Starting phenix.real_space_refine on Tue May 13 20:32:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cbn_45427/05_2025/9cbn_45427.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cbn_45427/05_2025/9cbn_45427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cbn_45427/05_2025/9cbn_45427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cbn_45427/05_2025/9cbn_45427.map" model { file = "/net/cci-nas-00/data/ceres_data/9cbn_45427/05_2025/9cbn_45427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cbn_45427/05_2025/9cbn_45427.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians S 34 5.16 5 C 5063 2.51 5 N 1279 2.21 5 O 1448 1.98 5 H 3143 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10967 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 3 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 546 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 73} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 3187 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 212, 3183 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 212, 3183 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 3221 Chain: "D" Number of atoms: 3216 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 212, 3208 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 212, 3208 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 3242 Chain: "E" Number of atoms: 890 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 115, 881 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 115, 881 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 894 Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 694 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 880 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "H" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 695 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "I" 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: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N MET C 636 " occ=0.81 ... (15 atoms not shown) pdb=" HE3 MET C 636 " occ=0.81 residue: pdb=" N MET D 636 " occ=0.87 ... (15 atoms not shown) pdb=" HE3 MET D 636 " occ=0.87 residue: pdb=" N ALYS E 81 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS E 81 " occ=0.50 Time building chain proxies: 12.07, per 1000 atoms: 1.10 Number of scatterers: 10967 At special positions: 0 Unit cell: (62.665, 113.295, 119.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 O 1448 8.00 N 1279 7.00 C 5063 6.00 H 3143 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.05 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=1.79 Simple disulfide: pdb=" SG CYS C 637 " - pdb=" SG CYS D 637 " distance=2.30 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 301 " - " ASN A 19 " " NAG J 1 " - " ASN G 60 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 23 sheets defined 3.3% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'C' and resid 623 through 627 removed outlier: 4.048A pdb=" N ILE C 627 " --> pdb=" O VAL C 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 624 removed outlier: 3.907A pdb=" N VAL D 624 " --> pdb=" O LYS D 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'F' and resid 30 through 34 Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'H' and resid 30 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.528A pdb=" N THR B 72 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.466A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LYS B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B 33 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 507 through 509 removed outlier: 4.147A pdb=" N ALA C 516 " --> pdb=" O VAL C 508 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL C 518 " --> pdb=" O LYS C 542 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS C 542 " --> pdb=" O VAL C 518 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 520 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 540 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS C 532 " --> pdb=" O GLN C 528 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TRP C 587 " --> pdb=" O ILE C 484 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 486 " --> pdb=" O THR C 437 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET C 640 " --> pdb=" O TYR C 432 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AA7, first strand: chain 'C' and resid 467 through 471 removed outlier: 6.666A pdb=" N HIS C 474 " --> pdb=" O LYS C 470 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 556 through 557 Processing sheet with id=AA9, first strand: chain 'D' and resid 475 through 477 removed outlier: 6.482A pdb=" N VAL D 508 " --> pdb=" O LYS D 515 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL