Starting phenix.real_space_refine on Tue Nov 18 04:22:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cbn_45427/11_2025/9cbn_45427.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cbn_45427/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cbn_45427/11_2025/9cbn_45427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cbn_45427/11_2025/9cbn_45427.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cbn_45427/11_2025/9cbn_45427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cbn_45427/11_2025/9cbn_45427.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'HIS:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} 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: {'ARG:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1, '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: {'ASP:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 2, 'GLU:plan': 2} 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: {'ASP:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 2, 'GLU:plan': 2} 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: {'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2} 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: {'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2} 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, 'ASP:plan': 1, 'ARG: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, 'ASP:plan': 1, 'ARG: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, 'ASP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 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, 'ASP:plan': 3, 'ASN:plan1': 1} 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: 2.86, per 1000 atoms: 0.26 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: 0.97 Conformation dependent library (CDL) restraints added in 603.2 milliseconds 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: 0.34 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: 2.20 Time building geometry restraints manager: 1.28 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: 27.610 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: 0.100 Extract box with map and model: 0.440 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.050 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.690 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.002 0.000 ARG E 66 TYR 0.015 0.001 TYR A 94 PHE 0.018 0.001 PHE D 494 TRP 0.020 0.002 TRP D 604 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.01972 ( 8022) covalent geometry : angle 1.54095 (10961) SS BOND : bond 0.13831 ( 7) SS BOND : angle 13.85116 ( 14) hydrogen bonds : bond 0.27763 ( 235) hydrogen bonds : angle 12.38436 ( 658) link_BETA1-4 : bond 0.04004 ( 4) link_BETA1-4 : angle 6.65818 ( 12) link_NAG-ASN : bond 0.01053 ( 2) link_NAG-ASN : angle 4.63280 ( 6) *********************** 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 : 0.347 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: 0.0992 time to fit residues: 22.9154 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 : 0.358 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 523 GLN ** D 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 60 ASN F 6 GLN 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 = 0.4396 r_free = 0.4396 target = 0.193779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.170193 restraints weight = 25172.933| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.22 r_work: 0.3996 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4015 r_free = 0.4015 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8035 Z= 0.147 Angle : 0.640 10.646 10993 Z= 0.335 Chirality : 0.046 0.207 1289 Planarity : 0.004 0.057 1343 Dihedral : 13.694 107.638 1220 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 25.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.94 % Favored : 93.86 % Rotamer: Outliers : 3.40 % Allowed : 24.18 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.26), residues: 998 helix: -5.10 (0.46), residues: 6 sheet: -0.94 (0.27), residues: 372 loop : -1.44 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 558 TYR 0.018 0.001 TYR G 94 PHE 0.013 0.001 PHE F 94 TRP 0.015 0.001 TRP E 47 HIS 0.004 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8022) covalent geometry : angle 0.62725 (10961) SS BOND : bond 0.00644 ( 7) SS BOND : angle 1.76677 ( 14) hydrogen bonds : bond 0.04128 ( 235) hydrogen bonds : angle 7.68317 ( 658) link_BETA1-4 : bond 0.00493 ( 4) link_BETA1-4 : angle 2.79366 ( 12) link_NAG-ASN : bond 0.00465 ( 2) link_NAG-ASN : angle 2.78985 ( 6) *********************** 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 141 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.404 Fit side-chains REVERT: A 27 TYR cc_start: 0.7722 (p90) cc_final: 0.7403 (p90) REVERT: D 483 SER cc_start: 0.8104 (t) cc_final: 0.7812 (p) REVERT: D 597 ASP cc_start: 0.7797 (m-30) cc_final: 0.7284 (p0) REVERT: E 46 GLU cc_start: 0.7241 (mp0) cc_final: 0.6709 (mp0) outliers start: 26 outliers final: 19 residues processed: 