Starting phenix.real_space_refine on Tue Mar 3 16:23:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nyx_49945/03_2026/9nyx_49945_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nyx_49945/03_2026/9nyx_49945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nyx_49945/03_2026/9nyx_49945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nyx_49945/03_2026/9nyx_49945.map" model { file = "/net/cci-nas-00/data/ceres_data/9nyx_49945/03_2026/9nyx_49945_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nyx_49945/03_2026/9nyx_49945_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 58 5.16 5 C 4456 2.51 5 N 1042 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6762 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 835 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Chain: "C" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 849 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain breaks: 1 Chain: "B" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2452 Unusual residues: {'ACE': 1} Classifications: {'peptide': 308, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'ACE_C-N': 1, 'PTRANS': 18, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2452 Unusual residues: {'ACE': 1} Classifications: {'peptide': 308, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'ACE_C-N': 1, 'PTRANS': 18, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" 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: "F" 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: "G" 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: "H" 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: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU B 458 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU B 458 " occ=0.97 residue: pdb=" N LYS D 542 " occ=0.90 ... (7 atoms not shown) pdb=" NZ LYS D 542 " occ=0.90 Time building chain proxies: 1.42, per 1000 atoms: 0.21 Number of scatterers: 6762 At special positions: 0 Unit cell: (70.62, 107, 109.14, 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 58 16.00 O 1206 8.00 N 1042 7.00 C 4456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 409 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 588 " 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN B 403 " " NAG F 1 " - " ASN B 416 " " NAG G 1 " - " ASN D 403 " " NAG H 1 " - " ASN D 416 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 271.7 milliseconds 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 56.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 461 through 464 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'C' and resid 474 through 478 removed outlier: 3.772A pdb=" N THR C 478 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 removed outlier: 4.063A pdb=" N THR B 418 " --> pdb=" O SER B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 466 removed outlier: 3.802A pdb=" N PHE B 438 " --> pdb=" O GLU B 434 " (cutoff:3.500A) Proline residue: B 454 - end of helix Processing helix chain 'B' and resid 471 through 502 removed outlier: 3.534A pdb=" N PHE B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 541 Processing helix chain 'B' and resid 551 through 570 removed outlier: 3.599A pdb=" N CYS B 568 " --> pdb=" O MET B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 600 through 612 removed outlier: 3.595A pdb=" N PHE B 604 " --> pdb=" O ASN B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 629 Processing helix chain 'B' and resid 646 through 679 removed outlier: 3.779A pdb=" N GLU B 650 " --> pdb=" O LYS B 646 " (cutoff:3.500A) Proline residue: B 668 - end of helix Processing helix chain 'B' and resid 686 through 697 Proline residue: B 692 - end of helix Processing helix chain 'B' and resid 698 through 710 removed outlier: 3.575A pdb=" N TYR B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASN B 703 " --> pdb=" O SER B 699 " (cutoff:3.500A) Proline residue: B 704 - end of helix Processing helix chain 'B' and resid 711 through 722 Processing helix chain 'D' and resid 415 through 419 removed outlier: 3.993A pdb=" N THR D 418 " --> pdb=" O SER D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 466 removed outlier: 3.615A pdb=" N PHE D 438 " --> pdb=" O GLU D 434 " (cutoff:3.500A) Proline residue: D 454 - end of helix Processing helix chain 'D' and resid 471 through 502 removed outlier: 3.703A pdb=" N PHE D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR D 494 " --> pdb=" O GLY D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 542 Processing helix chain 'D' and resid 550 through 570 removed outlier: 4.126A pdb=" N MET D 556 " --> pdb=" O ASN D 552 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS D 568 " --> pdb=" O MET D 564 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 570 " --> pdb=" O LEU D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 575 Processing helix chain 'D' and resid 600 through 612 Processing helix chain 'D' and resid 613 through 630 Processing helix chain 'D' and resid 646 through 678 removed outlier: 4.037A pdb=" N GLU D 650 " --> pdb=" O LYS D 646 " (cutoff:3.500A) Proline residue: D 668 - end of helix Processing helix chain 'D' and resid 689 through 697 Processing helix chain 'D' and resid 698 through 710 removed outlier: 4.407A pdb=" N ASN D 703 " --> pdb=" O SER D 699 " (cutoff:3.500A) Proline residue: D 704 - end of helix Processing helix chain 'D' and resid 711 through 721 Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 437 removed outlier: 5.902A pdb=" N TRP A 434 " --> pdb=" O ARG A 425 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG A 425 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 436 " --> pdb=" O TRP A 423 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 484 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 458 through 460 removed outlier: 3.641A pdb=" N THR A 465 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 409 Processing sheet with id=AA4, first strand: chain 'C' and resid 432 through 434 removed outlier: 3.568A pdb=" N THR C 498 