D 518 " --> pdb=" O LYS D 542 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS D 542 " --> pdb=" O VAL D 518 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 520 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 475 through 477 removed outlier: 6.482A pdb=" N VAL D 508 " --> pdb=" O LYS D 515 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL D 518 " --> pdb=" O LYS D 542 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS D 542 " --> pdb=" O VAL D 518 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 520 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP D 587 " --> pdb=" O ILE D 484 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR D 437 " --> pdb=" O ALA D 485 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL D 487 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 435 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TRP D 489 " --> pdb=" O LYS D 433 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS D 433 " --> pdb=" O TRP D 489 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR D 634 " --> pdb=" O PHE D 438 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 453 through 454 Processing sheet with id=AB3, first strand: chain 'D' and resid 556 through 557 Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.616A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.545A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE E 92 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR E 108 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.545A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE E 92 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR E 93 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR E 113 " --> pdb=" O TYR E 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.990A pdb=" N ILE F 69 " --> pdb=" O LYS F 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 39 through 41 Processing sheet with id=AB9, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AC1, first strand: chain 'G' and resid 18 through 22 removed outlier: 3.705A pdb=" N VAL G 78 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.370A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR G 108 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.370A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC5, first strand: chain 'H' and resid 45 through 51 removed outlier: 3.550A pdb=" N LEU H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TRP H 37 " --> pdb=" O LEU H 49 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 658 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.27: 4344 1.27 - 1.70: 6766 1.70 - 2.12: 54 2.12 - 2.55: 0 2.55 - 2.98: 1 Bond restraints: 11165 Sorted by residual: bond pdb=" C PRO F 61 " pdb=" N ARG F 63 " ideal model delta sigma weight residual 1.332 2.980 -1.647 1.40e-02 5.10e+03 1.38e+04 bond pdb=" C GLY E 10 " pdb=" N LEU E 11 " ideal model delta sigma weight residual 1.332 1.575 -0.243 1.25e-02 6.40e+03 3.79e+02 bond pdb=" N MET D 636 " pdb=" H MET D 636 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.79e+01 bond pdb=" N VAL D 543 " pdb=" H VAL D 543 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" N VAL D 541 " pdb=" H VAL D 541 " ideal model delta sigma weight residual 0.860 1.031 -0.171 2.00e-02 2.50e+03 7.32e+01 ... (remaining 11160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.05: 18045 13.05 - 26.09: 17 26.09 - 39.14: 6 39.14 - 52.19: 1 52.19 - 65.24: 1 Bond angle restraints: 18070 Sorted by residual: angle pdb=" N TYR A 94 " pdb=" CA TYR A 94 " pdb=" C TYR A 94 " ideal model delta sigma weight residual 113.88 160.94 -47.06 1.23e+00 6.61e-01 1.46e+03 angle pdb=" O PRO F 61 " pdb=" C PRO F 61 " pdb=" N ARG F 63 " ideal model delta sigma weight residual 122.64 88.67 33.97 1.35e+00 5.49e-01 6.33e+02 angle pdb=" CA TYR D 576 " pdb=" N TYR D 576 " pdb=" H TYR D 576 " ideal model delta sigma weight residual 113.64 48.40 65.24 3.00e+00 1.11e-01 4.73e+02 angle pdb=" N MET A 103 " pdb=" CA MET A 103 " pdb=" C MET A 103 " ideal model delta sigma weight residual 112.47 138.27 -25.80 1.24e+00 6.50e-01 4.33e+02 angle pdb=" N SER F 95 " pdb=" CA SER F 95 " pdb=" CB SER F 95 " ideal model delta sigma weight residual 110.01 81.42 28.59 1.45e+00 4.76e-01 3.89e+02 ... (remaining 18065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.29: 5375 23.29 - 46.57: 350 46.57 - 69.86: 76 69.86 - 93.14: 20 93.14 - 116.43: 22 Dihedral angle restraints: 5843 sinusoidal: 2582 harmonic: 3261 Sorted by residual: dihedral pdb=" CA PRO F 61 " pdb=" C PRO F 61 " pdb=" N ARG F 63 " pdb=" CA ARG F 63 " ideal model delta harmonic sigma weight residual 180.00 78.65 101.35 0 5.00e+00 4.00e-02 4.11e+02 dihedral pdb=" C ASN G 60 " pdb=" N ASN G 60 " pdb=" CA ASN G 60 " pdb=" CB ASN G 60 " ideal model delta harmonic sigma weight residual -122.60 -77.15 -45.45 0 2.50e+00 1.60e-01 3.30e+02 dihedral pdb=" N MET A 103 " pdb=" C MET A 103 " pdb=" CA MET A 103 " pdb=" CB MET A 103 " ideal model delta harmonic sigma weight residual 122.80 158.98 -36.18 0 2.50e+00 1.60e-01 2.09e+02 ... (remaining 5840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 1276 0.352 - 0.704: 10 0.704 - 1.056: 1 1.056 - 1.408: 0 1.408 - 1.760: 2 Chirality restraints: 1289 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.04e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-02 2.50e+03 8.66e+02 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-02 2.50e+03 6.60e+02 ... (remaining 1286 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 528 " 0.135 2.00e-02 2.50e+03 4.32e-01 2.80e+03 pdb=" CD GLN C 528 " -0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN C 528 " -0.130 2.00e-02 2.50e+03 pdb=" NE2 GLN C 528 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN C 528 " -0.735 2.00e-02 2.50e+03 pdb="HE22 GLN C 528 " 0.739 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 301 " -0.280 2.00e-02 2.50e+03 2.40e-01 7.22e+02 pdb=" C7 NAG A 301 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG A 301 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG A 301 " 0.421 2.00e-02 2.50e+03 pdb=" O7 NAG A 301 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 614 " -0.182 2.00e-02 2.50e+03 2.03e-01 6.21e+02 pdb=" CG ASN D 614 " 0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN D 614 " 0.181 2.00e-02 2.50e+03 pdb=" ND2 ASN D 614 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN D 614 " 0.301 2.00e-02 2.50e+03 pdb="HD22 ASN D 614 " -0.303 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.87: 34 1.87 - 2.55: 6092 2.55 - 3.24: 23656 3.24 - 3.92: 34677 3.92 - 4.60: 53964 Nonbonded interactions: 118423 Sorted by model distance: nonbonded pdb="HD22 ASN D 445 " pdb=" HE1 PHE D 481 " model vdw 1.191 2.100 nonbonded pdb=" HE1 TRP D 604 " pdb=" CD1 TRP D 606 " model vdw 1.278 2.800 nonbonded pdb=" HE1 TRP D 604 " pdb=" NE1 TRP D 606 " model vdw 1.296 2.600 nonbonded pdb="HD22 ASN D 445 " pdb=" CE1 PHE D 481 " model vdw 1.501 2.800 nonbonded pdb=" H TYR D 576 " pdb=" HA TYR D 576 " model vdw 1.579 1.816 ... (remaining 118418 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 'C' and (resid 431 through 442 or (resid 443 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 444 through 483 or re \ sid 485 or (resid 486 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 487 through 506 or resid 508 through 511 or (resid \ 512 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 513 through 541 or (resid 542 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ )) or resid 543 throu \ gh 573 or (resid 574 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 575 through 580 or resid 582 through 594 or resid 59 \ 6 through 598 or resid 602 through 636 or (resid 637 and (name N or name CA or n \ ame C or name O or name CB or name SG )) or resid 639 through 644)) selection = (chain 'D' and (resid 431 through 439 or (resid 440 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 441 through 457 or (r \ esid 458 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 459 through 462 or (resid 463 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 464 or (resid 465 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 46 \ 6 through 470 or (resid 471 through 473 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 474 through 483 or resid 485 thro \ ugh 497 or (resid 498 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 499 through 506 or resid 508 through 516 or (resid \ 517 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 518 through 547 or (resid 548 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 549 through 580 or resid 582 thr \ ough 594 or resid 596 or (resid 597 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 598 or resid 601 through 631 or (resi \ d 632 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 633 through 637 or resid 639 through 644)) } ncs_group { reference = (chain 'E' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 15 or (resid 16 through 17 and (name N \ or name CA or name C or name O or name CB )) or resid 18 through 27 or (resid 2 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 29 through 4 \ 5 or (resid 46 and (name N or name CA or name C or name O or name CB )) or resid \ 47 through 61 or (resid 62 and (name N or name CA or name C or name O or name C \ B )) or resid 63 or (resid 64 through 65 and (name N or name CA or name C or nam \ e O or name CB )) or resid 66 through 80 or resid 82 or (resid 83 through 84 and \ (name N or