132 average time/residue: 0.0924 time to fit residues: 19.0940 Evaluate side-chains 130 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 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 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 79 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 C 448 ASN C 523 GLN ** D 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 60 ASN ** 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 = 0.4377 r_free = 0.4377 target = 0.191571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.168636 restraints weight = 24153.185| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 3.07 r_work: 0.3979 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3995 r_free = 0.3995 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3995 r_free = 0.3995 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8035 Z= 0.178 Angle : 0.610 10.641 10993 Z= 0.321 Chirality : 0.046 0.195 1289 Planarity : 0.004 0.046 1343 Dihedral : 12.034 102.088 1215 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 27.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.45 % Favored : 91.45 % Rotamer: Outliers : 5.36 % Allowed : 21.96 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.26), residues: 998 helix: 1.57 (2.86), residues: 6 sheet: -0.79 (0.27), residues: 372 loop : -1.56 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 66 TYR 0.023 0.002 TYR E 100 PHE 0.026 0.002 PHE C 494 TRP 0.017 0.002 TRP E 47 HIS 0.007 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8022) covalent geometry : angle 0.59869 (10961) SS BOND : bond 0.00236 ( 7) SS BOND : angle 1.62174 ( 14) hydrogen bonds : bond 0.03569 ( 235) hydrogen bonds : angle 6.72979 ( 658) link_BETA1-4 : bond 0.00480 ( 4) link_BETA1-4 : angle 2.68370 ( 12) link_NAG-ASN : bond 0.00118 ( 2) link_NAG-ASN : angle 2.62597 ( 6) *********************** 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 157 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.5542 (pt0) REVERT: D 483 SER cc_start: 0.8116 (t) cc_final: 0.7823 (p) REVERT: D 493 ASP cc_start: 0.7250 (t0) cc_final: 0.7010 (t0) REVERT: D 597 ASP cc_start: 0.7893 (m-30) cc_final: 0.7208 (p0) outliers start: 41 outliers final: 29 residues processed: 142 average time/residue: 0.0901 time to fit residues: 20.0927 Evaluate side-chains 140 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 78 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 63 SER 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 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 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 51 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain H residue 5 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN C 447 ASN C 448 ASN C 523 GLN ** D 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.191489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.167936 restraints weight = 25882.490| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 3.50 r_work: 0.3966 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3982 r_free = 0.3982 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3982 r_free = 0.3982 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1887 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= 0.159 Angle : 0.578 10.552 10993 Z= 0.303 Chirality : 0.045 0.214 1289 Planarity : 0.003 0.032 1343 Dihedral : 11.345 99.784 1215 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.74 % Favored : 93.16 % Rotamer: Outliers : 5.36 % Allowed : 22.61 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.26), residues: 998 helix: 0.93 (2.76), residues: 6 sheet: -0.69 (0.27), residues: 372 loop : -1.60 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 558 TYR 0.023 0.001 TYR E 100 PHE 0.012 0.001 PHE C 494 TRP 0.008 0.001 TRP E 52 HIS 0.005 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8022) covalent geometry : angle 0.56839 (10961) SS BOND : bond 0.00268 ( 7) SS BOND : angle 1.13944 ( 14) hydrogen bonds : bond 0.03048 ( 235) hydrogen bonds : angle 6.26614 ( 658) link_BETA1-4 : bond 0.00490 ( 4) link_BETA1-4 : angle 2.55872 ( 12) link_NAG-ASN : bond 0.00063 ( 2) link_NAG-ASN : angle 2.43304 ( 6) *********************** 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 158 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.5564 (pt0) REVERT: C 494 PHE cc_start: 0.8033 (m-80) cc_final: 0.7573 (m-80) REVERT: D 493 ASP cc_start: 0.7289 (t0) cc_final: 0.7052 (t0) REVERT: D 597 ASP cc_start: 0.7935 (m-30) cc_final: 0.7163 (p0) REVERT: G 38 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7373 (ptp-170) outliers start: 41 outliers final: 30 residues processed: 143 average time/residue: 0.0916 time to fit residues: 19.9854 Evaluate side-chains 146 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 55 ILE Chi-restraints excluded: chain B residue 67 SER 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 113 THR Chi-restraints excluded: chain F residue 21 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 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 G residue 71 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 523 GLN D 607 ASN ** E 60 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.182209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.158227 restraints weight = 26247.338| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.58 r_work: 0.3863 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 8035 Z= 0.354 Angle : 0.763 11.383 10993 Z= 0.401 Chirality : 0.051 0.244 1289 Planarity : 0.005 0.042 1343 Dihedral : 10.021 96.235 1215 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 31.