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 405 through 407 removed outlier: 3.775A pdb=" N PHE B 410 " --> pdb=" O GLY B 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 579 through 582 removed outlier: 3.892A pdb=" N SER B 587 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 579 through 582 removed outlier: 3.939A pdb=" N SER D 587 " --> pdb=" O GLU D 582 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1071 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: 0.93 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1969 1.34 - 1.45: 1288 1.45 - 1.57: 3603 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 6954 Sorted by residual: bond pdb=" C ACE B 401 " pdb=" N MET B 402 " ideal model delta sigma weight residual 1.329 1.486 -0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" C ACE D 401 " pdb=" N MET D 402 " ideal model delta sigma weight residual 1.329 1.470 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" N MET B 402 " pdb=" CA MET B 402 " ideal model delta sigma weight residual 1.458 1.521 -0.063 1.90e-02 2.77e+03 1.11e+01 bond pdb=" N MET D 402 " pdb=" CA MET D 402 " ideal model delta sigma weight residual 1.458 1.513 -0.055 1.90e-02 2.77e+03 8.45e+00 bond pdb=" C14 RET B 801 " pdb=" C15 RET B 801 " ideal model delta sigma weight residual 1.448 1.498 -0.050 2.00e-02 2.50e+03 6.33e+00 ... (remaining 6949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 9128 1.71 - 3.42: 288 3.42 - 5.12: 38 5.12 - 6.83: 9 6.83 - 8.54: 1 Bond angle restraints: 9464 Sorted by residual: angle pdb=" N GLY D 419 " pdb=" CA GLY D 419 " pdb=" C GLY D 419 " ideal model delta sigma weight residual 114.48 110.31 4.17 1.19e+00 7.06e-01 1.23e+01 angle pdb=" C VAL D 420 " pdb=" N VAL D 421 " pdb=" CA VAL D 421 " ideal model delta sigma weight residual 121.97 127.58 -5.61 1.80e+00 3.09e-01 9.71e+00 angle pdb=" C ASP A 460 " pdb=" N ASN A 461 " pdb=" CA ASN A 461 " ideal model delta sigma weight residual 120.63 125.54 -4.91 1.61e+00 3.86e-01 9.31e+00 angle pdb=" C PHE B 688 " pdb=" N MET B 689 " pdb=" CA MET B 689 " ideal model delta sigma weight residual 121.54 127.35 -5.81 1.91e+00 2.74e-01 9.26e+00 angle pdb=" C VAL B 610 " pdb=" N VAL B 611 " pdb=" CA VAL B 611 " ideal model delta sigma weight residual 123.16 119.96 3.20 1.06e+00 8.90e-01 9.09e+00 ... (remaining 9459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 3797 17.48 - 34.96: 228 34.96 - 52.44: 82 52.44 - 69.92: 20 69.92 - 87.40: 9 Dihedral angle restraints: 4136 sinusoidal: 1714 harmonic: 2422 Sorted by residual: dihedral pdb=" CH3 ACE D 401 " pdb=" C ACE D 401 " pdb=" N MET D 402 " pdb=" CA MET D 402 " ideal model delta sinusoidal sigma weight residual 180.00 105.85 74.15 1 5.00e+00 4.00e-02 2.79e+02 dihedral pdb=" CH3 ACE B 401 " pdb=" C ACE B 401 " pdb=" N MET B 402 " pdb=" CA MET B 402 " ideal model delta sinusoidal sigma weight residual -180.00 -116.40 -63.60 1 5.00e+00 4.00e-02 2.13e+02 dihedral pdb=" CA TYR A 444 " pdb=" C TYR A 444 " pdb=" N THR A 445 " pdb=" CA THR A 445 " ideal model delta harmonic sigma weight residual -180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 4133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 786 0.042 - 0.085: 246 0.085 - 0.127: 38 0.127 - 0.170: 1 0.170 - 0.212: 5 Chirality restraints: 1076 Sorted by residual: chirality pdb=" CA MET B 402 " pdb=" N MET B 402 " pdb=" C MET B 402 " pdb=" CB MET B 402 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA MET D 402 " pdb=" N MET D 402 " pdb=" C MET D 402 " pdb=" CB MET D 402 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 403 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 1073 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE D 401 " 0.090 2.00e-02 2.50e+03 3.29e-01 1.35e+03 pdb=" O ACE D 401 " -0.085 2.00e-02 2.50e+03 pdb=" CH3 ACE D 401 " -0.190 2.00e-02 2.50e+03 pdb=" N MET D 402 " 0.578 2.00e-02 2.50e+03 pdb=" CA MET D 402 " -0.393 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE B 401 " -0.073 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" O ACE B 401 " 0.037 2.00e-02 2.50e+03 pdb=" CH3 ACE B 401 " 0.200 2.00e-02 2.50e+03 pdb=" N MET B 402 " -0.520 2.00e-02 2.50e+03 pdb=" CA MET B 402 " 0.355 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET B 801 " 0.104 2.00e-02 2.50e+03 1.15e-01 1.67e+02 pdb=" C13 RET B 801 " -0.038 2.00e-02 2.50e+03 pdb=" C14 RET B 801 " -0.189 2.00e-02 2.50e+03 pdb=" C15 RET B 801 " 0.135 2.00e-02 2.50e+03 pdb=" C20 RET B 801 " -0.013 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 3907 2.99 - 3.47: 7513 3.47 - 3.95: 11500 3.95 - 4.42: 13662 4.42 - 4.90: 21099 Nonbonded interactions: 57681 Sorted by model distance: nonbonded pdb=" O4 NAG F 2 " pdb=" O2 BMA F 3 " model vdw 2.517 2.432 nonbonded pdb=" N THR D 594 " pdb=" CG2 THR D 594 " model vdw 2.572 2.832 nonbonded pdb=" C THR D 594 " pdb=" OG1 THR D 594 " model vdw 2.574 2.616 nonbonded pdb=" N VAL B 420 " pdb=" O VAL B 420 " model vdw 2.583 2.496 nonbonded pdb=" O2 BMA E 3 " pdb=" O3 BMA E 3 " model vdw 2.583 2.432 ... (remaining 57676 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' selection = (chain 'C' and (resid 3 through 11 or resid 404 through 503)) } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.17 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.004 0.157 6970 Z= 0.225 Angle : 0.736 8.539 9502 Z= 0.431 Chirality : 0.041 0.212 1076 Planarity : 0.014 0.329 1168 Dihedral : 13.883 87.402 2580 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.29 % Favored : 90.73 % Rotamer: Outliers : 6.23 % Allowed : 7.37 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.32), residues: 820 helix: 2.54 (0.25), residues: 410 sheet: -3.65 (0.56), residues: 69 loop : -2.78 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 578 TYR 0.010 0.001 TYR A 444 PHE 0.012 0.001 PHE D 622 TRP 0.007 0.001 TRP B 527 HIS 0.004 0.001 HIS B 596 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 6954) covalent geometry : angle 0.71694 ( 9464) SS BOND : bond 0.00244 ( 4) SS BOND : angle 1.07247 ( 8) hydrogen bonds : bond 