name CA or name C or name O or name CB )) or resid 85 through 110 or \ (resid 111 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 2 through 117)) selection = (chain 'G' and (resid 1 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 24 or (resid 25 and (name N or name CA \ or name C or name O or name CB )) or resid 26 through 42 or resid 45 through 60 \ or (resid 61 through 62 and (name N or name CA or name C or name O or name CB ) \ ) or resid 63 through 80 or resid 82 through 117)) } ncs_group { reference = (chain 'F' and (resid 2 through 5 or (resid 6 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 20 or (resid 21 and (name N \ or name CA or name C or name O or name CB )) or resid 22 through 53 or (resid 5 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 55 through 6 \ 1 or (resid 63 and (name N or name CA or name C or name O or name CB )) or resid \ 64 through 66 or (resid 67 through 69 and (name N or name CA or name C or name \ O or name CB )) or (resid 70 through 74 and (name N or name CA or name C or name \ O or name CB )) or resid 75 through 77 or (resid 78 and (name N or name CA or n \ ame C or name O or name CB )) or resid 84 through 94 or (resid 95 and (name N or \ name CA or name C or name O or name CB )) or resid 96 through 103 or (resid 104 \ through 105 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 06)) selection = (chain 'H' and (resid 2 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 13 or resid 17 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 42 or resid 44 or (resid 45 and (name N or name CA or name C or name \ O or name CB )) or resid 46 through 61 or resid 63 through 78 or resid 84 throug \ h 106)) } ncs_group { reference = (chain 'I' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O4 or name O5 o \ r name O6 or name O7 )) or (resid 3 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name O5 )))) selection = chain 'J' } 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=0.02 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: 14.990 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: 0.270 Extract box with map and model: 0.590 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 33.720 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.020 1.647 8035 Z= 1.422 Angle : 1.635 47.204 10993 Z= 1.083 Chirality : 0.104 1.760 1289 Planarity : 0.011 0.240 1343 Dihedral : 18.300 116.428 2713 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 31.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.22 % Allowed : 22.22 % Favored : 75.56 % Cbeta Deviations : 1.77 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.26), residues: 996 helix: -5.16 (0.42), residues: 6 sheet: -1.26 (0.26), residues: 412 loop : -1.36 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 604 HIS 0.005 0.001 HIS A 97 PHE 0.018 0.001 PHE D 494 TYR 0.015 0.001 TYR A 94 ARG 0.002 0.000 ARG E 66 Details of bonding type rmsd link_NAG-ASN : bond 0.01053 ( 2) link_NAG-ASN : angle 4.63280 ( 6) link_BETA1-4 : bond 0.04004 ( 4) link_BETA1-4 : angle 6.65818 ( 12) hydrogen bonds : bond 0.27763 ( 235) hydrogen bonds : angle 12.38436 ( 658) SS BOND : bond 0.13831 ( 7) SS BOND : angle 13.85116 ( 14) covalent geometry : bond 0.01972 ( 8022) covalent geometry : angle 1.54095 (10961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 440 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue VAL 472 is missing expected H atoms. Skipping. Residue SER 443 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7202 (p90) cc_final: 0.6938 (p90) REVERT: D 597 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7358 (p0) outliers start: 17 outliers final: 4 residues processed: 152 average time/residue: 0.2086 time to fit residues: 47.5109 Evaluate side-chains 127 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 104 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN B 92 ASN C 447 ASN C 523 GLN ** D 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 60 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.194471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.168986 restraints weight = 32540.036| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 4.22 r_work: 0.3929 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3948 r_free = 0.3948 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8035 Z= 0.141 Angle : 0.637 10.643 10993 Z= 0.333 Chirality : 0.046 0.188 1289 Planarity : 0.004 0.057 1343 Dihedral : 13.675 107.814 1220 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 25.