Starting phenix.real_space_refine on Thu Nov 14 08:19:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0h_28757/11_2024/8f0h_28757.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0h_28757/11_2024/8f0h_28757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0h_28757/11_2024/8f0h_28757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0h_28757/11_2024/8f0h_28757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0h_28757/11_2024/8f0h_28757.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0h_28757/11_2024/8f0h_28757.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3134 2.51 5 N 839 2.21 5 O 962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4959 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 960 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Conformer: "A" Number of residues, atoms: 123, 958 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 976 Chain: "C" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1528 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "H" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 887 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "L" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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 Time building chain proxies: 5.48, per 1000 atoms: 1.11 Number of scatterers: 4959 At special positions: 0 Unit cell: (67.1, 110, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 962 8.00 N 839 7.00 C 3134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " BETA1-6 " NAG M 1 " - " FUC M 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG M 1 " - " ASN C 343 " Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 658.9 milliseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 14 sheets defined 8.4% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.729A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.453A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.612A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.232A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.678A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.543A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 60 removed outlier: 6.709A pdb=" N GLY B 50 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR B 60 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL B 48 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 33 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 37 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 60 removed outlier: 6.709A pdb=" N GLY B 50 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR B 60 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL B 48 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 33 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 37 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 94 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.669A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.382A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AA9, first strand: chain 'D' and resid 44 through 47 removed outlier: 5.303A pdb=" N LEU D 45 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN D 36 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP D 91 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS D 96 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.956A pdb=" N GLY H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.956A pdb=" N GLY H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.158A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.599A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 405 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: 1.57 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1594 1.34 - 1.46: 1215 1.46 - 1.58: 2244 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 5084 Sorted by residual: bond pdb=" N ILE L 75 " pdb=" CA ILE L 75 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.17e-02 7.31e+03 6.93e+00 bond pdb=" N THR L 72 " pdb=" CA THR L 72 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.53e+00 bond pdb=" N PHE L 73 " pdb=" CA PHE L 73 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.21e-02 6.83e+03 5.86e+00 bond pdb=" N THR L 74 " pdb=" CA THR L 74 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.77e+00 bond pdb=" N SER L 77 " pdb=" CA