Starting phenix.real_space_refine on Fri Dec 27 10:19:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d8p_46645/12_2024/9d8p_46645.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d8p_46645/12_2024/9d8p_46645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d8p_46645/12_2024/9d8p_46645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d8p_46645/12_2024/9d8p_46645.map" model { file = "/net/cci-nas-00/data/ceres_data/9d8p_46645/12_2024/9d8p_46645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d8p_46645/12_2024/9d8p_46645.cif" } resolution = 3.2 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= -0.001 sd= 0.011 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 22 5.16 5 C 2625 2.51 5 N 698 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4073 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2749 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 98 Chain: "B" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 649 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 79} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 647 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Time building chain proxies: 3.58, per 1000 atoms: 0.88 Number of scatterers: 4073 At special positions: 0 Unit cell: (75.226, 95.978, 80.414, 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 22 16.00 O 728 8.00 N 698 7.00 C 2625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 368 " 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 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 487.8 milliseconds 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 8 sheets defined 19.9% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 118 through 122 Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 418 through 423 removed outlier: 3.642A pdb=" N ALA A 421 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 432 Processing helix chain 'A' and resid 434 through 442 Processing helix chain 'B' and resid 23 through 36 Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 46 Processing helix chain 'C' and resid 66 through 84 removed outlier: 4.175A pdb=" N LYS C 72 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 48 removed outlier: 4.609A pdb=" N LEU A 395 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.593A pdb=" N VAL A 140 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 162 Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 201 removed outlier: 6.822A pdb=" N ARG A 200 " --> pdb=" O TRP A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 267 removed outlier: 4.240A pdb=" N HIS A 290 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 298 " --> pdb=" O ASN A 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 320 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 383 through 385 removed outlier: 6.363A pdb=" N LYS A 390 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 43 through 45 removed outlier: 7.150A pdb=" N PHE B 4 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL B 75 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET B 6 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU B 77 " --> pdb=" O MET B 6 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG B 8 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 13 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N LYS C 32 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N PHE B 15 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N VAL C 60 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS C 20 " --> pdb=" O VAL C 60 " (cutoff:3.500A) 153 hydrogen bonds defined for protein. 399 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: 1.06 Time building geometry restraints manager: 1.10 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: 1308 1.34 - 1.46: 916 1.46 - 1.57: 1921 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 4177 Sorted by residual: bond pdb=" CB ASP C 111 " pdb=" CG ASP C 111 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.25e+00 bond pdb=" SD MET C 75 " pdb=" CE MET C 75 " ideal model delta sigma weight residual 1.791 1.770 0.021 2.50e-02 1.60e+03 7.37e-01 bond pdb=" CB ASP B 17 " pdb=" CG ASP B 17 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.31e-01 bond pdb=" CA ASP B 17 " pdb=" CB ASP B 17 " ideal model delta sigma weight residual 1.536 1.549 -0.014 2.08e-02 2.31e+03 4.30e-01 bond pdb=" CA ASP C 111 " pdb=" CB ASP C 111 " ideal model delta sigma weight residual 1.533 1.542 -0.009 1.37e-02 5.33e+03 4.24e-01 ... (remaining 4172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 5478 1.03 - 2.07: 157 2.07 - 3.10: 40 3.10 - 4.14: 9 4.14 - 5.17: 5 Bond angle restraints: 5689 Sorted by residual: angle pdb=" CA LYS C 20 " pdb=" CB LYS C 20 " pdb=" CG LYS C 20 " ideal model delta sigma weight residual 114.10 118.24 -4.14 2.00e+00 2.50e-01 4.28e+00 angle pdb=" N ASP C 111 " pdb=" CA ASP C 111 " pdb=" C ASP C 111 " ideal model delta sigma weight residual 110.91 108.58 2.33 1.17e+00 7.31e-01 3.98e+00 angle pdb=" CA ASP C 111 " pdb=" CB ASP C 111 " pdb=" CG ASP C 111 " ideal model delta sigma weight residual 112.60 114.57 -1.97 1.00e+00 1.00e+00 3.87e+00 angle pdb=" CB ASP C 111 " pdb=" CG ASP C 111 " pdb=" OD1 ASP C 111 " ideal model delta sigma weight residual 118.40 122.84 -4.44 2.30e+00 1.89e-01 3.72e+00 angle pdb=" CB LYS C 20 " pdb=" CG LYS C 20 " pdb=" CD LYS C 20 " ideal model delta sigma weight residual 111.30 107.68 3.62 2.30e+00 1.89e-01 2.48e+00 ... (remaining 5684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.09: 2061 15.09 - 30.17: 263 30.17 - 45.26: 86 45.26 - 60.35: 26 60.35 - 75.43: 1 Dihedral angle restraints: 2437 sinusoidal: 903 harmonic: 1534 Sorted by residual: dihedral pdb=" CG ARG A 262 " pdb=" CD ARG A 262 " pdb=" NE ARG A 262 " pdb=" CZ ARG A 262 " ideal model delta sinusoidal sigma weight residual -180.00 -136.61 -43.39 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" N LEU B 27 " pdb=" CA LEU B 27 " pdb=" CB LEU B 27 " pdb=" CG LEU B 27 " ideal model delta sinusoidal sigma weight residual -60.00 -119.06 59.06 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU A 196 " pdb=" CB LEU A 196 " pdb=" CG LEU A 196 " pdb=" CD1 LEU A 196 " ideal model delta sinusoidal sigma weight residual 180.00 123.32 56.68 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 2434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 410 0.029 - 0.059: 146 0.059 - 0.088: 44 0.088 - 0.117: 36 0.117 - 0.147: 6 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA ILE A 274 " pdb=" N ILE A 274 " pdb=" C ILE A 274 " pdb=" CB ILE A 274 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA ILE A 379 " pdb=" N ILE A 379 " pdb=" C ILE A 379 " pdb=" CB ILE A 379 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA ILE C 65 " pdb=" N ILE C 65 " pdb=" C ILE C 65 " pdb=" CB ILE C 65 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 639 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 111 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C ASP C 111 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP C 111 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS C 112 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 174 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C ILE A 174 " -0.017 2.00e-02 2.50e+03 pdb=" O ILE A 174 " 0.006 2.00e-02 2.50e+03 pdb=" N PRO A 175 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 372 " 0.016 5.00e-02 4.00e+02 2.44e-02 9.50e-01 pdb=" N PRO A 373 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.014 5.00e-02 4.00e+02 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 463 2.75 - 3.29: 3767 3.29 - 3.83: 6757 3.83 - 4.36: 7858 4.36 - 4.90: 14014 Nonbonded interactions: 32859 Sorted by model distance: nonbonded pdb=" OH TYR A 292 " pdb=" OD1 ASN A 297 " model vdw 2.213 3.040 nonbonded pdb=" O PRO A 112 " pdb=" OH TYR A 125 " model vdw 2.213 3.040 nonbonded pdb=" NH2 ARG A 129 " pdb=" O MET A 150 " model vdw 2.277 3.120 nonbonded pdb=" OH TYR A 208 " pdb=" O LEU D 73 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR A 365 " pdb=" NH2 ARG D 74 " model vdw 2.300 3.120 ... (remaining 32854 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: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 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 0.029 4177 Z= 0.171 Angle : 0.480 5.174 5689 Z= 0.245 Chirality : 0.041 0.147 642 Planarity : 0.003 0.024 726 Dihedral : 15.510 75.432 1450 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 28.57 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.36 (0.38), residues: 519 helix: 1.44 (0.54), residues: 93 sheet: 0.09 (0.43), residues: 173 loop : 0.02 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 353 HIS 0.002 0.001 HIS A 263 PHE 0.005 0.001 PHE B 4 TYR 0.012 0.001 TYR C 79 ARG 0.001 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.497 Fit side-chains REVERT: B 91 GLU cc_start: 0.8299 (mp0) cc_final: 0.7753 (mp0) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1810 time to fit residues: 9.7608 Evaluate side-chains 40 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.0370 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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: 0.8364 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4177 Z= 0.284 Angle : 0.502 4.881 5689 Z= 0.259 Chirality : 0.042 0.139 642 Planarity : 0.003 0.028 726 Dihedral : 4.226 45.332 575 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.18 % Allowed : 26.88 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.11 (0.37), residues: 519 helix: 1.39 (0.53), residues: 94 sheet: -0.21 (0.43), residues: 159 loop : -0.11 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.002 0.001 HIS A 142 PHE 0.005 0.001 PHE B 4 TYR 0.017 0.001 TYR C 79 ARG 0.002 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.531 Fit side-chains REVERT: A 261 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.7741 (p90) REVERT: A 389 ASN cc_start: 0.9169 (t0) cc_final: 0.8772 (t0) REVERT: B 91 GLU cc_start: 0.8310 (mp0) cc_final: 0.7779 (mp0) REVERT: C 102 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8233 (mt-10) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.1311 time to fit residues: 9.0911 Evaluate side-chains 49 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.0000 chunk 42 optimal weight: 0.0670 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.2922 ------------------------------------------------------------------------------- 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: 0.8342 moved from start: 0.