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.63 % Favored : 94.16 % Rotamer: Outliers : 3.14 % Allowed : 24.71 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.26), residues: 998 helix: -5.10 (0.47), residues: 6 sheet: -0.93 (0.27), residues: 372 loop : -1.43 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.004 0.001 HIS G 35 PHE 0.014 0.001 PHE F 94 TYR 0.019 0.001 TYR G 94 ARG 0.004 0.001 ARG D 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 2) link_NAG-ASN : angle 2.76460 ( 6) link_BETA1-4 : bond 0.00621 ( 4) link_BETA1-4 : angle 2.74908 ( 12) hydrogen bonds : bond 0.03997 ( 235) hydrogen bonds : angle 7.64410 ( 658) SS BOND : bond 0.00434 ( 7) SS BOND : angle 1.65033 ( 14) covalent geometry : bond 0.00315 ( 8022) covalent geometry : angle 0.62511 (10961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 440 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue VAL 472 is missing expected H atoms. Skipping. Residue SER 443 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.955 Fit side-chains REVERT: A 27 TYR cc_start: 0.7771 (p90) cc_final: 0.7448 (p90) REVERT: D 483 SER cc_start: 0.8162 (t) cc_final: 0.7871 (p) REVERT: D 493 ASP cc_start: 0.7292 (t0) cc_final: 0.7091 (t0) REVERT: D 597 ASP cc_start: 0.7851 (m-30) cc_final: 0.7294 (p0) REVERT: E 46 GLU cc_start: 0.7321 (mp0) cc_final: 0.6794 (mp0) outliers start: 24 outliers final: 17 residues processed: 129 average time/residue: 0.1957 time to fit residues: 39.1425 Evaluate side-chains 127 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 523 GLN ** D 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN E 58 ASN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.185484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.160906 restraints weight = 30284.883| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 3.61 r_work: 0.3875 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 8035 Z= 0.288 Angle : 0.722 10.863 10993 Z= 0.381 Chirality : 0.050 0.210 1289 Planarity : 0.005 0.040 1343 Dihedral : 11.968 100.095 1215 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 30.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.87 % Favored : 89.03 % Rotamer: Outliers : 5.75 % Allowed : 22.61 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.25), residues: 998 helix: -2.19 (1.61), residues: 12 sheet: -0.87 (0.27), residues: 361 loop : -1.82 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 106 HIS 0.011 0.002 HIS F 97 PHE 0.027 0.003 PHE C 494 TYR 0.031 0.002 TYR E 100 ARG 0.007 0.001 ARG D 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 2) link_NAG-ASN : angle 2.48828 ( 6) link_BETA1-4 : bond 0.00499 ( 4) link_BETA1-4 : angle 2.70805 ( 12) hydrogen bonds : bond 0.03963 ( 235) hydrogen bonds : angle 6.97691 ( 658) SS BOND : bond 0.00261 ( 7) SS BOND : angle 2.21923 ( 14) covalent geometry : bond 0.00677 ( 8022) covalent geometry : angle 0.71039 (10961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 440 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue VAL 472 is missing expected H atoms. Skipping. Residue SER 443 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 118 time to evaluate : 0.889 Fit side-chains REVERT: A 27 TYR cc_start: 0.7859 (p90) cc_final: 0.7485 (p90) REVERT: A 62 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.5601 (pt0) REVERT: B 96 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7969 (mt) REVERT: D 483 SER cc_start: 0.8200 (t) cc_final: 0.7899 (p) REVERT: D 493 ASP cc_start: 0.7442 (t0) cc_final: 0.7162 (t0) REVERT: G 38 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7494 (ptp-170) REVERT: H 96 ASN cc_start: 0.7730 (t0) cc_final: 0.7448 (t0) outliers start: 44 outliers final: 31 residues processed: 143 average time/residue: 0.1963 time to fit residues: 42.9734 Evaluate side-chains 148 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 10.9990 chunk 90 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN C 448 ASN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.190897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.167150 restraints weight = 28096.101| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.68 r_work: 0.3952 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8035 Z= 0.134 Angle : 0.570 11.304 10993 Z= 0.298 Chirality : 0.045 0.209 1289 Planarity : 0.003 0.034 1343 Dihedral : 10.976 98.361 1215 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 26.