SER L 77 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.28e-02 6.10e+03 5.16e+00 ... (remaining 5079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 6641 1.07 - 2.14: 196 2.14 - 3.21: 54 3.21 - 4.28: 12 4.28 - 5.35: 5 Bond angle restraints: 6908 Sorted by residual: angle pdb=" N PHE C 338 " pdb=" CA PHE C 338 " pdb=" C PHE C 338 " ideal model delta sigma weight residual 114.56 109.83 4.73 1.27e+00 6.20e-01 1.39e+01 angle pdb=" C ASN L 76 " pdb=" CA ASN L 76 " pdb=" CB ASN L 76 " ideal model delta sigma weight residual 117.23 112.26 4.97 1.36e+00 5.41e-01 1.34e+01 angle pdb=" N ILE L 75 " pdb=" CA ILE L 75 " pdb=" C ILE L 75 " ideal model delta sigma weight residual 113.07 108.17 4.90 1.36e+00 5.41e-01 1.30e+01 angle pdb=" CA LEU L 78 " pdb=" C LEU L 78 " pdb=" O LEU L 78 " ideal model delta sigma weight residual 122.37 118.24 4.13 1.15e+00 7.56e-01 1.29e+01 angle pdb=" N VAL B 64 " pdb=" CA VAL B 64 " pdb=" C VAL B 64 " ideal model delta sigma weight residual 106.21 109.83 -3.62 1.07e+00 8.73e-01 1.15e+01 ... (remaining 6903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 2936 23.94 - 47.88: 66 47.88 - 71.83: 6 71.83 - 95.77: 6 95.77 - 119.71: 1 Dihedral angle restraints: 3015 sinusoidal: 1205 harmonic: 1810 Sorted by residual: dihedral pdb=" CA ILE L 29 " pdb=" C ILE L 29 " pdb=" N ASN L 30 " pdb=" CA ASN L 30 " ideal model delta harmonic sigma weight residual 180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" C2 FUC M 3 " pdb=" C1 FUC M 3 " pdb=" O5 FUC M 3 " pdb=" C5 FUC M 3 " ideal model delta sinusoidal sigma weight residual 57.68 -62.03 119.71 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C1 FUC M 3 " pdb=" C5 FUC M 3 " pdb=" O5 FUC M 3 " pdb=" C4 FUC M 3 " ideal model delta sinusoidal sigma weight residual 59.12 -34.07 93.19 1 3.00e+01 1.11e-03 1.13e+01 ... (remaining 3012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 575 0.042 - 0.085: 109 0.085 - 0.127: 54 0.127 - 0.169: 2 0.169 - 0.212: 1 Chirality restraints: 741 Sorted by residual: chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 9.14e-01 chirality pdb=" CA LEU L 78 " pdb=" N LEU L 78 " pdb=" C LEU L 78 " pdb=" CB LEU L 78 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 738 not shown) Planarity restraints: 893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 95 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO L 96 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO C 521 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 100 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO H 101 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 101 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 101 " 0.017 5.00e-02 4.00e+02 ... (remaining 890 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1089 2.78 - 3.31: 4566 3.31 - 3.84: 8336 3.84 - 4.37: 10055 4.37 - 4.90: 17201 Nonbonded interactions: 41247 Sorted by model distance: nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.350 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.352 3.040 nonbonded pdb=" OG SER C 469 " pdb=" OE1 GLU C 471 " model vdw 2.372 3.040 nonbonded pdb=" O PHE B 29 " pdb=" NH2 ARG B 72 " model vdw 2.378 3.120 ... (remaining 41242 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.330 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.360 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.003 0.035 5084 Z= 0.162 Angle : 0.500 5.351 6908 Z= 0.300 Chirality : 0.040 0.212 741 Planarity : 0.004 0.044 892 Dihedral : 10.682 119.710 1851 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.38 % Allowed : 4.71 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.33), residues: 624 helix: -1.83 (1.16), residues: 21 sheet: 0.74 (0.40), residues: 176 loop : -0.84 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 107 HIS 0.001 0.001 HIS D 96 PHE 0.006 0.001 PHE H 67 TYR 0.018 0.001 TYR L 91 ARG 0.002 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8246 (tp40) cc_final: 0.7954 (mm-40) REVERT: C 385 THR cc_start: 0.8740 (t) cc_final: 0.8465 (p) REVERT: D 77 VAL cc_start: 0.6240 (t) cc_final: 0.5985 (p) REVERT: H 59 TYR cc_start: 0.8847 (m-80) cc_final: 0.8626 (m-80) REVERT: L 82 ASP cc_start: 0.7534 (m-30) cc_final: 0.6658 (m-30) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.2564 time to fit residues: 