_final: 0.6886 (mm-40) REVERT: I 54 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8404 (ttp80) REVERT: C 104 MET cc_start: 0.8909 (ttt) cc_final: 0.8557 (ttt) REVERT: C 166 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.8078 (mtm-85) REVERT: C 217 TYR cc_start: 0.9062 (m-80) cc_final: 0.8685 (m-80) REVERT: C 232 LYS cc_start: 0.8593 (pttm) cc_final: 0.7802 (tmtt) REVERT: C 381 GLU cc_start: 0.7852 (tt0) cc_final: 0.7583 (mt-10) REVERT: D 632 ASP cc_start: 0.8950 (t70) cc_final: 0.8662 (t70) REVERT: J 38 ARG cc_start: 0.8986 (ptp90) cc_final: 0.8641 (ptp90) REVERT: J 81 GLN cc_start: 0.8668 (tm-30) cc_final: 0.7605 (tm-30) REVERT: E 143 ARG cc_start: 0.8207 (ttt-90) cc_final: 0.7623 (ttm110) REVERT: E 157 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8307 (mt) REVERT: M 23 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7786 (ttm170) REVERT: M 72 ASP cc_start: 0.8531 (t0) cc_final: 0.8127 (t0) REVERT: N 47 MET cc_start: 0.7522 (mtt) cc_final: 0.7110 (mtt) REVERT: N 85 ASP cc_start: 0.8152 (m-30) cc_final: 0.7838 (m-30) outliers start: 44 outliers final: 40 residues processed: 382 average time/residue: 0.3384 time to fit residues: 198.0131 Evaluate side-chains 383 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 342 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain B residue 544 LEU 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 75 ILE Chi-restraints excluded: chain I residue 89 SER 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 599 SER Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain K residue 24 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 83 GLU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 157 LEU 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 544 LEU 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 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 21 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 97 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 76 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.148697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.123100 restraints weight = 29020.081| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.50 r_work: 0.3388 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21481 Z= 0.156 Angle : 0.570 11.115 29274 Z= 0.285 Chirality : 0.044 0.273 3423 Planarity : 0.004 0.103 3618 Dihedral : 5.106 58.657 4140 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.20 % Rotamer: Outliers : 2.07 % Allowed : 15.46 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2523 helix: 1.87 (0.28), residues: 381 sheet: 0.31 (0.18), residues: 813 loop : -0.49 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 47 HIS 0.003 0.001 HIS E 366 PHE 0.011 0.001 PHE A 53 TYR 0.016 0.001 TYR M 27 ARG 0.009 0.000 ARG J 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 51) link_NAG-ASN : angle 2.49657 ( 153) link_ALPHA1-6 : bond 0.00614 ( 1) link_ALPHA1-6 : angle 1.58963 ( 3) link_BETA1-4 : bond 0.00363 ( 11) link_BETA1-4 : angle 1.42887 ( 33) link_ALPHA1-3 : bond 0.00995 ( 2) link_ALPHA1-3 : angle 1.30374 ( 6) hydrogen bonds : bond 0.03504 ( 584) hydrogen bonds : angle 4.44449 ( 1569) SS BOND : bond 0.00303 ( 41) SS BOND : angle 0.92227 ( 82) covalent geometry : bond 0.00370 (21375) covalent geometry : angle 0.53849 (28997) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10962.83 seconds wall clock time: 189 minutes 11.31 seconds (11351.31 seconds total)