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.63 % Favored : 94.27 % Rotamer: Outliers : 4.05 % Allowed : 24.05 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.26), residues: 998 helix: -0.21 (2.40), residues: 6 sheet: -0.68 (0.27), residues: 365 loop : -1.70 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 36 HIS 0.004 0.001 HIS G 35 PHE 0.011 0.001 PHE C 494 TYR 0.018 0.001 TYR E 100 ARG 0.003 0.001 ARG D 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 2) link_NAG-ASN : angle 2.39093 ( 6) link_BETA1-4 : bond 0.00564 ( 4) link_BETA1-4 : angle 2.61999 ( 12) hydrogen bonds : bond 0.02949 ( 235) hydrogen bonds : angle 6.20597 ( 658) SS BOND : bond 0.00264 ( 7) SS BOND : angle 1.08519 ( 14) covalent geometry : bond 0.00309 ( 8022) covalent geometry : angle 0.56040 (10961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 440 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue VAL 472 is missing expected H atoms. Skipping. Residue SER 443 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7831 (p90) cc_final: 0.7431 (p90) REVERT: A 62 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.5587 (pt0) REVERT: D 493 ASP cc_start: 0.7414 (t0) cc_final: 0.7128 (t0) REVERT: H 96 ASN cc_start: 0.7644 (t0) cc_final: 0.7265 (t0) outliers start: 31 outliers final: 25 residues processed: 137 average time/residue: 0.2081 time to fit residues: 43.9969 Evaluate side-chains 141 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 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 = 0.4358 r_free = 0.4358 target = 0.189818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.166883 restraints weight = 24567.749| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 3.03 r_work: 0.3963 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8035 Z= 0.156 Angle : 0.587 10.583 10993 Z= 0.302 Chirality : 0.045 0.229 1289 Planarity : 0.003 0.034 1343 Dihedral : 9.421 98.193 1215 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.95 % Favored : 90.95 % Rotamer: Outliers : 5.75 % Allowed : 22.48 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.26), residues: 998 helix: -1.12 (2.31), residues: 6 sheet: -0.66 (0.27), residues: 375 loop : -1.72 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 37 HIS 0.005 0.001 HIS B 34 PHE 0.015 0.002 PHE G 103 TYR 0.024 0.001 TYR E 100 ARG 0.004 0.000 ARG D 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 2) link_NAG-ASN : angle 2.58987 ( 6) link_BETA1-4 : bond 0.00445 ( 4) link_BETA1-4 : angle 3.36224 ( 12) hydrogen bonds : bond 0.02847 ( 235) hydrogen bonds : angle 5.93553 ( 658) SS BOND : bond 0.00219 ( 7) SS BOND : angle 1.11292 ( 14) covalent geometry : bond 0.00366 ( 8022) covalent geometry : angle 0.57260 (10961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 440 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue VAL 472 is missing expected H atoms. Skipping. Residue SER 443 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7830 (p90) cc_final: 0.7467 (p90) REVERT: A 62 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.5565 (pt0) REVERT: B 96 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7833 (mt) outliers start: 44 outliers final: 36 residues processed: 143 average time/residue: 0.2053 time to fit residues: 45.6487 Evaluate side-chains 150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 637 CYS Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 99 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 79 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN C 447 ASN C 448 ASN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.193270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.169002 restraints weight = 30090.453| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 3.98 r_work: 0.3972 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8035 Z= 0.096 Angle : 0.521 10.424 10993 Z= 0.276 Chirality : 0.043 0.147 1289 Planarity : 0.003 0.036 1343 Dihedral : 7.954 94.586 1215 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.05 % Allowed : 24.44 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.26), residues: 998 helix: -1.10 (2.36), residues: 6 sheet: -0.60 (0.27), residues: 376 loop : -1.52 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 37 HIS 0.003 0.001 HIS D 533 PHE 0.024 0.001 PHE C 494 TYR 0.017 0.001 TYR E 100 ARG 0.002 0.000 ARG D 572 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 2) link_NAG-ASN : angle 2.80880 ( 6) link_BETA1-4 : bond 0.00539 ( 4) link_BETA1-4 : angle 2.04355 ( 12) hydrogen bonds : bond 0.02533 ( 235) hydrogen bonds : angle 5.59458 ( 658) SS BOND : bond 0.00446 ( 7) SS BOND : angle 1.17678 ( 14) covalent geometry : bond 0.00221 ( 8022) covalent geometry : angle 0.51189 (10961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 440 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue VAL 472 is missing expected H atoms. Skipping. Residue SER 443 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7823 (p90) cc_final: 0.7369 (p90) REVERT: A 62 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.5606 (pt0) REVERT: D 493 ASP cc_start: 0.7299 (t0) cc_final: 0.7065 (t0) outliers start: 31 outliers final: 23 residues processed: 140 average time/residue: 0.1918 time to fit