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.88 % Favored : 87.02 % Rotamer: Outliers : 6.93 % Allowed : 21.96 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.25), residues: 998 helix: -3.41 (1.24), residues: 12 sheet: -0.86 (0.28), residues: 356 loop : -2.12 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 66 TYR 0.033 0.003 TYR E 100 PHE 0.022 0.003 PHE C 438 TRP 0.025 0.003 TRP F 98 HIS 0.009 0.002 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00840 ( 8022) covalent geometry : angle 0.75065 (10961) SS BOND : bond 0.00281 ( 7) SS BOND : angle 1.86889 ( 14) hydrogen bonds : bond 0.03808 ( 235) hydrogen bonds : angle 6.75516 ( 658) link_BETA1-4 : bond 0.00473 ( 4) link_BETA1-4 : angle 3.44227 ( 12) link_NAG-ASN : bond 0.00266 ( 2) link_NAG-ASN : angle 2.56376 ( 6) *********************** 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 175 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 122 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7895 (p90) cc_final: 0.7511 (p90) REVERT: B 96 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8068 (mt) REVERT: D 483 SER cc_start: 0.8161 (t) cc_final: 0.7887 (p) REVERT: D 493 ASP cc_start: 0.7523 (t0) cc_final: 0.7292 (t0) REVERT: G 38 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7556 (ptp-170) outliers start: 53 outliers final: 41 residues processed: 156 average time/residue: 0.0821 time to fit residues: 19.8074 Evaluate side-chains 159 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 83 LEU 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 523 GLN 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 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 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 G residue 71 LYS Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 17 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 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 64 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 448 ASN C 523 GLN C 584 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.188313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.162546 restraints weight = 35767.463| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 4.23 r_work: 0.3867 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2421 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= 0.136 Angle : 0.594 10.590 10993 Z= 0.316 Chirality : 0.045 0.169 1289 Planarity : 0.003 0.038 1343 Dihedral : 8.580 97.057 1215 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 28.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.84 % Favored : 93.06 % Rotamer: Outliers : 4.18 % Allowed : 24.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.25), residues: 998 helix: -3.46 (1.19), residues: 12 sheet: -0.84 (0.27), residues: 378 loop : -1.87 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 558 TYR 0.019 0.001 TYR E 100 PHE 0.035 0.001 PHE C 494 TRP 0.015 0.001 TRP H 37 HIS 0.005 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8022) covalent geometry : angle 0.57920 (10961) SS BOND : bond 0.00183 ( 7) SS BOND : angle 2.06551 ( 14) hydrogen bonds : bond 0.02965 ( 235) hydrogen bonds : angle 6.17184 ( 658) link_BETA1-4 : bond 0.00387 ( 4) link_BETA1-4 : angle 2.70542 ( 12) link_NAG-ASN : bond 0.00323 ( 2) link_NAG-ASN : angle 2.96284 ( 6) *********************** 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 144 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7901 (p90) cc_final: 0.7538 (p90) REVERT: A 62 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.5634 (pt0) REVERT: D 493 ASP cc_start: 0.7506 (t0) cc_final: 0.7237 (t0) REVERT: H 96 ASN cc_start: 0.8200 (t0) cc_final: 0.7249 (t0) outliers start: 32 outliers final: 26 residues processed: 137 average time/residue: 0.0866 time to fit residues: 18.7104 Evaluate side-chains 138 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 92 ASN Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 GLN Chi-restraints excluded: chain C residue 549 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 6 GLU Chi-restraints excluded: chain E residue 48 LEU 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 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 106 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 0.0570 chunk 36 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN C 448 ASN C 523 GLN C 584 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.189519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.166293 restraints weight = 22629.457| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.11 r_work: 0.3958 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 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 = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8035 Z= 0.112 Angle : 0.546 10.525 10993 Z= 0.291 Chirality : 0.044 0.155 1289 Planarity : 0.003 0.038 1343 Dihedral : 7.953 91.333 1215 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 26.