Starting phenix.real_space_refine on Wed Sep 17 04:27:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d8p_46645/09_2025/9d8p_46645.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d8p_46645/09_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_46645/09_2025/9d8p_46645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d8p_46645/09_2025/9d8p_46645.map" model { file = "/net/cci-nas-00/data/ceres_data/9d8p_46645/09_2025/9d8p_46645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d8p_46645/09_2025/9d8p_46645.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 3, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 3, 'TYR:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1} 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: {'ARG:plan': 2, 'GLU:plan': 3, '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: 1.36, per 1000 atoms: 0.33 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: 0.33 Conformation dependent library (CDL) restraints added in 166.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.17 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: 0.71 Time building geometry restraints manager: 0.48 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: 4.120 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.530 Find NCS groups from input model: 0.020 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.330 ------------------------------------------------------------------------------- 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 : 9.90 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 96 TYR 0.012 0.001 TYR C 79 PHE 0.005 0.001 PHE B 4 TRP 0.005 0.001 TRP A 353 HIS 0.002 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4177) covalent geometry : angle 0.47994 ( 5689) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.42141 ( 2) hydrogen bonds : bond 0.10144 ( 153) hydrogen bonds : angle 5.25157 ( 399) *********************** 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 : 0.105 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: 0.0688 time to fit residues: 3.7048 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 : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0050 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3263 r_free = 0.3263 target = 0.081785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.070148 restraints weight = 10507.511| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.12 r_work: 0.2928 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0485 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= 0.168 Angle : 0.493 4.896 5691 Z= 0.255 Chirality : 0.041 0.138 642 Planarity : 0.003 0.025 726 Dihedral : 4.139 43.976 575 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.94 % Allowed : 27.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.37), residues: 519 helix: 1.39 (0.53), residues: 94 sheet: -0.20 (0.44), residues: 159 loop : -0.08 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.016 0.001 TYR C 79 PHE 0.004 0.001 PHE B 4 TRP 0.007 0.001 TRP A 353 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 4177) covalent geometry : angle 0.49342 ( 5689) SS BOND : bond 0.00170 ( 1) SS BOND : angle 0.46459 ( 2) hydrogen bonds : bond 0.03332 ( 153) hydrogen bonds : angle 4.81884 ( 399) *********************** 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 51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.124 Fit side-chains REVERT: A 261 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.7682 (p90) REVERT: A 389 ASN cc_start: 0.9159 (t0) cc_final: 0.8741 (t0) REVERT: B 91 GLU cc_start: 0.8448 (mp0) cc_final: 0.7762 (mp0) REVERT: C 102 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8231 (mt-10) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 0.0570 time to fit residues: 3.7325 Evaluate side-chains 47 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.0040 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.080885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.069165 restraints weight = 10577.450| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.14 r_work: 0.2903 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4178 Z= 0.206 Angle : 0.518 6.571 5691 Z= 0.266 Chirality : 0.042 0.138 642 Planarity : 0.003 0.025 726 Dihedral : 4.376 49.196 575 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.91 % Allowed : 26.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.37), residues: 519 helix: 1.19 (0.52), residues: 94 sheet: -0.23 (0.43), residues: 159 loop : -0.13 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 262 TYR 0.019 0.001 TYR C 79 PHE 0.006 0.001 PHE B 4 TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 4177) covalent geometry : angle 0.51809 ( 5689) SS BOND : bond 0.00225 ( 1) SS BOND : angle 0.53374 ( 2) hydrogen bonds : bond 0.03337 ( 153) hydrogen bonds : angle 4.83205 ( 399) *********************** 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 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.165 Fit side-chains REVERT: A 237 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8848 (tp) REVERT: A 261 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.7674 (p90) REVERT: A 389 ASN cc_start: 0.9218 (t0) cc_final: 0.8771 (t0) REVERT: B 91 GLU cc_start: 0.8468 (mp0) cc_final: 0.7762 (mp0) REVERT: C 80 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8718 (tptm) REVERT: C 102 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8244 (mt-10) outliers start: 12 outliers final: 7 residues processed: 52 average time/residue: 0.0582 time to fit residues: 4.0998 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 : 0.222 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 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 = 0.3233 r_free = 0.3233 target = 0.079753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.068410 restraints weight = 10720.665| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.08 r_work: 0.2900 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0811 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= 0.189 Angle : 0.500 4.803 5691 Z= 0.257 Chirality : 0.042 0.141 642 Planarity : 0.003 0.026 726 Dihedral : 4.434 49.683 575 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.15 % Allowed : 26.