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4177 Z= 0.165 Angle : 0.472 6.974 5689 Z= 0.241 Chirality : 0.041 0.139 642 Planarity : 0.003 0.025 726 Dihedral : 4.076 43.288 575 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.45 % Allowed : 27.85 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.13 (0.37), residues: 519 helix: 1.25 (0.52), residues: 94 sheet: -0.20 (0.44), residues: 159 loop : -0.03 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 353 HIS 0.002 0.001 HIS C 68 PHE 0.003 0.001 PHE A 107 TYR 0.012 0.001 TYR C 79 ARG 0.001 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.492 Fit side-chains REVERT: A 389 ASN cc_start: 0.9146 (t0) cc_final: 0.8752 (t0) REVERT: B 91 GLU cc_start: 0.8246 (mp0) cc_final: 0.7778 (mp0) outliers start: 6 outliers final: 5 residues processed: 46 average time/residue: 0.1321 time to fit residues: 8.3843 Evaluate side-chains 47 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 99 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.8370 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4177 Z= 0.298 Angle : 0.500 4.912 5689 Z= 0.257 Chirality : 0.042 0.137 642 Planarity : 0.003 0.025 726 Dihedral : 4.295 47.254 575 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.91 % Allowed : 27.36 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.10 (0.37), residues: 519 helix: 1.28 (0.52), residues: 94 sheet: -0.22 (0.43), residues: 159 loop : -0.06 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.002 0.001 HIS A 142 PHE 0.005 0.001 PHE B 4 TYR 0.019 0.001 TYR C 79 ARG 0.002 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.503 Fit side-chains REVERT: A 113 ASP cc_start: 0.8552 (t0) cc_final: 0.8348 (t0) REVERT: A 237 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8897 (tp) REVERT: A 261 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.7745 (p90) REVERT: A 389 ASN cc_start: 0.9243 (t0) cc_final: 0.8818 (t0) REVERT: B 91 GLU cc_start: 0.8298 (mp0) cc_final: 0.7763 (mp0) REVERT: C 20 LYS cc_start: 0.7761 (tttm) cc_final: 0.7559 (tttm) REVERT: C 80 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8822 (tptm) REVERT: C 102 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8292 (mt-10) outliers start: 12 outliers final: 7 residues processed: 54 average time/residue: 0.1541 time to fit residues: 11.0763 Evaluate side-chains 55 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 80 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4177 Z= 0.349 Angle : 0.524 4.384 5689 Z= 0.271 Chirality : 0.043 0.136 642 Planarity : 0.003 0.025 726 Dihedral : 4.503 49.669 575 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.87 % Allowed : 27.12 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.09 (0.37), residues: 519 helix: 1.25 (0.52), residues: 94 sheet: 0.03 (0.41), residues: 169 loop : -0.27 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS A 142 PHE 0.006 0.001 PHE B 4 TYR 0.021 0.002 TYR C 79 ARG 0.002 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.516 Fit side-chains REVERT: A 261 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.7747 (p90) REVERT: A 389 ASN cc_start: 0.9258 (t0) cc_final: 0.8809 (t0) REVERT: B 91 GLU cc_start: 0.8275 (mp0) cc_final: 0.7660 (mp0) REVERT: C 80 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8832 (tptm) REVERT: C 102 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8384 (mt-10) outliers start: 16 outliers final: 10 residues processed: 57 average time/residue: 0.1454 time to fit residues: 11.2153 Evaluate side-chains 54 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 80 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4177 Z= 0.289 Angle : 0.506 4.062 5689 Z= 0.261 Chirality : 0.042 0.138 642 Planarity : 0.003 0.026 726 Dihedral : 4.494 49.240 575 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.39 % Allowed : 27.85 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.10 (0.37), residues: 519 helix: 1.28 (0.52), residues: 94 sheet: -0.05 (0.40), residues: 171 loop : -0.19 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.002 0.001 HIS A 263 PHE 0.004 0.001 PHE B 4 TYR 0.018 0.001 TYR C 79 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.487 Fit side-chains REVERT: A 261 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.7760 (p90) REVERT: A 389 ASN cc_start: 0.9273 (t0) cc_final: 0.8830 (t0) REVERT: B 91 GLU cc_start: 0.8262 (mp0) cc_final: 0.7658 (mp0) REVERT: C 80 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8810 (tptm) outliers start: 14 outliers final: 10 residues processed: 55 average time/residue: 0.1440 time to fit residues: 10.4490 Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 80 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 0.0670 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4177 Z= 0.320 Angle : 0.534 5.346 5689 Z= 0.274 Chirality : 0.043 0.137 642 Planarity : 0.003 0.025 726 Dihedral : 4.628 50.445 575 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.15 % Allowed : 28.09 