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.26), residues: 998 helix: -1.45 (2.35), residues: 6 sheet: -0.70 (0.27), residues: 377 loop : -1.70 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 66 TYR 0.018 0.001 TYR E 100 PHE 0.021 0.001 PHE C 494 TRP 0.011 0.001 TRP H 37 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8022) covalent geometry : angle 0.53649 (10961) SS BOND : bond 0.00204 ( 7) SS BOND : angle 1.57820 ( 14) hydrogen bonds : bond 0.02772 ( 235) hydrogen bonds : angle 5.87909 ( 658) link_BETA1-4 : bond 0.00344 ( 4) link_BETA1-4 : angle 2.01058 ( 12) link_NAG-ASN : bond 0.00129 ( 2) link_NAG-ASN : angle 2.51831 ( 6) *********************** 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 142 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7834 (p90) cc_final: 0.7470 (p90) REVERT: A 62 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.5562 (pt0) REVERT: D 493 ASP cc_start: 0.7372 (t0) cc_final: 0.7133 (t0) REVERT: H 96 ASN cc_start: 0.8009 (t0) cc_final: 0.7034 (t0) outliers start: 31 outliers final: 25 residues processed: 136 average time/residue: 0.0904 time to fit residues: 19.4274 Evaluate side-chains 138 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 63 SER 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 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 113 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 51 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 chunk 87 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 overall best weight: 0.9284 ------------------------------------------------------------------------------- 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 448 ASN C 523 GLN C 584 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.186139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.162081 restraints weight = 30357.955| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.82 r_work: 0.3907 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 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 = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8035 Z= 0.141 Angle : 0.548 10.548 10993 Z= 0.292 Chirality : 0.044 0.160 1289 Planarity : 0.003 0.036 1343 Dihedral : 7.516 84.027 1215 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.31 % Allowed : 24.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.26), residues: 998 helix: -3.14 (1.38), residues: 12 sheet: -0.67 (0.28), residues: 381 loop : -1.72 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 558 TYR 0.022 0.001 TYR E 100 PHE 0.021 0.001 PHE C 494 TRP 0.013 0.001 TRP H 37 HIS 0.004 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8022) covalent geometry : angle 0.54043 (10961) SS BOND : bond 0.00180 ( 7) SS BOND : angle 1.49812 ( 14) hydrogen bonds : bond 0.02628 ( 235) hydrogen bonds : angle 5.70674 ( 658) link_BETA1-4 : bond 0.00354 ( 4) link_BETA1-4 : angle 1.88044 ( 12) link_NAG-ASN : bond 0.00161 ( 2) link_NAG-ASN : angle 2.18429 ( 6) *********************** 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 148 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7856 (p90) cc_final: 0.7481 (p90) REVERT: A 62 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.5583 (pt0) REVERT: D 493 ASP cc_start: 0.7381 (t0) cc_final: 0.7119 (t0) outliers start: 33 outliers final: 26 residues processed: 140 average time/residue: 0.0899 time to fit residues: 19.6174 Evaluate side-chains 140 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 C residue 493 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 GLN Chi-restraints excluded: chain C residue 549 VAL 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 6 GLU Chi-restraints excluded: chain E residue 48 LEU 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 F residue 104 THR Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 24 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.0502 ------------------------------------------------------------------------------- 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 C 523 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.185890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.162536 restraints weight = 26816.085| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 3.61 r_work: 0.3925 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8035 Z= 0.152 Angle : 0.557 10.534 10993 Z= 0.297 Chirality : 0.044 0.162 1289 Planarity : 0.003 0.036 1343 Dihedral : 7.364 80.983 1215 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 4.31 % Allowed : 23.