55.4218 Evaluate side-chains 123 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 26 optimal weight: 0.3980 chunk 16 optimal weight: 0.4980 chunk 31 optimal weight: 0.0050 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN H 104 HIS L 30 ASN L 34 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 5084 Z= 0.248 Angle : 0.661 11.478 6908 Z= 0.349 Chirality : 0.045 0.164 741 Planarity : 0.005 0.046 892 Dihedral : 8.271 102.918 760 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.07 % Allowed : 13.94 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.33), residues: 624 helix: -2.94 (0.78), residues: 27 sheet: 0.62 (0.39), residues: 174 loop : -0.81 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.004 0.001 HIS C 519 PHE 0.020 0.001 PHE C 429 TYR 0.019 0.002 TYR B 80 ARG 0.007 0.001 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8214 (m-80) cc_final: 0.7949 (m-80) REVERT: C 430 THR cc_start: 0.9002 (p) cc_final: 0.8792 (p) REVERT: D 37 GLN cc_start: 0.7777 (tt0) cc_final: 0.7387 (tt0) REVERT: D 52 ASP cc_start: 0.7677 (t0) cc_final: 0.7323 (t0) REVERT: D 73 THR cc_start: 0.8145 (m) cc_final: 0.7779 (p) REVERT: L 2 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8491 (mp) outliers start: 11 outliers final: 5 residues processed: 149 average time/residue: 0.2439 time to fit residues: 43.8477 Evaluate side-chains 130 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5084 Z= 0.281 Angle : 0.663 11.964 6908 Z= 0.346 Chirality : 0.045 0.159 741 Planarity : 0.005 0.048 892 Dihedral : 8.032 95.524 760 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.01 % Allowed : 15.25 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.32), residues: 624 helix: -2.98 (0.76), residues: 27 sheet: 0.61 (0.39), residues: 174 loop : -1.00 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 PHE 0.011 0.001 PHE C 429 TYR 0.021 0.002 TYR B 80 ARG 0.006 0.001 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASP cc_start: 0.8390 (m-30) cc_final: 0.8175 (m-30) REVERT: B 95 TYR cc_start: 0.8080 (m-80) cc_final: 0.7813 (m-80) REVERT: D 6 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6417 (pp30) REVERT: D 73 THR cc_start: 0.8203 (m) cc_final: 0.7884 (p) outliers start: 16 outliers final: 12 residues processed: 137 average time/residue: 0.2293 time to fit residues: 39.1686 Evaluate side-chains 132 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN H 3 GLN H 104 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5084 Z= 0.295 Angle : 0.675 12.604 6908 Z= 0.350 Chirality : 0.045 0.156 741 Planarity : 0.005 0.051 892 Dihedral : 7.773 88.317 760 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.33 % Allowed : 15.44 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.32), residues: 624 helix: -3.15 (0.74), residues: 27 sheet: 0.31 (0.38), residues: 185 loop : -1.11 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 PHE 0.011 0.001 PHE H 79 TYR 0.023 0.002 TYR B 80 ARG 0.007 0.001 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7709 (tp-100) REVERT: B 30 ASP cc_start: 0.8533 (p0) cc_final: 0.8203 (p0) REVERT: B 76 LYS cc_start: 0.9101 (ptpp) cc_final: 0.8752 (ptpp) REVERT: B 87 ARG cc_start: 0.7442 (mtm-85) cc_final: 0.6981 (mtm180) REVERT: B 90 ASP cc_start: 0.8288 (m-30) cc_final: 0.7993 (m-30) REVERT: B 95 TYR cc_start: 0.8107 (m-80) cc_final: 0.7891 (m-80) REVERT: C 386 LYS cc_start: 0.9171 (mmtm) cc_final: 0.8905 (mmtt) REVERT: D 34 TRP cc_start: 0.8624 (m100) cc_final: 0.8281 (m100) REVERT: D 52 ASP cc_start: 0.7847 (m-30) cc_final: 0.7592 (m-30) outliers start: 23 outliers final: 12 residues processed: 134 average time/residue: 0.2294 time to fit residues: 37.4459 Evaluate side-chains 124 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5084 Z= 0.314 Angle : 0.681 13.059 6908 Z= 0.353 Chirality : 0.046 0.188 741 Planarity : 0.005 0.050 892 Dihedral : 7.313 75.568 760 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.14 % Allowed : 15.82 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.32), residues: 624 helix: -2.88 (0.74), residues: 27 sheet: 0.15 (0.38), residues: 184 loop : -1.11 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.002 0.001 HIS H 104 PHE 0.012 0.001 PHE H 79 TYR 0.021 0.002 TYR B 80 ARG 0.008 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 31 