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.08 (0.37), residues: 519 helix: 1.29 (0.52), residues: 94 sheet: -0.07 (0.40), residues: 171 loop : -0.22 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS A 263 PHE 0.005 0.001 PHE A 329 TYR 0.019 0.001 TYR C 79 ARG 0.002 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.456 Fit side-chains REVERT: A 261 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.7764 (p90) REVERT: A 389 ASN cc_start: 0.9284 (t0) cc_final: 0.8838 (t0) REVERT: B 91 GLU cc_start: 0.8280 (mp0) cc_final: 0.7659 (mp0) REVERT: C 80 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8817 (tptm) outliers start: 13 outliers final: 11 residues processed: 55 average time/residue: 0.1543 time to fit residues: 11.1904 Evaluate side-chains 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 80 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 48 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4177 Z= 0.219 Angle : 0.495 4.439 5689 Z= 0.253 Chirality : 0.041 0.138 642 Planarity : 0.003 0.026 726 Dihedral : 4.476 47.866 575 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.63 % Allowed : 27.60 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.37), residues: 519 helix: 1.36 (0.52), residues: 93 sheet: -0.04 (0.41), residues: 171 loop : -0.17 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.002 0.001 HIS A 263 PHE 0.005 0.001 PHE C 29 TYR 0.014 0.001 TYR C 79 ARG 0.001 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.591 Fit side-chains REVERT: A 389 ASN cc_start: 0.9267 (t0) cc_final: 0.8824 (t0) REVERT: B 91 GLU cc_start: 0.8262 (mp0) cc_final: 0.7636 (mp0) REVERT: C 80 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8812 (tptm) outliers start: 15 outliers final: 13 residues processed: 57 average time/residue: 0.1364 time to fit residues: 10.4602 Evaluate side-chains 58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 80 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 0.0170 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4177 Z= 0.301 Angle : 0.535 5.067 5689 Z= 0.275 Chirality : 0.042 0.136 642 Planarity : 0.003 0.025 726 Dihedral : 4.597 49.028 575 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.87 % Allowed : 27.36 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.09 (0.37), residues: 519 helix: 1.38 (0.52), residues: 93 sheet: -0.08 (0.40), residues: 171 loop : -0.22 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS A 263 PHE 0.005 0.001 PHE A 329 TYR 0.019 0.001 TYR C 79 ARG 0.002 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.530 Fit side-chains REVERT: A 261 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.7635 (p90) REVERT: A 389 ASN cc_start: 0.9283 (t0) cc_final: 0.8830 (t0) REVERT: B 91 GLU cc_start: 0.8286 (mp0) cc_final: 0.7648 (mp0) REVERT: C 80 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8821 (tptm) outliers start: 16 outliers final: 14 residues processed: 56 average time/residue: 0.1323 time to fit residues: 10.0493 Evaluate side-chains 58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 80 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 0.0370 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4177 Z= 0.212 Angle : 0.512 5.150 5689 Z= 0.265 Chirality : 0.042 0.147 642 Planarity : 0.003 0.026 726 Dihedral : 4.526 46.658 575 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.15 % Allowed : 28.09 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.11 (0.37), residues: 519 helix: 1.39 (0.52), residues: 93 sheet: -0.11 (0.40), residues: 171 loop : -0.17 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.003 0.001 HIS A 263 PHE 0.004 0.001 PHE A 329 TYR 0.014 0.001 TYR C 79 ARG 0.005 0.000 ARG A 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.499 Fit side-chains REVERT: A 389 ASN cc_start: 0.9265 (t0) cc_final: 0.8813 (t0) REVERT: B 91 GLU cc_start: 0.8269 (mp0) cc_final: 0.7630 (mp0) REVERT: C 80 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8814 (tptm) outliers start: 13 outliers final: 12 residues processed: 53 average time/residue: 0.1456 time to fit residues: 10.2763 Evaluate side-chains 55 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 80 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 1 optimal weight: 0.0870 chunk 33 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.081106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.069710 restraints weight = 10615.875| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.07 r_work: 0.2925 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4177 Z= 0.194 Angle : 0.504 5.111 5689 Z= 0.258 Chirality : 0.041 0.139 642 Planarity : 0.003 0.026 726 Dihedral : 4.355 43.261 575 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.91 % Allowed : 28.33 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.37), residues: 519 helix: 1.34 (0.53), residues: 94 sheet: -0.11 (0.41), residues: 171 loop : -0.09 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.003 0.001 HIS A 263 PHE 0.004 0.001 PHE A 329 TYR 0.013 0.001 TYR C 79 ARG 0.001 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1334.18 seconds wall clock time: 24 minutes 52.82 seconds (1492.82 seconds total)