residues: 41.8015 Evaluate side-chains 138 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 50 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.183311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.159626 restraints weight = 27470.573| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 3.64 r_work: 0.3887 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3902 r_free = 0.3902 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3902 r_free = 0.3902 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8035 Z= 0.230 Angle : 0.619 10.642 10993 Z= 0.329 Chirality : 0.046 0.202 1289 Planarity : 0.004 0.033 1343 Dihedral : 7.845 87.894 1215 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 28.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 5.62 % Allowed : 22.61 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.26), residues: 998 helix: -3.25 (1.33), residues: 12 sheet: -0.62 (0.28), residues: 357 loop : -1.79 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 98 HIS 0.006 0.002 HIS F 97 PHE 0.026 0.002 PHE C 494 TYR 0.029 0.002 TYR E 100 ARG 0.004 0.001 ARG D 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00041 ( 2) link_NAG-ASN : angle 2.12061 ( 6) link_BETA1-4 : bond 0.00353 ( 4) link_BETA1-4 : angle 2.01545 ( 12) hydrogen bonds : bond 0.03006 ( 235) hydrogen bonds : angle 5.92004 ( 658) SS BOND : bond 0.00163 ( 7) SS BOND : angle 1.85065 ( 14) covalent geometry : bond 0.00544 ( 8022) covalent geometry : angle 0.61037 (10961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 440 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue VAL 472 is missing expected H atoms. Skipping. Residue SER 443 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7856 (p90) cc_final: 0.7467 (p90) REVERT: A 62 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.5556 (pt0) REVERT: B 96 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8042 (mt) REVERT: D 493 ASP cc_start: 0.7378 (t0) cc_final: 0.7152 (t0) REVERT: G 71 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7929 (ttmt) outliers start: 43 outliers final: 34 residues processed: 146 average time/residue: 0.1939 time to fit residues: 44.0622 Evaluate side-chains 150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 99 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN C 447 ASN C 448 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.189344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.165030 restraints weight = 30069.415| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 3.84 r_work: 0.3922 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3936 r_free = 0.3936 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8035 Z= 0.124 Angle : 0.534 10.471 10993 Z= 0.284 Chirality : 0.043 0.158 1289 Planarity : 0.003 0.038 1343 Dihedral : 7.372 81.699 1215 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.84 % Allowed : 23.40 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.26), residues: 998 helix: -1.35 (2.43), residues: 6 sheet: -0.67 (0.27), residues: 381 loop : -1.63 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 37 HIS 0.004 0.001 HIS D 533 PHE 0.023 0.001 PHE C 494 TYR 0.020 0.001 TYR E 100 ARG 0.003 0.000 ARG D 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 2) link_NAG-ASN : angle 1.90765 ( 6) link_BETA1-4 : bond 0.00372 ( 4) link_BETA1-4 : angle 1.90890 ( 12) hydrogen bonds : bond 0.02599 ( 235) hydrogen bonds : angle 5.56885 ( 658) SS BOND : bond 0.00182 ( 7) SS BOND : angle 1.28800 ( 14) covalent geometry : bond 0.00289 ( 8022) covalent geometry : angle 0.52703 (10961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 440 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue VAL 472 is missing expected H atoms. Skipping. Residue SER 443 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7862 (p90) cc_final: 0.7427 (p90) REVERT: A 62 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.5587 (pt0) REVERT: D 493 ASP cc_start: 0.7354 (t0) cc_final: 0.7090 (t0) outliers start: 37 outliers final: 32 residues processed: 142 average time/residue: 0.2007 time to fit residues: 44.3316 Evaluate side-chains 146 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 99 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 584 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.185994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.162098 restraints weight = 27237.209| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 3.61 r_work: 0.3897 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3912 r_free = 0.3912 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3912 r_free = 0.3912 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8035 Z= 0.208 Angle : 0.591 10.593 10993 Z= 0.315 Chirality : 0.045 0.191 1289 Planarity : 0.004 0.035 1343 Dihedral : 7.309 77.753 1215 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 28.