ASP cc_start: 0.8362 (m-30) cc_final: 0.8126 (m-30) REVERT: B 76 LYS cc_start: 0.9094 (ptpp) cc_final: 0.8744 (ptpp) REVERT: B 87 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7052 (mtm180) REVERT: B 90 ASP cc_start: 0.8183 (m-30) cc_final: 0.7822 (m-30) REVERT: D 34 TRP cc_start: 0.8736 (m100) cc_final: 0.8354 (m100) REVERT: D 52 ASP cc_start: 0.8082 (m-30) cc_final: 0.7787 (m-30) REVERT: D 95 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8237 (t0) outliers start: 22 outliers final: 17 residues processed: 130 average time/residue: 0.2413 time to fit residues: 38.1351 Evaluate side-chains 131 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 59 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.0570 chunk 31 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5084 Z= 0.231 Angle : 0.668 11.831 6908 Z= 0.344 Chirality : 0.045 0.186 741 Planarity : 0.005 0.056 892 Dihedral : 6.801 62.819 760 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.77 % Allowed : 17.14 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.32), residues: 624 helix: -2.94 (0.72), residues: 27 sheet: 0.22 (0.38), residues: 184 loop : -1.02 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 PHE 0.010 0.001 PHE C 486 TYR 0.022 0.002 TYR B 80 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.904 Fit side-chains REVERT: B 13 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7549 (tp-100) REVERT: B 31 ASP cc_start: 0.8252 (m-30) cc_final: 0.7967 (m-30) REVERT: B 76 LYS cc_start: 0.9070 (ptpp) cc_final: 0.8740 (ptpp) REVERT: B 87 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7069 (mtm180) REVERT: B 90 ASP cc_start: 0.8097 (m-30) cc_final: 0.7677 (m-30) REVERT: C 509 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8482 (mmt180) REVERT: D 34 TRP cc_start: 0.8673 (m100) cc_final: 0.8336 (m100) REVERT: D 52 ASP cc_start: 0.8161 (m-30) cc_final: 0.7861 (m-30) REVERT: D 53 ARG cc_start: 0.8127 (ttm110) cc_final: 0.7863 (ttm110) REVERT: D 95 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8232 (t0) outliers start: 20 outliers final: 15 residues processed: 134 average time/residue: 0.2947 time to fit residues: 49.3460 Evaluate side-chains 130 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5084 Z= 0.277 Angle : 0.698 11.425 6908 Z= 0.361 Chirality : 0.045 0.169 741 Planarity : 0.005 0.052 892 Dihedral : 6.347 55.627 760 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.14 % Allowed : 17.89 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.32), residues: 624 helix: -2.95 (0.71), residues: 27 sheet: 0.21 (0.38), residues: 184 loop : -1.07 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 PHE 0.010 0.001 PHE H 79 TYR 0.023 0.002 TYR L 91 ARG 0.009 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.990 Fit side-chains REVERT: B 13 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7616 (tp-100) REVERT: B 31 ASP cc_start: 0.8215 (m-30) cc_final: 0.7908 (m-30) REVERT: B 76 LYS cc_start: 0.9074 (ptpp) cc_final: 0.8768 (ptpp) REVERT: B 87 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7127 (mtm180) REVERT: B 90 ASP cc_start: 0.8074 (m-30) cc_final: 0.7617 (m-30) REVERT: C 386 LYS cc_start: 0.8801 (mmtm) cc_final: 0.8582 (mmtm) REVERT: D 52 ASP cc_start: 0.8213 (m-30) cc_final: 0.7854 (m-30) REVERT: D 95 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8252 (t0) outliers start: 22 outliers final: 18 residues processed: 130 average time/residue: 0.2344 time to fit residues: 37.3605 Evaluate side-chains 132 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5084 Z= 0.271 Angle : 0.678 10.942 6908 Z= 0.353 Chirality : 0.045 0.164 741 Planarity : 0.006 0.056 892 Dihedral : 5.775 55.471 760 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.95 % Allowed : 18.08 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.32), residues: 624 helix: -2.90 (0.73), residues: 27 sheet: 0.25 (0.39), residues: 179 loop : -1.07 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 PHE 0.010 0.001 PHE H 79 TYR 0.024 0.002 TYR B 80 ARG 0.006 0.001 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.577 Fit side-chains REVERT: B 13 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7518 (tp-100) REVERT: B 31 ASP cc_start: 0.8174 (m-30) cc_final: 0.7859 (m-30) REVERT: B 76 LYS cc_start: 0.9059 (ptpp) cc_final: 