0.15068 ( 372) hydrogen bonds : angle 6.23407 ( 1071) Misc. bond : bond 0.01224 ( 2) link_BETA1-4 : bond 0.00747 ( 6) link_BETA1-4 : angle 2.81427 ( 18) link_NAG-ASN : bond 0.00518 ( 4) link_NAG-ASN : angle 3.28111 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 252 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.9107 (tp) cc_final: 0.8656 (tt) REVERT: A 419 TYR cc_start: 0.8974 (m-80) cc_final: 0.8623 (m-80) REVERT: A 440 ARG cc_start: 0.8825 (mtm110) cc_final: 0.8477 (mtm110) REVERT: A 460 ASP cc_start: 0.8343 (t70) cc_final: 0.8081 (t0) REVERT: A 469 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7777 (tm-30) REVERT: A 474 LYS cc_start: 0.9472 (mtpp) cc_final: 0.9207 (mtpp) REVERT: A 480 VAL cc_start: 0.9264 (t) cc_final: 0.9053 (t) REVERT: C 422 ASN cc_start: 0.8528 (m-40) cc_final: 0.8142 (m-40) REVERT: C 434 TRP cc_start: 0.8345 (t60) cc_final: 0.7537 (t60) REVERT: C 444 TYR cc_start: 0.8264 (t80) cc_final: 0.8031 (t80) REVERT: C 446 ASP cc_start: 0.8680 (t0) cc_final: 0.7882 (t0) REVERT: C 447 TYR cc_start: 0.8015 (m-80) cc_final: 0.7498 (m-80) REVERT: C 460 ASP cc_start: 0.8464 (t70) cc_final: 0.8229 (t0) REVERT: B 422 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.7975 (mmt-90) REVERT: B 466 HIS cc_start: 0.7826 (OUTLIER) cc_final: 0.7480 (m-70) REVERT: B 535 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: B 536 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8700 (mmp80) REVERT: B 556 MET cc_start: 0.8518 (mtt) cc_final: 0.8263 (mtt) REVERT: B 564 MET cc_start: 0.9105 (tpt) cc_final: 0.8850 (mmm) REVERT: B 598 GLU cc_start: 0.8414 (mp0) cc_final: 0.7958 (mp0) REVERT: B 654 MET cc_start: 0.9262 (ttm) cc_final: 0.8858 (tpp) REVERT: B 687 ILE cc_start: 0.8407 (pt) cc_final: 0.8122 (mp) REVERT: B 689 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8804 (tpt) REVERT: B 703 ASN cc_start: 0.9025 (m-40) cc_final: 0.8707 (m-40) REVERT: D 406 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7815 (tm-30) REVERT: D 422 ARG cc_start: 0.8811 (mmt-90) cc_final: 0.8314 (mmt-90) REVERT: D 426 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8614 (mp0) REVERT: D 429 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.7020 (pm20) REVERT: D 478 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9057 (tt) REVERT: D 484 ASP cc_start: 0.9331 (m-30) cc_final: 0.9085 (m-30) REVERT: D 536 ARG cc_start: 0.9321 (mmm160) cc_final: 0.9022 (mmp-170) REVERT: D 544 MET cc_start: 0.8454 (mmt) cc_final: 0.8165 (mmt) REVERT: D 551 GLU cc_start: 0.8029 (pm20) cc_final: 0.7627 (pt0) REVERT: D 587 SER cc_start: 0.8738 (m) cc_final: 0.8532 (t) REVERT: D 591 ASP cc_start: 0.8914 (t0) cc_final: 0.8660 (t0) REVERT: D 656 ILE cc_start: 0.9624 (mt) cc_final: 0.9412 (mp) REVERT: D 658 MET cc_start: 0.9308 (mtp) cc_final: 0.9006 (mtp) REVERT: D 699 SER cc_start: 0.9316 (t) cc_final: 0.9092 (m) REVERT: D 712 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8871 (tptp) outliers start: 44 outliers final: 8 residues processed: 272 average time/residue: 0.0959 time to fit residues: 33.4236 Evaluate side-chains 199 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 712 LYS Chi-restraints excluded: chain D residue 716 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS B 512 ASN ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 GLN D 512 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.083944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.069828 restraints weight = 17955.071| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.09 r_work: 0.2942 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6970 Z= 0.170 Angle : 0.759 8.565 9502 Z= 0.368 Chirality : 0.044 0.193 1076 Planarity : 0.005 0.045 1168 Dihedral : 10.845 85.685 1180 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.15 % Favored : 89.88 % Rotamer: Outliers : 4.67 % Allowed : 13.31 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.31), residues: 820 helix: 2.29 (0.25), residues: 420 sheet: -3.38 (0.58), residues: 63 loop : -2.88 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 653 TYR 0.013 0.001 TYR D 702 PHE 0.012 0.001 PHE C 414 TRP 0.009 0.001 TRP D 436 HIS 0.003 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6954) covalent geometry : angle 0.74069 ( 9464) SS BOND : bond 0.00234 ( 4) SS BOND : angle 1.05306 ( 8) hydrogen bonds : bond 0.04209 ( 372) hydrogen bonds : angle 4.89486 ( 1071) Misc. bond : bond 0.00077 ( 2) link_BETA1-4 : bond 0.00799 ( 6) link_BETA1-4 : angle 2.80460 ( 18) link_NAG-ASN : bond 0.00432 ( 4) link_NAG-ASN : angle 3.37299 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.9084 (tp) cc_final: 0.8614 (tt) REVERT: A 419 TYR cc_start: 0.9001 (m-80) cc_final: 0.8724 (m-80) REVERT: A 440 ARG cc_start: 0.8879 (mtm110) cc_final: 0.8578 (mtm110) REVERT: A 460 ASP cc_start: 0.8669 (t70) cc_final: 0.8411 (t0) REVERT: A 469 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7736 (tm-30) REVERT: A 474 LYS cc_start: 0.9330 (mtpp) cc_final: 0.9091 (mtpp) REVERT: A 500 VAL cc_start: 0.9723 (t) cc_final: 0.9518 (m) REVERT: C 430 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8818 (mmtp) REVERT: C 444 TYR cc_start: 0.8326 (t80) cc_final: 0.8058 (t80) REVERT: C 446 ASP cc_start: 0.8924 (t0) cc_final: 0.8490 (t0) REVERT: C 447 TYR cc_start: 0.8329 (m-80) cc_final: 0.7915 (m-80) REVERT: C 467 TYR cc_start: 0.7804 (m-80) cc_final: 0.7501 (m-10) REVERT: C 499 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8118 (tm-30) REVERT: C 500 VAL cc_start: 0.8436 (m) cc_final: 0.8123 (p) REVERT: B 535 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8268 (mm-30) REVERT: B 548 ARG cc_start: 0.9090 (tpp-160) cc_final: 0.8711 (mmp80) REVERT: B 556 MET cc_start: 0.8535 (mtt) cc_final: 0.8310 (mtt) REVERT: B 564 MET cc_start: 0.9231 (tpt) cc_final: 0.9027 (mmm) REVERT: B 598 GLU cc_start: 0.8585 (mp0) cc_final: 0.8143 (mp0) REVERT: B 649 LYS cc_start: 0.9428 (mppt) cc_final: 0.9190 (mmtm) REVERT: B 687 ILE cc_start: 0.8353 (pt) cc_final: 0.7976 (mm) REVERT: B 703 ASN cc_start: 0.9094 (m-40) cc_final: 0.8790 (m-40) REVERT: D 406 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7875 (tm-30) REVERT: D 422 ARG cc_start: 0.8968 (mmt-90) cc_final: 0.8279 (mmt-90) REVERT: D 426 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8673 (mp0) REVERT: D 429 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6848 (pm20) REVERT: D 478 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9056 (tt) REVERT: D 712 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9020 (tptp) REVERT: D 715 ARG cc_start: 0.9105 (ttm110) cc_final: 0.8651 (ptp90) outliers start: 33 outliers final: 17 residues processed: 204 average time/residue: 0.0929 time to fit residues: 24.3494 Evaluate side-chains 185 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 712 LYS Chi-restraints excluded: chain D residue 716 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 67 optimal weight: 0.0980 chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN ** D 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.083419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.069069 restraints weight = 17771.800| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.17 r_work: 0.2897 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6970 Z= 0.161 Angle : 0.730 11.921 9502 Z= 0.355 Chirality : 0.043 0.215 1076 Planarity : 0.005 0.044 1168 Dihedral : 10.362 89.814 1171 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.17 % Favored : 90.85 % Rotamer: Outliers : 4.11 % Allowed : 16.86 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.31), residues: 820 helix: 2.21 (0.25), residues: 420 sheet: -3.06 (0.62), residues: 63 loop : -2.79 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 536 TYR 0.013 0.001 TYR C 482 PHE 0.018 0.001 PHE B 453 TRP 0.010 0.001 TRP D 436 HIS 0.002 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6954) covalent geometry : angle 0.70952 ( 9464) SS BOND : bond 0.00243 ( 4) SS BOND : angle 1.23580 ( 8) hydrogen bonds : bond 0.03891 ( 372) hydrogen bonds : angle 4.68366 ( 1071) Misc. bond : bond 0.00084 ( 2) link_BETA1-4 : bond 0.00744 ( 6) link_BETA1-4 : angle 2.81392 ( 18) link_NAG-ASN : bond 0.00391 ( 4) link_NAG-ASN : angle 3.39619 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.8939 (tp) cc_final: 0.8500 (tt) REVERT: A 419 TYR cc_start: 0.8961 (m-80) cc_final: 0.8630 (m-80) REVERT: A 430 LYS cc_start: 0.9064 (mtmm) cc_final: 0.8539 (mtmm) REVERT: A 440 ARG cc_start: 0.8855 (mtm110) cc_final: 0.8445 (mtm110) REVERT: A 460 ASP cc_start: 0.8712 (t70) cc_final: 0.8403 (t0) REVERT: A 469 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7532 (tm-30) REVERT: A 474 LYS cc_start: 0.9322 (mtpp) cc_final: 0.9078 (mtpp) REVERT: A 500 VAL cc_start: 0.9725 (t) cc_final: 0.9483 (m) REVERT: C 430 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8824 (mmtp) REVERT: C 433 GLU cc_start: 0.8207 (mt-10) cc_final: 0.8005 (mt-10) REVERT: C 444 TYR cc_start: 0.8334 (t80) cc_final: 0.8054 (t80) REVERT: C 446 ASP cc_start: 0.8783 (t0) cc_final: 0.8370 (t0) REVERT: C 447 TYR cc_start: 0.8353 (m-80) cc_final: 0.7773 (m-80) REVERT: C 463 LYS cc_start: 0.9372 (mtmm) cc_final: 0.9045 (mtmm) REVERT: C 466 LEU cc_start: 0.8572 (tt) cc_final: 0.8336 (pp) REVERT: C 467 TYR cc_start: 0.7688 (m-80) cc_final: 0.7101 (m-10) REVERT: C 500 VAL cc_start: 0.8445 (m) cc_final: 0.8222 (p) REVERT: B 535 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8114 (mm-30) REVERT: B 556 MET cc_start: 0.8479 (mtt) cc_final: 0.8219 (mtt) REVERT: B 564 MET cc_start: 0.9151 (tpt) cc_final: 0.8851 (mmm) REVERT: B 598 GLU cc_start: 0.8567 (mp0) cc_final: 0.8081 (mp0) REVERT: B 649 LYS cc_start: 0.9546 (mppt) cc_final: 0.9249 (mmtm) REVERT: B 687 ILE cc_start: 0.8224 (pt) cc_final: 0.7817 (mm) REVERT: B 703 ASN cc_start: 0.8988 (m-40) cc_final: 0.8681 (m-40) REVERT: D 406 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7916 (tm-30) REVERT: D 422 ARG cc_start: 0.8881 (mmt-90) cc_final: 0.8148 (mmt-90) REVERT: D 426 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8651 (mp0) REVERT: D 429 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: D 478 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9021 (tt) REVERT: D 535 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8524 (pp20) REVERT: D 551 GLU cc_start: 0.8280 (pm20) cc_final: 0.7723 (pt0) REVERT: D 591 ASP cc_start: 0.9161 (t0) cc_final: 0.8820 (t0) REVERT: D 712 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8938 (tptp) REVERT: D 715 ARG cc_start: 0.9160 (ttm110) cc_final: 0.8602 (ptp90) outliers start: 29 outliers final: 20 residues processed: 204 average time/residue: 0.0918 time to fit residues: 24.2412 Evaluate side-chains 198 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 592 TYR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 712 LYS Chi-restraints excluded: chain D residue 716 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** D 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.083031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.069136 restraints weight = 18185.831| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.07 r_work: 0.2916 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6970 Z= 0.170 Angle : 0.708 9.832 9502 Z= 0.344 Chirality : 0.043 0.212 1076 Planarity : 0.005 0.044 1168 Dihedral : 9.724 89.275 1171 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.15 % Favored : 89.88 % Rotamer: Outliers : 5.10 % Allowed : 15.72 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.31), residues: 820 helix: 2.23 (0.25), residues: 420 sheet: -2.72 (0.64), residues: 63 loop : -2.71 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 536 TYR 0.014 0.001 TYR C 482 PHE 0.012 0.001 PHE B 457 TRP 0.010 0.001 TRP D 436 HIS 0.002 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6954) covalent geometry : angle 0.68663 ( 9464) SS BOND : bond 0.00249 ( 4) SS BOND : angle 1.09921 ( 8) hydrogen bonds : bond 0.03638 ( 372) hydrogen bonds : angle 4.54143 ( 1071) Misc. bond : bond 0.00090 ( 2) link_BETA1-4 : bond 0.00740 ( 