Starting phenix.real_space_refine on Wed Jun 4 20:40:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d8p_46645/06_2025/9d8p_46645.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d8p_46645/06_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_46645/06_2025/9d8p_46645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d8p_46645/06_2025/9d8p_46645.map" model { file = "/net/cci-nas-00/data/ceres_data/9d8p_46645/06_2025/9d8p_46645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d8p_46645/06_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-5710/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: 3.68, per 1000 atoms: 0.90 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: 0.95 Conformation dependent library (CDL) restraints added in 524.2 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: 0.48 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: 1.09 Time building geometry restraints manager: 1.16 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: 2.090 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.760 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.910 ------------------------------------------------------------------------------- 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 4178 Z= 0.116 Angle : 0.480 5.174 5691 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 Details of bonding type rmsd hydrogen bonds : bond 0.10144 ( 153) hydrogen bonds : angle 5.25157 ( 399) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.42141 ( 2) covalent geometry : bond 0.00263 ( 4177) covalent geometry : angle 0.47994 ( 5689) *********************** 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 : 0.430 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: 0.1720 time to fit residues: 9.2474 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 : 0.428 ------------------------------------------------------------------------------- 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 4178 Z= 0.184 Angle : 0.502 4.880 5691 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 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 153) hydrogen bonds : angle 4.83563 ( 399) SS BOND : bond 0.00168 ( 1) SS BOND : angle 0.47265 ( 2) covalent geometry : bond 0.00429 ( 4177) covalent geometry : angle 0.50174 ( 5689) *********************** 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 : 0.499 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: 0.1433 time to fit residues: 9.9512 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 : 0.672 ------------------------------------------------------------------------------- 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 4178 Z= 0.199 Angle : 0.514 6.473 5691 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 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 153) hydrogen bonds : angle 4.85163 ( 399) SS BOND : bond 0.00228 ( 1) SS BOND : angle 0.54210 ( 2) covalent geometry : bond 0.00466 ( 4177) covalent geometry : angle 0.51396 ( 5689) *********************** 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 : 0.582 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: 0.1411 time to fit residues: 9.6519 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 : 0.438 ------------------------------------------------------------------------------- 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 4178 Z= 0.190 Angle : 0.500 4.820 5691 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 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 153) hydrogen bonds : angle 4.82064 ( 399) SS BOND : bond 0.00207 ( 1) SS BOND : angle 0.55497 ( 2) covalent geometry : bond 0.00446 ( 4177) covalent geometry : angle 0.50015 ( 5689) *********************** 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 : 0.469 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: 0.1352 time to fit residues: 9.8154 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 : 0.478 ------------------------------------------------------------------------------- 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 4178 Z= 0.180 Angle : 0.498 4.498 5691 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 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 153) hydrogen bonds : angle 4.78370 ( 399) SS BOND : bond 0.00200 ( 1) SS BOND : angle 0.54036 ( 2) covalent geometry : bond 0.00423 ( 4177) covalent geometry : angle 0.49767 ( 5689) *********************** 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 : 0.482 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: 0.1732 time to fit residues: 13.0079 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 : 0.624 ------------------------------------------------------------------------------- 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: 0.5980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.080459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.069119 restraints weight = 10743.238| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.07 r_work: 0.2915 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4178 Z= 0.150 Angle : 0.481 4.158 5691 Z= 0.248 Chirality : 0.041 0.138 642 Planarity : 0.003 0.026 726 Dihedral : 4.404 48.671 575 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.36 % Allowed : 27.36 % 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: 0.15 (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 0.006 0.001 TRP A 353 HIS 0.002 0.001 HIS A 263 PHE 0.003 0.001 PHE A 107 TYR 0.015 0.001 TYR C 79 ARG 0.001 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03011 ( 153) hydrogen bonds : angle 4.71078 ( 399) SS BOND : bond 0.00157 ( 1) SS BOND : angle 0.49338 ( 2) covalent geometry : bond 0.00355 ( 4177) covalent geometry : angle 0.48133 ( 5689) *********************** 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 : 0.436 Fit side-chains REVERT: A 261 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.7715 (p90) REVERT: A 389 ASN cc_start: 0.9226 (t0) cc_final: 0.8778 (t0) REVERT: B 59 GLU cc_start: 0.8502 (pm20) cc_final: 0.8293 (pm20) REVERT: B 91 GLU cc_start: 0.8419 (mp0) cc_final: 0.7658 (mp0) REVERT: C 80 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8673 (tptm) outliers start: 18 outliers final: 13 residues processed: 57 average time/residue: 0.1307 time to fit residues: 10.0285 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 : 0.439 ------------------------------------------------------------------------------- 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: 0.0970 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 20 optimal weight: 0.0770 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.2736 ------------------------------------------------------------------------------- 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 = 0.3268 r_free = 0.3268 target = 0.081553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.070184 restraints weight = 10694.122| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.11 r_work: 0.2939 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4178 Z= 0.108 Angle : 0.472 4.542 5691 Z= 0.244 Chirality : 0.041 0.139 642 Planarity : 0.003 0.026 726 Dihedral : 4.238 44.796 575 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.18 % Allowed : 29.78 % 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: 0.25 (0.37), residues: 519 helix: 1.35 (0.53), residues: 94 sheet: -0.04 (0.41), residues: 173 loop : -0.00 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 194 HIS 0.002 0.001 HIS C 68 PHE 0.004 0.001 PHE C 29 TYR 0.011 0.001 TYR C 79 ARG 