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 5.23 % Allowed : 23.14 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.26), residues: 998 helix: -3.34 (1.31), residues: 12 sheet: -0.73 (0.27), residues: 381 loop : -1.75 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 98 HIS 0.005 0.001 HIS G 35 PHE 0.023 0.002 PHE C 494 TYR 0.027 0.002 TYR E 100 ARG 0.004 0.001 ARG D 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 2) link_NAG-ASN : angle 1.73133 ( 6) link_BETA1-4 : bond 0.00320 ( 4) link_BETA1-4 : angle 1.96266 ( 12) hydrogen bonds : bond 0.02814 ( 235) hydrogen bonds : angle 5.73332 ( 658) SS BOND : bond 0.00163 ( 7) SS BOND : angle 1.49382 ( 14) covalent geometry : bond 0.00490 ( 8022) covalent geometry : angle 0.58474 (10961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 440 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue VAL 472 is missing expected H atoms. Skipping. Residue SER 443 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7878 (p90) cc_final: 0.7460 (p90) REVERT: A 62 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.5574 (pt0) REVERT: D 493 ASP cc_start: 0.7359 (t0) cc_final: 0.7095 (t0) outliers start: 40 outliers final: 34 residues processed: 140 average time/residue: 0.1929 time to fit residues: 42.2167 Evaluate side-chains 148 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.0020 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN C 448 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.180280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.157300 restraints weight = 26561.741| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.16 r_work: 0.3802 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8035 Z= 0.092 Angle : 0.521 10.404 10993 Z= 0.273 Chirality : 0.043 0.146 1289 Planarity : 0.003 0.039 1343 Dihedral : 6.696 69.005 1215 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.14 % Allowed : 25.23 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.26), residues: 998 helix: -1.32 (2.46), residues: 6 sheet: -0.56 (0.28), residues: 381 loop : -1.55 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 36 HIS 0.003 0.001 HIS D 533 PHE 0.019 0.001 PHE C 494 TYR 0.017 0.001 TYR E 100 ARG 0.002 0.000 ARG D 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 2) link_NAG-ASN : angle 1.84761 ( 6) link_BETA1-4 : bond 0.00465 ( 4) link_BETA1-4 : angle 1.87656 ( 12) hydrogen bonds : bond 0.02424 ( 235) hydrogen bonds : angle 5.30911 ( 658) SS BOND : bond 0.00201 ( 7) SS BOND : angle 1.16557 ( 14) covalent geometry : bond 0.00212 ( 8022) covalent geometry : angle 0.51420 (10961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 440 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue VAL 472 is missing expected H atoms. Skipping. Residue SER 443 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Residue SER 581 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7775 (p90) cc_final: 0.7319 (p90) REVERT: D 493 ASP cc_start: 0.7230 (t0) cc_final: 0.6984 (t0) outliers start: 23 outliers final: 18 residues processed: 132 average time/residue: 0.1889 time to fit residues: 39.0027 Evaluate side-chains 134 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN C 448 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.179941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.156877 restraints weight = 25276.344| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 3.02 r_work: 0.3791 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 8035 Z= 0.190 Angle : 0.961 59.182 10993 Z= 0.578 Chirality : 0.043 0.144 1289 Planarity : 0.003 0.040 1343 Dihedral : 6.667 68.942 1214 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 25.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.40 % Allowed : 24.97 % Favored : 71.63 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.26), residues: 998 helix: -1.33 (2.46), residues: 6 sheet: -0.56 (0.28), residues: 381 loop : -1.55 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 36 HIS 0.003 0.001 HIS G 35 PHE 0.017 0.001 PHE C 494 TYR 0.018 0.001 TYR E 100 ARG 0.002 0.000 ARG D 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 2) link_NAG-ASN : angle 1.84612 ( 6) link_BETA1-4 : bond 0.00382 ( 4) link_BETA1-4 : angle 1.88821 ( 12) hydrogen bonds : bond 0.02460 ( 235) hydrogen bonds : angle 5.31017 ( 658) SS BOND : bond 0.00249 ( 7) SS BOND : angle 1.17986 ( 14) covalent geometry : bond 0.00368 ( 8022) covalent geometry : angle 0.95803 (10961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6305.94 seconds wall clock time: 109 minutes 54.68 seconds (6594.68 seconds total)