6) link_BETA1-4 : angle 2.83231 ( 18) link_NAG-ASN : bond 0.00392 ( 4) link_NAG-ASN : angle 3.48443 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.9077 (tp) cc_final: 0.8617 (tt) REVERT: A 419 TYR cc_start: 0.9029 (m-80) cc_final: 0.8727 (m-80) REVERT: A 440 ARG cc_start: 0.8871 (mtm110) cc_final: 0.8475 (mtm110) REVERT: A 460 ASP cc_start: 0.8743 (t70) cc_final: 0.8431 (t0) REVERT: A 468 LEU cc_start: 0.9374 (tt) cc_final: 0.9011 (tt) REVERT: A 469 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7627 (tm-30) REVERT: A 474 LYS cc_start: 0.9346 (mtpp) cc_final: 0.9095 (mtpp) REVERT: A 500 VAL cc_start: 0.9707 (t) cc_final: 0.9494 (m) REVERT: C 430 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8902 (mmtp) REVERT: C 433 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8223 (mt-10) REVERT: C 444 TYR cc_start: 0.8375 (t80) cc_final: 0.8140 (t80) REVERT: C 446 ASP cc_start: 0.8886 (t0) cc_final: 0.8462 (t0) REVERT: C 447 TYR cc_start: 0.8296 (m-80) cc_final: 0.7679 (m-80) REVERT: C 467 TYR cc_start: 0.7834 (m-80) cc_final: 0.7553 (m-10) REVERT: B 458 LEU cc_start: 0.9370 (tp) cc_final: 0.9132 (tp) REVERT: B 535 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8088 (mm-30) REVERT: B 556 MET cc_start: 0.8491 (mtt) cc_final: 0.8220 (mtt) REVERT: B 564 MET cc_start: 0.9244 (tpt) cc_final: 0.8975 (mmm) REVERT: B 598 GLU cc_start: 0.8570 (mp0) cc_final: 0.8105 (mp0) REVERT: B 649 LYS cc_start: 0.9501 (mppt) cc_final: 0.9198 (mmtm) REVERT: B 687 ILE cc_start: 0.8299 (pt) cc_final: 0.7910 (mm) REVERT: B 703 ASN cc_start: 0.9050 (m-40) cc_final: 0.8735 (m-40) REVERT: D 406 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8012 (tm-30) REVERT: D 422 ARG cc_start: 0.8955 (mmt-90) cc_final: 0.8458 (mmt-90) REVERT: D 426 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8644 (mp0) REVERT: D 429 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6830 (pm20) REVERT: D 450 MET cc_start: 0.8984 (mtm) cc_final: 0.8733 (mtm) REVERT: D 578 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8269 (pmt100) REVERT: D 591 ASP cc_start: 0.9162 (t0) cc_final: 0.8703 (t0) REVERT: D 712 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8925 (tptp) REVERT: D 715 ARG cc_start: 0.9173 (ttm110) cc_final: 0.8657 (ptp90) outliers start: 36 outliers final: 21 residues processed: 201 average time/residue: 0.0931 time to fit residues: 24.1120 Evaluate side-chains 191 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 592 TYR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 712 LYS Chi-restraints excluded: chain D residue 716 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.067803 restraints weight = 18087.365| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.17 r_work: 0.2870 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6970 Z= 0.184 Angle : 0.729 10.791 9502 Z= 0.351 Chirality : 0.043 0.207 1076 Planarity : 0.005 0.043 1168 Dihedral : 9.224 89.449 1169 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.54 % Favored : 90.49 % Rotamer: Outliers : 4.82 % Allowed : 17.00 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.31), residues: 820 helix: 2.21 (0.25), residues: 420 sheet: -2.04 (0.74), residues: 53 loop : -2.73 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 470 TYR 0.013 0.001 TYR D 702 PHE 0.012 0.001 PHE A 416 TRP 0.012 0.001 TRP C 423 HIS 0.002 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 6954) covalent geometry : angle 0.70812 ( 9464) SS BOND : bond 0.00304 ( 4) SS BOND : angle 1.36587 ( 8) hydrogen bonds : bond 0.03626 ( 372) hydrogen bonds : angle 4.50758 ( 1071) Misc. bond : bond 0.00090 ( 2) link_BETA1-4 : bond 0.00730 ( 6) link_BETA1-4 : angle 2.82214 ( 18) link_NAG-ASN : bond 0.00344 ( 4) link_NAG-ASN : angle 3.54227 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.9052 (tp) cc_final: 0.8602 (tt) REVERT: A 419 TYR cc_start: 0.9013 (m-80) cc_final: 0.8663 (m-80) REVERT: A 440 ARG cc_start: 0.8852 (mtm110) cc_final: 0.8422 (mtm110) REVERT: A 460 ASP cc_start: 0.8725 (t70) cc_final: 0.8380 (t0) REVERT: A 468 LEU cc_start: 0.9363 (tt) cc_final: 0.8950 (tt) REVERT: A 469 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7603 (tm-30) REVERT: A 474 LYS cc_start: 0.9357 (mtpp) cc_final: 0.8938 (mtpp) REVERT: A 476 GLU cc_start: 0.9292 (mp0) cc_final: 0.9053 (pm20) REVERT: A 500 VAL cc_start: 0.9692 (t) cc_final: 0.9456 (m) REVERT: C 430 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8970 (mmtp) REVERT: C 433 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8151 (mt-10) REVERT: C 444 TYR cc_start: 0.8361 (t80) cc_final: 0.8143 (t80) REVERT: C 446 ASP cc_start: 0.8801 (t0) cc_final: 0.8393 (t0) REVERT: C 447 TYR cc_start: 0.8348 (m-80) cc_final: 0.7661 (m-80) REVERT: C 460 ASP cc_start: 0.8194 (t0) cc_final: 0.7639 (t0) REVERT: C 467 TYR cc_start: 0.7733 (m-80) cc_final: 0.7380 (m-10) REVERT: B 535 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8127 (mm-30) REVERT: B 556 MET cc_start: 0.8479 (mtt) cc_final: 0.8187 (mtt) REVERT: B 564 MET cc_start: 0.9165 (tpt) cc_final: 0.8875 (mmm) REVERT: B 598 GLU cc_start: 0.8567 (mp0) cc_final: 0.8112 (mp0) REVERT: B 649 LYS cc_start: 0.9536 (mppt) cc_final: 0.9251 (mmtm) REVERT: B 687 ILE cc_start: 0.8205 (pt) cc_final: 0.7797 (mm) REVERT: B 703 ASN cc_start: 0.9021 (m-40) cc_final: 0.8696 (m-40) REVERT: D 422 ARG cc_start: 0.8914 (mmt-90) cc_final: 0.8382 (mmt-90) REVERT: D 426 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8639 (mp0) REVERT: D 429 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6821 (pm20) REVERT: D 523 GLU cc_start: 0.9513 (mm-30) cc_final: 0.9201 (mm-30) REVERT: D 551 GLU cc_start: 0.8243 (pm20) cc_final: 0.7630 (pt0) REVERT: D 591 ASP cc_start: 0.9105 (t0) cc_final: 0.8267 (t0) REVERT: D 594 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8929 (t) REVERT: D 712 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8855 (tptp) REVERT: D 715 ARG cc_start: 0.9190 (ttm110) cc_final: 0.8633 (ptp90) outliers start: 34 outliers final: 22 residues processed: 199 average time/residue: 