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.26), residues: 998 helix: -3.23 (1.34), residues: 12 sheet: -0.66 (0.28), residues: 381 loop : -1.71 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 558 TYR 0.023 0.001 TYR E 100 PHE 0.019 0.001 PHE C 494 TRP 0.012 0.001 TRP H 37 HIS 0.004 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8022) covalent geometry : angle 0.54993 (10961) SS BOND : bond 0.00156 ( 7) SS BOND : angle 1.43418 ( 14) hydrogen bonds : bond 0.02682 ( 235) hydrogen bonds : angle 5.68021 ( 658) link_BETA1-4 : bond 0.00315 ( 4) link_BETA1-4 : angle 1.89513 ( 12) link_NAG-ASN : bond 0.00161 ( 2) link_NAG-ASN : angle 2.14695 ( 6) *********************** 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 147 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7856 (p90) cc_final: 0.7489 (p90) REVERT: A 62 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.5563 (pt0) outliers start: 33 outliers final: 29 residues processed: 141 average time/residue: 0.0943 time to fit residues: 20.6989 Evaluate side-chains 144 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 63 SER 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 549 VAL 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 6 GLU Chi-restraints excluded: chain E residue 48 LEU 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 36 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 24 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.0020 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.0270 chunk 0 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 0.7448 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.178666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153289 restraints weight = 36320.332| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 4.19 r_work: 0.3713 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2653 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= 0.121 Angle : 0.541 10.467 10993 Z= 0.287 Chirality : 0.043 0.157 1289 Planarity : 0.003 0.038 1343 Dihedral : 7.140 77.168 1215 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.31 % Allowed : 23.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.26), residues: 998 helix: -1.27 (2.50), residues: 6 sheet: -0.60 (0.28), residues: 381 loop : -1.64 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 558 TYR 0.020 0.001 TYR E 100 PHE 0.019 0.001 PHE C 494 TRP 0.011 0.001 TRP H 37 HIS 0.003 0.001 HIS D 533 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8022) covalent geometry : angle 0.53389 (10961) SS BOND : bond 0.00154 ( 7) SS BOND : angle 1.32957 ( 14) hydrogen bonds : bond 0.02575 ( 235) hydrogen bonds : angle 5.59579 ( 658) link_BETA1-4 : bond 0.00373 ( 4) link_BETA1-4 : angle 1.87044 ( 12) link_NAG-ASN : bond 0.00192 ( 2) link_NAG-ASN : angle 2.14619 ( 6) ********************** 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 147 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7884 (p90) cc_final: 0.7538 (p90) REVERT: A 62 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.5652 (pt0) REVERT: C 523 GLN cc_start: 0.8344 (pp30) cc_final: 0.7371 (pt0) outliers start: 33 outliers final: 29 residues processed: 140 average time/residue: 0.0914 time to fit residues: 19.9634 Evaluate side-chains 143 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 63 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 549 VAL 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 107 ASP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 24 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.182708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.158814 restraints weight = 28843.972| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.70 r_work: 0.3875 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8035 Z= 0.240 Angle : 0.626 10.630 10993 Z= 0.334 Chirality : 0.046 0.188 1289 Planarity : 0.004 0.033 1343 Dihedral : 7.173 72.874 1215 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 29.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.27 % Favored : 87.73 % Rotamer: Outliers : 4.44 % Allowed : 23.53 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.26), residues: 998 helix: -3.36 (1.32), residues: 12 sheet: -0.73 (0.28), residues: 378 loop : -1.80 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 558 TYR 0.029 0.002 TYR E 100 PHE 0.019 0.002 PHE C 494 TRP 0.017 0.002 TRP F 98 HIS 0.006 0.002 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 8022) covalent geometry : angle 0.61931 (10961) SS BOND : bond 0.00195 ( 7) SS BOND : angle 1.61808 ( 14) hydrogen bonds : bond 0.02973 ( 235) hydrogen bonds : angle 5.90986 ( 658) link_BETA1-4 : bond 0.00285 ( 4) link_BETA1-4 : angle 2.00570 ( 12) link_NAG-ASN : bond 0.00147 ( 2) link_NAG-ASN : angle 2.01643 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3466.16 seconds wall clock time: 59 minutes 57.72 seconds (3597.72 seconds total)