0.001 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.02724 ( 153) hydrogen bonds : angle 4.61369 ( 399) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.43974 ( 2) covalent geometry : bond 0.00255 ( 4177) covalent geometry : angle 0.47200 ( 5689) *********************** 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 55 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.693 Fit side-chains REVERT: A 389 ASN cc_start: 0.9205 (t0) cc_final: 0.8745 (t0) REVERT: B 91 GLU cc_start: 0.8387 (mp0) cc_final: 0.7632 (mp0) REVERT: C 80 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8656 (tptm) REVERT: C 102 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8219 (mt-10) outliers start: 9 outliers final: 8 residues processed: 52 average time/residue: 0.1921 time to fit residues: 13.7304 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 : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 434 THR Chi-restraints excluded: chain B residue 27 LEU 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: 0.0040 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 chunk 23 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 = 0.080827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.069511 restraints weight = 10568.810| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.07 r_work: 0.2928 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4178 Z= 0.142 Angle : 0.488 4.798 5691 Z= 0.251 Chirality : 0.041 0.137 642 Planarity : 0.003 0.025 726 Dihedral : 4.237 43.747 575 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.15 % Allowed : 28.57 % 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: 0.24 (0.37), residues: 519 helix: 1.41 (0.53), residues: 94 sheet: -0.05 (0.41), residues: 173 loop : -0.04 (0.39), residues: 252 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 0.004 0.001 PHE A 329 TYR 0.015 0.001 TYR C 79 ARG 0.001 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.02868 ( 153) hydrogen bonds : angle 4.62138 ( 399) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.43386 ( 2) covalent geometry : bond 0.00336 ( 4177) covalent geometry : angle 0.48830 ( 5689) *********************** 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 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.505 Fit side-chains REVERT: A 389 ASN cc_start: 0.9204 (t0) cc_final: 0.8746 (t0) REVERT: B 91 GLU cc_start: 0.8393 (mp0) cc_final: 0.7626 (mp0) REVERT: C 80 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8660 (tptm) REVERT: C 102 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8260 (mt-10) outliers start: 13 outliers final: 10 residues processed: 52 average time/residue: 0.1502 time to fit residues: 10.3561 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 : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9990 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 48 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.080309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.068923 restraints weight = 10690.321| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.09 r_work: 0.2915 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4178 Z= 0.175 Angle : 0.508 4.201 5691 Z= 0.264 Chirality : 0.041 0.135 642 Planarity : 0.003 0.025 726 Dihedral : 4.337 44.606 575 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.66 % Allowed : 29.30 % 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: 0.18 (0.37), residues: 519 helix: 1.41 (0.53), residues: 94 sheet: -0.10 (0.41), residues: 173 loop : -0.09 (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 C 27 PHE 0.005 0.001 PHE A 329 TYR 0.017 0.001 TYR C 79 ARG 0.002 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03021 ( 153) hydrogen bonds : angle 4.69313 ( 399) SS BOND : bond 0.00198 ( 1) SS BOND : angle 0.46697 ( 2) covalent geometry : bond 0.00412 ( 4177) covalent geometry : angle 0.50839 ( 5689) *********************** 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 55 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.466 Fit side-chains REVERT: A 389 ASN cc_start: 0.9215 (t0) cc_final: 0.8762 (t0) REVERT: B 91 GLU cc_start: 0.8410 (mp0) cc_final: 0.7633 (mp0) REVERT: C 80 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8665 (tptm) outliers start: 11 outliers final: 10 residues processed: 52 average time/residue: 0.1968 time to fit residues: 13.5995 Evaluate side-chains 54 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 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 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 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: 0.8980 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 chunk 8 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.3436 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.081071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.069661 restraints weight = 10762.426| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.10 r_work: 0.2930 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4178 Z= 0.124 Angle : 0.495 4.548 5691 Z= 0.258 Chirality : 0.041 0.138 642 Planarity : 0.003 0.026 726 Dihedral : 4.266 42.738 575 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.42 % Allowed : 29.54 % 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: 0.20 (0.37), residues: 519 helix: 1.40 (0.53), residues: 94 sheet: -0.08 (0.41), residues: 173 loop : -0.07 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 0.004 0.000 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.02809 ( 153) hydrogen bonds : angle 4.62661 ( 399) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.45280 ( 2) covalent geometry : bond 0.00293 ( 4177) covalent geometry : angle 0.49468 ( 5689) ********************** 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 53 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.447 Fit side-chains REVERT: A 389 ASN cc_start: 0.9200 (t0) cc_final: 0.8749 (t0) REVERT: B 91 GLU cc_start: 0.8418 (mp0) cc_final: 0.7619 (mp0) REVERT: C 28 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8493 (mm-30) REVERT: C 80 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8658 (tptm) outliers start: 10 outliers final: 8 residues processed: 50 average time/residue: 0.1856 time to fit residues: 12.7212 Evaluate side-chains 52 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 434 THR Chi-restraints excluded: chain B residue 27 LEU 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: 0.0980 chunk 39 optimal weight: 0.0010 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.081119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.069791 restraints weight = 10589.545| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.07 r_work: 0.2930 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4178 Z= 0.125 Angle : 0.492 4.554 5691 Z= 0.253 Chirality : 0.041 0.138 642 Planarity : 0.003 0.026 726 Dihedral : 4.187 42.245 575 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.39 % Allowed : 28.33 % 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: 0.24 (0.37), residues: 519 helix: 1.44 (0.53), residues: 94 sheet: -0.07 (0.41), residues: 173 loop : -0.04 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 Details of bonding type rmsd hydrogen bonds : bond 0.02798 ( 153) hydrogen bonds : angle 4.62084 ( 399) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.42009 ( 2) covalent geometry : bond 0.00296 ( 4177) covalent geometry : angle 0.49225 ( 5689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2872.51 seconds wall clock time: 52 minutes 34.89 seconds (3154.89 seconds total)