0.0966 time to fit residues: 24.6375 Evaluate side-chains 192 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 592 TYR Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 699 SER Chi-restraints excluded: chain D residue 712 LYS Chi-restraints excluded: chain D residue 716 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** D 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.082747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.068973 restraints weight = 18199.191| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.03 r_work: 0.2916 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6970 Z= 0.162 Angle : 0.724 10.622 9502 Z= 0.353 Chirality : 0.044 0.214 1076 Planarity : 0.005 0.042 1168 Dihedral : 9.009 88.053 1164 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.66 % Favored : 90.37 % Rotamer: Outliers : 4.53 % Allowed : 19.12 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.30), residues: 820 helix: 2.09 (0.25), residues: 420 sheet: -1.83 (0.76), residues: 50 loop : -2.61 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 536 TYR 0.014 0.001 TYR A 447 PHE 0.016 0.001 PHE B 453 TRP 0.011 0.001 TRP A 423 HIS 0.002 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6954) covalent geometry : angle 0.70359 ( 9464) SS BOND : bond 0.00343 ( 4) SS BOND : angle 1.17319 ( 8) hydrogen bonds : bond 0.03591 ( 372) hydrogen bonds : angle 4.45027 ( 1071) Misc. bond : bond 0.00063 ( 2) link_BETA1-4 : bond 0.00780 ( 6) link_BETA1-4 : angle 2.79910 ( 18) link_NAG-ASN : bond 0.00398 ( 4) link_NAG-ASN : angle 3.46027 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.9122 (tp) cc_final: 0.8593 (tt) REVERT: A 419 TYR cc_start: 0.9050 (m-80) cc_final: 0.8740 (m-80) REVERT: A 440 ARG cc_start: 0.8888 (mtm110) cc_final: 0.8510 (mtm110) REVERT: A 460 ASP cc_start: 0.8757 (t70) cc_final: 0.8429 (t0) REVERT: A 468 LEU cc_start: 0.9432 (tt) cc_final: 0.9036 (tt) REVERT: A 474 LYS cc_start: 0.9362 (mtpp) cc_final: 0.8939 (mtpp) REVERT: A 476 GLU cc_start: 0.9238 (mp0) cc_final: 0.9028 (pm20) REVERT: C 433 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8254 (mt-10) REVERT: C 446 ASP cc_start: 0.8863 (t0) cc_final: 0.8477 (t0) REVERT: C 447 TYR cc_start: 0.8408 (m-80) cc_final: 0.7841 (m-80) REVERT: B 542 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8936 (mmtt) REVERT: B 556 MET cc_start: 0.8404 (mtt) cc_final: 0.8114 (mtt) REVERT: B 564 MET cc_start: 0.9202 (tpt) cc_final: 0.8945 (mmm) REVERT: B 598 GLU cc_start: 0.8526 (mp0) cc_final: 0.8118 (mp0) REVERT: B 649 LYS cc_start: 0.9452 (mppt) cc_final: 0.9177 (mmtm) REVERT: B 703 ASN cc_start: 0.9061 (m-40) cc_final: 0.8724 (m-40) REVERT: D 422 ARG cc_start: 0.8956 (mmt-90) cc_final: 0.8420 (mmt-90) REVERT: D 426 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8635 (mp0) REVERT: D 429 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6792 (pm20) REVERT: D 578 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7951 (pmt100) REVERT: D 591 ASP cc_start: 0.9010 (t0) cc_final: 0.8213 (t0) REVERT: D 594 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.9028 (t) REVERT: D 712 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8832 (tptp) REVERT: D 715 ARG cc_start: 0.9175 (ttm110) cc_final: 0.8608 (ptp90) outliers start: 32 outliers final: 25 residues processed: 192 average time/residue: 0.1006 time to fit residues: 24.4640 Evaluate side-chains 191 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 592 TYR Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 699 SER Chi-restraints excluded: chain D residue 712 LYS Chi-restraints excluded: chain D residue 716 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 48 optimal weight: 0.0050 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.069721 restraints weight = 17850.108| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.03 r_work: 0.2930 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6970 Z= 0.147 Angle : 0.735 11.801 9502 Z= 0.357 Chirality : 0.044 0.221 1076 Planarity : 0.005 0.056 1168 Dihedral : 8.946 88.004 1164 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.66 % Favored : 90.37 % Rotamer: Outliers : 4.67 % Allowed : 18.98 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.31), residues: 820 helix: 2.14 (0.25), residues: 420 sheet: -1.54 (0.77), residues: 50 loop : -2.52 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 536 TYR 0.017 0.001 TYR A 447 PHE 0.012 0.001 PHE A 416 TRP 0.012 0.001 TRP A 423 HIS 0.002 0.000 HIS B 596 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6954) covalent geometry : angle 0.71689 ( 9464) SS BOND : bond 0.00281 ( 4) SS BOND : angle 1.23536 ( 8) hydrogen bonds : bond 0.03460 ( 372) hydrogen bonds : angle 4.37091 ( 1071) Misc. bond : bond 0.00051 ( 2) link_BETA1-4 : bond 0.00725 ( 6) link_BETA1-4 : angle 2.60864 ( 18) link_NAG-ASN : bond 0.00421 ( 4) link_NAG-ASN : angle 3.36165 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.9078 (tp) cc_final: 0.8605 (tt) REVERT: A 419 TYR cc_start: 0.9042 (m-80) cc_final: 0.8727 (m-80) REVERT: A 440 ARG cc_start: 0.8876 (mtm110) cc_final: 0.8492 (mtm110) REVERT: A 460 ASP cc_start: 0.8717 (t70) cc_final: 0.8435 (t0) REVERT: A 468 LEU cc_start: 0.9379 (tt) cc_final: 0.8994 (tt) REVERT: A 476 GLU cc_start: 0.9243 (mp0) cc_final: 0.8990 (pm20) REVERT: C 433 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8294 (mt-10) REVERT: C 446 ASP cc_start: 0.8902 (t0) cc_final: 0.8654 (t0) REVERT: C 447 TYR cc_start: 0.8408 (m-80) cc_final: 0.7819 (m-80) REVERT: B 535 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8193 (mm-30) REVERT: B 556 MET cc_start: 0.8386 (mtt) cc_final: 0.8087 (mtt) REVERT: B 561 THR cc_start: 0.9748 (p) cc_final: 0.9440 (p) REVERT: B 564 MET cc_start: 0.9203 (tpt) cc_final: 0.8943 (mmm) REVERT: B 598 GLU cc_start: 0.8491 (mp0) cc_final: 0.8106 (mp0) REVERT: B 703 ASN cc_start: 0.9059 (m-40) cc_final: 0.8727 (m-40) REVERT: D 422 ARG cc_start: 0.8950 (mmt-90) cc_final: 0.8388 (mmt-90) REVERT: D 426 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8648 (mp0) REVERT: D 429 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6825 (pm20) REVERT: D 578 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8055 (pmt100) REVERT: D 591 ASP cc_start: 0.9005 (t0) cc_final: 0.8317 (t0) REVERT: D 712 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8810 (tptp) REVERT: D 715 ARG cc_start: 0.9179 (ttm110) cc_final: 0.8603 (ptp90) outliers start: 33 outliers final: 26 residues processed: 191 average time/residue: 0.0960 time to fit residues: 23.4865 Evaluate side-chains 195 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 592 TYR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 699 SER Chi-restraints excluded: chain D residue 712 LYS Chi-restraints excluded: chain D residue 716 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 73 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 0.0570 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** D 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.069275 restraints weight = 17992.867| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.12 r_work: 0.2939 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6970 Z= 0.153 Angle : 0.755 11.989 9502 Z= 0.367 Chirality : 0.044 0.229 1076 Planarity : 0.005 0.048 1168 Dihedral : 8.835 86.843 1164 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.54 % Favored : 90.49 % Rotamer: Outliers : 5.24 % Allowed : 19.69 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.31), residues: 820 helix: 2.06 (0.25), residues: 420 sheet: -1.31 (0.84), residues: 44 loop : -2.44 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 536 TYR 0.020 0.001 TYR A 447 PHE 0.019 0.001 PHE B 453 TRP 0.018 0.001 TRP C 423 HIS 0.002 0.000 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 6954) covalent geometry : angle 0.73761 ( 9464) SS BOND : bond 0.00274 ( 4) SS BOND : angle 1.31506 ( 8) hydrogen bonds : bond 0.03473 ( 372) hydrogen bonds : angle 4.35897 ( 1071) Misc. bond : bond 0.00050 ( 2) link_BETA1-4 : bond 0.00704 ( 6) link_BETA1-4 : angle 2.52247 ( 18) link_NAG-ASN : bond 0.00399 ( 4) link_NAG-ASN : angle 3.33149 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.9127 (tp) cc_final: 0.8670 (tt) REVERT: A 419 TYR cc_start: 0.9050 (m-80) cc_final: 0.8752 (m-80) REVERT: A 440 ARG cc_start: 0.8888 (mtm110) cc_final: 0.8533 (mtm110) REVERT: A 460 ASP cc_start: 0.8752 (t70) cc_final: 0.8415 (t0) REVERT: A 468 LEU cc_start: 0.9401 (tt) cc_final: 0.9072 (tt) REVERT: A 476 GLU cc_start: 0.9212 (mp0) cc_final: 0.8986 (pm20) REVERT: C 433 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8291 (mt-10) REVERT: C 446 ASP cc_start: 0.8914 (t0) cc_final: 0.8621 (t0) REVERT: C 447 TYR cc_start: 0.8396 (m-80) cc_final: 0.7846 (m-80) REVERT: B 535 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8209 (mm-30) REVERT: B 556 MET cc_start: 0.8373 (mtt) cc_final: 0.8071 (mtt) REVERT: B 561 THR cc_start: 0.9739 (p) cc_final: 0.9433 (p) REVERT: B 564 MET cc_start: 0.9184 (tpt) cc_final: 0.8943 (mmm) REVERT: B 598 GLU cc_start: 0.8489 (mp0) cc_final: 0.8141 (mp0) REVERT: B 703 ASN cc_start: 0.9076 (m-40) cc_final: 0.8748 (m-40) REVERT: D 422 ARG cc_start: 0.8978 (mmt-90) cc_final: 0.8442 (mmt-90) REVERT: D 426 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8673 (mp0) REVERT: D 429 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6865 (pm20) REVERT: D 548 ARG cc_start: 0.9099 (mmm-85) cc_final: 0.8873 (mmp80) REVERT: D 578 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8062 (pmt100) REVERT: D 591 ASP cc_start: 0.9005 (t0) cc_final: 0.8243 (t0) REVERT: D 712 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8800 (tptp) REVERT: D 715 ARG cc_start: 0.9167 (ttm110) cc_final: 0.8615 (ptp90) outliers start: 37 outliers final: 28 residues processed: 190 average time/residue: 0.0922 time to fit residues: 22.4975 Evaluate side-chains 201 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 586 CYS Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 592 TYR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 699 SER Chi-restraints excluded: chain D residue 712 LYS Chi-restraints excluded: chain D residue 716 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 71 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.068849 restraints weight = 18091.441| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.11 r_work: 0.2930 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6970 Z= 0.168 Angle : 0.750 11.572 9502 Z= 0.365 Chirality : 0.044 0.215 1076 Planarity : 0.005 0.043 1168 Dihedral : 8.580 85.081 1160 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.66 % Favored : 90.37 % Rotamer: Outliers : 5.52 % Allowed : 19.41 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.31), residues: 820 helix: 2.09 (0.25), residues: 420 sheet: -1.41 (0.77), residues: 53 loop : -2.39 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 536 TYR 0.017 0.001 TYR A 447 PHE 0.012 0.001 PHE A 416 TRP 0.014 0.001 TRP C 423 HIS 0.002 0.001 HIS D 466 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 6954) covalent geometry : angle 0.73362 ( 9464) SS BOND : bond 0.00286 ( 4) SS BOND : angle 1.36941 ( 8) hydrogen bonds : bond 0.03488 ( 372) hydrogen bonds : angle 4.37298 ( 1071) Misc. bond : bond 0.00057 ( 2) link_BETA1-4 : bond 0.00708 ( 6) link_BETA1-4 : angle 2.43589 ( 18) link_NAG-ASN : bond 0.00316 ( 4) link_NAG-ASN : angle 3.36015 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.9143 (tp) cc_final: 0.8796 (tt) REVERT: A 419 TYR cc_start: 0.9052 (m-80) cc_final: 0.8756 (m-80) REVERT: A 440 ARG cc_start: 0.8906 (mtm110) cc_final: 0.8550 (mtm110) REVERT: A 460 ASP cc_start: 0.8732 (t70) cc_final: 0.8406 (t0) REVERT: A 468 LEU cc_start: 0.9490 (tt) cc_final: 0.9099 (tt) REVERT: A 474 LYS cc_start: 0.9343 (mtpp) cc_final: 0.8961 (mtpp) REVERT: C 433 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8399 (mt-10) REVERT: C 446 ASP cc_start: 0.8962 (t0) cc_final: 0.8663 (t0) REVERT: C 447 TYR cc_start: 0.8443 (m-80) cc_final: 0.7882 (m-80) REVERT: C 499 