0.8768 (ptpp) REVERT: B 87 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.7044 (mtm180) REVERT: B 90 ASP cc_start: 0.8095 (m-30) cc_final: 0.7589 (m-30) REVERT: C 386 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8515 (mmtm) REVERT: D 52 ASP cc_start: 0.8294 (m-30) cc_final: 0.7919 (m-30) REVERT: D 53 ARG cc_start: 0.8098 (ttm110) cc_final: 0.7838 (ttm110) REVERT: D 95 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8278 (t0) outliers start: 21 outliers final: 18 residues processed: 134 average time/residue: 0.2521 time to fit residues: 41.1265 Evaluate side-chains 135 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5084 Z= 0.318 Angle : 0.704 11.019 6908 Z= 0.370 Chirality : 0.046 0.167 741 Planarity : 0.006 0.053 892 Dihedral : 5.547 54.811 760 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.39 % Allowed : 19.59 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.32), residues: 624 helix: -2.85 (0.74), residues: 27 sheet: 0.16 (0.39), residues: 176 loop : -1.13 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 34 HIS 0.003 0.001 HIS H 104 PHE 0.011 0.001 PHE H 79 TYR 0.027 0.002 TYR B 80 ARG 0.009 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.589 Fit side-chains REVERT: B 13 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7719 (tp-100) REVERT: B 31 ASP cc_start: 0.8211 (m-30) cc_final: 0.7902 (m-30) REVERT: B 76 LYS cc_start: 0.9068 (ptpp) cc_final: 0.8782 (ptpp) REVERT: B 87 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7113 (mtm180) REVERT: B 90 ASP cc_start: 0.8272 (m-30) cc_final: 0.7768 (m-30) REVERT: C 386 LYS cc_start: 0.8889 (mmtm) cc_final: 0.8527 (mmtm) REVERT: D 52 ASP cc_start: 0.8398 (m-30) cc_final: 0.8010 (m-30) REVERT: D 95 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8318 (t0) outliers start: 18 outliers final: 16 residues processed: 127 average time/residue: 0.2422 time to fit residues: 37.2860 Evaluate side-chains 132 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.0370 chunk 7 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5084 Z= 0.274 Angle : 0.696 10.535 6908 Z= 0.364 Chirality : 0.045 0.161 741 Planarity : 0.006 0.055 892 Dihedral : 5.532 55.582 760 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.39 % Allowed : 20.72 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.32), residues: 624 helix: -2.84 (0.74), residues: 27 sheet: 0.15 (0.39), residues: 176 loop : -1.13 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.002 0.001 HIS C 519 PHE 0.011 0.001 PHE H 27 TYR 0.026 0.002 TYR B 80 ARG 0.011 0.001 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8506 (ttt90) cc_final: 0.8205 (ttt90) REVERT: B 31 ASP cc_start: 0.8208 (m-30) cc_final: 0.7932 (m-30) REVERT: B 76 LYS cc_start: 0.9053 (ptpp) cc_final: 0.8792 (ptpp) REVERT: B 87 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7359 (mtm180) REVERT: B 90 ASP cc_start: 0.8267 (m-30) cc_final: 0.7732 (m-30) REVERT: C 386 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8574 (mmtm) REVERT: D 52 ASP cc_start: 0.8396 (m-30) cc_final: 0.8038 (m-30) REVERT: D 95 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8331 (t0) outliers start: 18 outliers final: 15 residues processed: 129 average time/residue: 0.2193 time to fit residues: 34.4435 Evaluate side-chains 132 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 0.0020 overall best weight: 0.3126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.100135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.077842 restraints weight = 10183.173| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.13 r_work: 0.3009 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5084 Z= 0.202 Angle : 0.660 9.720 6908 Z= 0.342 Chirality : 0.044 0.160 741 Planarity : 0.005 0.055 892 Dihedral : 5.420 54.826 760 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.01 % Allowed : 20.90 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.32), residues: 624 helix: -2.85 (0.74), residues: 27 sheet: 0.24 (0.39), residues: 176 loop : -1.08 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 34 HIS 0.003 0.001 HIS C 519 PHE 0.014 0.001 PHE H 27 TYR 0.023 0.001 TYR B 80 ARG 0.010 0.001 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2122.12 seconds wall clock time: 41 minutes 7.09 seconds (2467.09 seconds total)