Starting phenix.real_space_refine on Wed Mar 5 23:47:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d8p_46645/03_2025/9d8p_46645.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d8p_46645/03_2025/9d8p_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_46645/03_2025/9d8p_46645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d8p_46645/03_2025/9d8p_46645.map" model { file = "/net/cci-nas-00/data/ceres_data/9d8p_46645/03_2025/9d8p_46645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d8p_46645/03_2025/9d8p_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-5624/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: 3.78, per 1000 atoms: 0.93 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: 0.96 Conformation dependent library (CDL) restraints added in 973.6 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: 0.47 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: 1.17 Time building geometry restraints manager: 1.14 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: 3.780 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.920 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: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.140 ------------------------------------------------------------------------------- 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 : 0.460 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: 0.1734 time to fit residues: 9.3043 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 : 0.458 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.081380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.069738 restraints weight = 10582.616| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.12 r_work: 0.2920 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 4.880 5689 Z= 0.259 Chirality : 0.042 0.139 642 Planarity : 0.003 0.028 726 Dihedral : 4.226 45.331 575 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 : 0.438 Fit side-chains REVERT: A 261 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.7692 (p90) REVERT: A 389 ASN cc_start: 0.9134 (t0) cc_final: 0.8727 (t0) REVERT: B 91 GLU cc_start: 0.8461 (mp0) cc_final: 0.7776 (mp0) REVERT: C 102 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8249 (mt-10) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.1345 time to fit residues: 9.3026 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 : 0.442 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.069136 restraints weight = 10561.233| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.14 r_work: 0.2908 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4177 Z= 0.309 Angle : 0.514 6.473 5689 Z= 0.264 Chirality : 0.042 0.139 642 Planarity : 0.003 0.025 726 Dihedral : 4.419 49.823 575 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.66 % Allowed : 26.88 % Favored : 70.46 % 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: 0.02 (0.37), residues: 519 helix: 1.18 (0.52), residues: 94 sheet: -0.24 (0.43), residues: 159 loop : -0.13 (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 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 53 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.464 Fit side-chains REVERT: A 237 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8848 (tp) REVERT: A 261 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.7677 (p90) REVERT: A 389 ASN cc_start: 0.9212 (t0) cc_final: 0.8764 (t0) REVERT: B 91 GLU cc_start: 0.8465 (mp0) cc_final: 0.7758 (mp0) outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 0.1309 time to fit residues: 8.9875 Evaluate side-chains 52 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.079874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.068503 restraints weight = 10812.317| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.10 r_work: 0.2899 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0841 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= 0.296 Angle : 0.500 4.820 5689 Z= 0.257 Chirality : 0.042 0.139 642 Planarity : 0.003 0.026 726 Dihedral : 4.454 50.231 575 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.39 % Allowed : 26.63 % Favored : 69.98 % 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: 1.20 (0.52), residues: 94 sheet: -0.07 (0.41), residues: 173 loop : -0.17 (0.39), residues: 252 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 0.018 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 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.478 Fit side-chains REVERT: A 237 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8860 (tp) REVERT: A 261 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.7701 (p90) REVERT: A 389 ASN cc_start: 0.9233 (t0) cc_final: 0.8799 (t0) REVERT: B 59 GLU cc_start: 0.8526 (pm20) cc_final: 0.8309 (pm20) REVERT: B 91 GLU cc_start: 0.8493 (mp0) cc_final: 0.7766 (mp0) REVERT: C 80 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8721 (tptm) REVERT: C 102 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8411 (mt-10) outliers start: 14 outliers final: 8 residues processed: 54 average