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8203 (tm-30) REVERT: B 535 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8207 (mm-30) REVERT: B 556 MET cc_start: 0.8388 (mtt) cc_final: 0.8094 (mtt) REVERT: B 561 THR cc_start: 0.9731 (p) cc_final: 0.9423 (p) REVERT: B 564 MET cc_start: 0.9187 (tpt) cc_final: 0.8947 (mmm) REVERT: B 598 GLU cc_start: 0.8512 (mp0) cc_final: 0.8175 (mp0) REVERT: B 703 ASN cc_start: 0.9074 (m-40) cc_final: 0.8757 (m-40) REVERT: D 422 ARG cc_start: 0.8987 (mmt-90) cc_final: 0.8443 (mmt-90) REVERT: D 426 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8682 (mp0) REVERT: D 429 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6881 (pm20) REVERT: D 578 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8044 (pmt100) REVERT: D 591 ASP cc_start: 0.8959 (t0) cc_final: 0.8226 (t0) REVERT: D 712 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8791 (tptp) REVERT: D 715 ARG cc_start: 0.9191 (ttm110) cc_final: 0.8633 (ptp90) outliers start: 39 outliers final: 30 residues processed: 186 average time/residue: 0.1003 time to fit residues: 23.8000 Evaluate side-chains 197 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 586 CYS Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 592 TYR Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 699 SER Chi-restraints excluded: chain D residue 712 LYS Chi-restraints excluded: chain D residue 716 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** D 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.068094 restraints weight = 18028.877| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.06 r_work: 0.2912 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6970 Z= 0.194 Angle : 0.773 12.506 9502 Z= 0.378 Chirality : 0.045 0.211 1076 Planarity : 0.005 0.042 1168 Dihedral : 8.579 82.279 1160 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.78 % Favored : 90.24 % Rotamer: Outliers : 4.82 % Allowed : 19.97 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.31), residues: 820 helix: 2.07 (0.25), residues: 420 sheet: -1.05 (0.78), residues: 52 loop : -2.40 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 548 TYR 0.031 0.001 TYR A 447 PHE 0.019 0.001 PHE B 453 TRP 0.013 0.001 TRP C 423 HIS 0.002 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 6954) covalent geometry : angle 0.75642 ( 9464) SS BOND : bond 0.00346 ( 4) SS BOND : angle 1.46554 ( 8) hydrogen bonds : bond 0.03582 ( 372) hydrogen bonds : angle 4.38535 ( 1071) Misc. bond : bond 0.00073 ( 2) link_BETA1-4 : bond 0.00705 ( 6) link_BETA1-4 : angle 2.36927 ( 18) link_NAG-ASN : bond 0.00285 ( 4) link_NAG-ASN : angle 3.44989 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.9038 (tp) cc_final: 0.8732 (tt) REVERT: A 419 TYR cc_start: 0.9062 (m-80) cc_final: 0.8756 (m-80) REVERT: A 440 ARG cc_start: 0.8918 (mtm110) cc_final: 0.8553 (mtm110) REVERT: A 460 ASP cc_start: 0.8750 (t70) cc_final: 0.8474 (t0) REVERT: A 468 LEU cc_start: 0.9450 (tt) cc_final: 0.8950 (tt) REVERT: C 446 ASP cc_start: 0.8913 (t0) cc_final: 0.8621 (t0) REVERT: C 447 TYR cc_start: 0.8498 (m-80) cc_final: 0.7939 (m-80) REVERT: B 535 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8217 (mm-30) REVERT: B 556 MET cc_start: 0.8391 (mtt) cc_final: 0.8093 (mtt) REVERT: B 561 THR cc_start: 0.9729 (p) cc_final: 0.9424 (p) REVERT: B 564 MET cc_start: 0.9203 (tpt) cc_final: 0.8949 (mmm) REVERT: B 598 GLU cc_start: 0.8509 (mp0) cc_final: 0.8198 (mp0) REVERT: B 703 ASN cc_start: 0.9072 (m-40) cc_final: 0.8759 (m-40) REVERT: D 422 ARG cc_start: 0.8997 (mmt-90) cc_final: 0.8447 (mmt-90) REVERT: D 426 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8700 (mp0) REVERT: D 429 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7007 (pm20) REVERT: D 578 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8129 (pmt100) REVERT: D 591 ASP cc_start: 0.8997 (t0) cc_final: 0.8636 (t0) REVERT: D 712 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8784 (tptp) REVERT: D 715 ARG cc_start: 0.9182 (ttm110) cc_final: 0.8594 (ptp90) outliers start: 34 outliers final: 26 residues processed: 179 average time/residue: 0.0909 time to fit residues: 20.9328 Evaluate side-chains 189 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 485 LYS Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 586 CYS Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 561 THR Chi-restraints excluded: chain D residue 578 ARG Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 592 TYR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 699 SER Chi-restraints excluded: chain D residue 712 LYS Chi-restraints excluded: chain D residue 716 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 8 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.082395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.068269 restraints weight = 18165.111| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.10 r_work: 0.2917 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6970 Z= 0.178 Angle : 0.780 12.254 9502 Z= 0.382 Chirality : 0.044 0.220 1076 Planarity : 0.005 0.040 1168 Dihedral : 8.559 81.398 1160 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.41 % Favored : 90.61 % Rotamer: Outliers : 4.82 % Allowed : 20.68 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.31), residues: 820 helix: 2.05 (0.25), residues: 420 sheet: -1.20 (0.83), residues: 46 loop : -2.32 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 548 TYR 0.030 0.001 TYR A 447 PHE 0.013 0.001 PHE A 416 TRP 0.013 0.001 TRP C 423 HIS 0.002 0.001 HIS D 466 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 6954) covalent geometry : angle 0.76477 ( 9464) SS BOND : bond 0.00308 ( 4) SS BOND : angle 1.23284 ( 8) hydrogen bonds : bond 0.03578 ( 372) hydrogen bonds : angle 4.36848 ( 1071) Misc. bond : bond 0.00062 ( 2) link_BETA1-4 : bond 0.00695 ( 6) link_BETA1-4 : angle 2.30834 ( 18) link_NAG-ASN : bond 0.00316 ( 4) link_NAG-ASN : angle 3.41399 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.85 seconds wall clock time: 29 minutes 28.78 seconds (1768.78 seconds total)