time/residue: 0.1461 time to fit residues: 10.4544 Evaluate side-chains 55 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.079938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.068532 restraints weight = 11004.040| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.13 r_work: 0.2902 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4177 Z= 0.280 Angle : 0.498 4.498 5689 Z= 0.258 Chirality : 0.042 0.137 642 Planarity : 0.003 0.026 726 Dihedral : 4.480 50.211 575 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.63 % Allowed : 27.36 % 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: 0.10 (0.37), residues: 519 helix: 1.20 (0.52), residues: 94 sheet: -0.06 (0.41), residues: 173 loop : -0.15 (0.39), residues: 252 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 A 329 TYR 0.017 0.001 TYR C 79 ARG 0.001 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: 15 poor density : 45 time to evaluate : 0.488 Fit side-chains REVERT: A 261 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.7705 (p90) REVERT: A 389 ASN cc_start: 0.9250 (t0) cc_final: 0.8823 (t0) REVERT: B 59 GLU cc_start: 0.8524 (pm20) cc_final: 0.8308 (pm20) REVERT: B 91 GLU cc_start: 0.8432 (mp0) cc_final: 0.7678 (mp0) REVERT: C 80 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8726 (tptm) REVERT: C 102 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8445 (mt-10) outliers start: 15 outliers final: 11 residues processed: 57 average time/residue: 0.1396 time to fit residues: 10.7299 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 : 0.468 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 0.0980 chunk 24 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.069029 restraints weight = 10742.970| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.10 r_work: 0.2911 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4177 Z= 0.243 Angle : 0.484 4.135 5689 Z= 0.250 Chirality : 0.041 0.138 642 Planarity : 0.003 0.026 726 Dihedral : 4.420 48.931 575 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.36 % Allowed : 27.12 % Favored : 68.52 % 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: 1.28 (0.52), residues: 94 sheet: -0.06 (0.41), residues: 173 loop : -0.11 (0.39), residues: 252 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 0.003 0.001 PHE A 396 TYR 0.015 0.001 TYR C 79 ARG 0.001 0.000 ARG A 262 *********************** 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 63 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.434 Fit side-chains REVERT: A 261 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.7711 (p90) REVERT: A 389 ASN cc_start: 0.9233 (t0) cc_final: 0.8785 (t0) REVERT: B 59 GLU cc_start: 0.8510 (pm20) cc_final: 0.8299 (pm20) REVERT: B 91 GLU cc_start: 0.8424 (mp0) cc_final: 0.7656 (mp0) REVERT: C 80 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8671 (tptm) outliers start: 18 outliers final: 13 residues processed: 57 average time/residue: 0.1289 time to fit residues: 9.8547 Evaluate side-chains 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.068243 restraints weight = 10829.400| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.10 r_work: 0.2900 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0976 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= 0.313 Angle : 0.516 4.234 5689 Z= 0.268 Chirality : 0.042 0.141 642 Planarity : 0.003 0.026 726 Dihedral : 4.575 50.369 575 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.36 % Allowed : 27.60 % Favored : 68.04 % 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: 0.12 (0.37), residues: 519 helix: 1.30 (0.52), residues: 94 sheet: -0.10 (0.41), residues: 173 loop : -0.13 (0.39), residues: 252 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 0.005 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 64 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.510 Fit side-chains REVERT: A 237 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8831 (tp) REVERT: A 261 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.7718 (p90) REVERT: A 389 ASN cc_start: 0.9235 (t0) cc_final: 0.8785 (t0) REVERT: B 59 GLU cc_start: 0.8532 (pm20) cc_final: 0.8312 (pm20) REVERT: B 91 GLU cc_start: 0.8430 (mp0) cc_final: 0.7656 (mp0) REVERT: C 80 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8680 (tptm) REVERT: C 102 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8355 (mt-10) outliers start: 18 outliers final: 14 residues processed: 61 average time/residue: 0.1513 time to fit residues: 12.3964 Evaluate side-chains 61 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 237 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.079809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.068575 restraints weight = 10593.938| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.06 r_work: 0.2900 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4177 Z= 0.288 Angle : 0.508 4.129 5689 Z= 0.262 Chirality : 0.042 0.137 642 Planarity : 0.003 0.026 726 Dihedral : 4.588 50.235 575 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.08 % Allowed : 26.63 % Favored : 68.28 % 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: 0.12 (0.37), residues: 519 helix: 1.29 (0.52), residues: 94 sheet: -0.12 (0.40), residues: 173 loop : -0.11 (0.39), residues: 252 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 A 329 TYR 0.017 0.001 TYR C 79 ARG 0.001 0.000 ARG A 316 *********************** 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 65 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.536 Fit side-chains REVERT: A 237 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8834 (tp) REVERT: A 261 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.7576 (p90) REVERT: A 389 ASN cc_start: 0.9245 (t0) cc_final: 0.8790 (t0) REVERT: B 91 GLU cc_start: 0.8438 (mp0) cc_final: 0.7650 (mp0) REVERT: C 80 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8671 (tptm) REVERT: C 102 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8385 (mt-10) outliers start: 21 outliers final: 14 residues processed: 61 average time/residue: 0.1630 time to fit residues: 13.5330 Evaluate side-chains 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 237 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.0370 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 0.0370 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.068977 restraints weight = 10682.149| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.09 r_work: 0.2918 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0992 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= 0.224 Angle : 0.509 4.718 5689 Z= 0.264 Chirality : 0.042 0.139 642 Planarity : 0.003 0.026 726 Dihedral : 4.532 48.188 575 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.39 % Allowed : 28.81 % Favored : 67.80 % 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: 0.12 (0.37), residues: 519 helix: 1.33 (0.52), residues: 94 sheet: -0.12 (0.41), residues: 173 loop : -0.14 (0.39), residues: 252 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 C 29 TYR 0.014 0.001 TYR C 79 ARG 0.001 0.000 ARG A 96 *********************** 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 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.478 Fit side-chains REVERT: A 389 ASN cc_start: 0.9220 (t0) cc_final: 0.8765 (t0) REVERT: B 91 GLU cc_start: 0.8442 (mp0) cc_final: 0.7627 (mp0) REVERT: C 80 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8675 (tptm) REVERT: C 102 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8307 (mt-10) outliers start: 14 outliers final: 13 residues processed: 54 average time/residue: 0.1801 time to fit residues: 12.8139 Evaluate side-chains 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 0.9980 chunk 46 optimal weight: 0.0770 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.069452 restraints weight = 10775.085| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.10 r_work: 0.2926 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0976 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= 0.207 Angle : 0.501 4.405 5689 Z= 0.258 Chirality : 0.041 0.138 642 Planarity : 0.003 0.026 726 Dihedral : 4.354 44.811 575 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.91 % Allowed : 29.06 % Favored : 68.04 % 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: 1.37 (0.52), residues: 94 sheet: -0.11 (0.41), residues: 173 loop : -0.10 (0.39), residues: 252 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 262 ********************** 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 55 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 389 ASN cc_start: 0.9213 (t0) cc_final: 0.8765 (t0) REVERT: B 91 GLU cc_start: 0.8434 (mp0) cc_final: 0.7616 (mp0) REVERT: C 80 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8667 (tptm) outliers start: 12 outliers final: 11 residues processed: 52 average time/residue: 0.1329 time to fit residues: 9.3420 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 : 0.431 ------------------------------------------------------------------------------- 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 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 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 1 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.079923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.068624 restraints weight = 10653.461| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.06 r_work: 0.2905 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4177 Z= 0.282 Angle : 0.525 5.396 5689 Z= 0.272 Chirality : 0.042 0.136 642 Planarity : 0.003 0.026 726 Dihedral : 4.475 45.032 575 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.39 % Allowed : 28.57 % Favored : 68.04 % 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: 1.41 (0.53), residues: 94 sheet: -0.17 (0.40), residues: 173 loop : -0.16 (0.39), residues: 252 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 0.017 0.001 TYR C 79 ARG 0.003 0.000 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.56 seconds wall clock time: 44 minutes 46.80 seconds (2686.80 seconds total)