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.37), residues: 519 helix: 1.16 (0.52), residues: 94 sheet: -0.08 (0.41), residues: 173 loop : -0.16 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 262 TYR 0.018 0.001 TYR C 79 PHE 0.005 0.001 PHE B 4 TRP 0.007 0.001 TRP A 353 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 4177) covalent geometry : angle 0.49949 ( 5689) SS BOND : bond 0.00200 ( 1) SS BOND : angle 0.55268 ( 2) hydrogen bonds : bond 0.03218 ( 153) hydrogen bonds : angle 4.82128 ( 399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.164 Fit side-chains REVERT: A 237 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8852 (tp) REVERT: A 261 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.7704 (p90) REVERT: A 389 ASN cc_start: 0.9232 (t0) cc_final: 0.8799 (t0) REVERT: B 59 GLU cc_start: 0.8521 (pm20) cc_final: 0.8307 (pm20) REVERT: B 91 GLU cc_start: 0.8474 (mp0) cc_final: 0.7775 (mp0) outliers start: 13 outliers final: 9 residues processed: 54 average time/residue: 0.0598 time to fit residues: 4.3588 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 : 0.157 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 42 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.080297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.068976 restraints weight = 10697.199| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.09 r_work: 0.2914 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0856 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= 0.156 Angle : 0.488 4.606 5691 Z= 0.253 Chirality : 0.041 0.138 642 Planarity : 0.003 0.026 726 Dihedral : 4.383 48.390 575 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.37), residues: 519 helix: 1.21 (0.52), residues: 94 sheet: -0.06 (0.41), residues: 173 loop : -0.12 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 242 TYR 0.015 0.001 TYR C 79 PHE 0.004 0.001 PHE A 329 TRP 0.007 0.001 TRP A 353 HIS 0.002 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 4177) covalent geometry : angle 0.48800 ( 5689) SS BOND : bond 0.00163 ( 1) SS BOND : angle 0.49534 ( 2) hydrogen bonds : bond 0.03020 ( 153) hydrogen bonds : angle 4.74124 ( 399) *********************** 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 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.163 Fit side-chains REVERT: A 261 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.7712 (p90) REVERT: A 389 ASN cc_start: 0.9234 (t0) cc_final: 0.8801 (t0) REVERT: B 91 GLU cc_start: 0.8409 (mp0) cc_final: 0.7660 (mp0) REVERT: C 80 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8678 (tptm) REVERT: C 102 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8250 (mt-10) outliers start: 13 outliers final: 10 residues processed: 57 average time/residue: 0.0565 time to fit residues: 4.3695 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 : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 80 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.079560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.068266 restraints weight = 10933.261| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.09 r_work: 0.2895 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4178 Z= 0.205 Angle : 0.516 4.530 5691 Z= 0.266 Chirality : 0.042 0.136 642 Planarity : 0.003 0.025 726 Dihedral : 4.527 50.025 575 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.87 % Allowed : 28.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.37), residues: 519 helix: 1.27 (0.52), residues: 94 sheet: -0.07 (0.41), residues: 173 loop : -0.21 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 262 TYR 0.019 0.001 TYR C 79 PHE 0.005 0.001 PHE B 4 TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 4177) covalent geometry : angle 0.51628 ( 5689) SS BOND : bond 0.00228 ( 1) SS BOND : angle 0.56958 ( 2) hydrogen bonds : bond 0.03233 ( 153) hydrogen bonds : angle 4.79979 ( 399) *********************** 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 60 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.165 Fit side-chains REVERT: A 237 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8831 (tp) REVERT: A 261 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.7695 (p90) REVERT: A 389 ASN cc_start: 0.9246 (t0) cc_final: 0.8787 (t0) REVERT: B 91 GLU cc_start: 0.8442 (mp0) cc_final: 0.7665 (mp0) REVERT: C 80 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8663 (tptm) REVERT: C 102 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8363 (mt-10) outliers start: 16 outliers final: 10 residues processed: 57 average time/residue: 0.0520 time to fit residues: 4.0813 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 : 0.161 ------------------------------------------------------------------------------- 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 237 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 80 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.0060 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6134 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.079822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.068427 restraints weight = 11020.890| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.14 r_work: 0.2898 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4178 Z= 0.183 Angle : 0.511 4.310 5691 Z= 0.264 Chirality : 0.042 0.144 642 Planarity : 0.003 0.026 726 Dihedral : 4.560 49.742 575 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.12 % Allowed : 27.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.37), residues: 519 helix: 1.27 (0.52), residues: 94 sheet: -0.11 (0.40), residues: 173 loop : -0.17 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 316 TYR 0.017 0.001 TYR C 79 PHE 0.005 0.001 PHE B 4 TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 4177) covalent geometry : angle 0.51074 ( 5689) SS BOND : bond 0.00200 ( 1) SS BOND : angle 0.52713 ( 2) hydrogen bonds : bond 0.03125 ( 153) hydrogen bonds : angle 4.78555 ( 399) *********************** 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 60 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.166 Fit side-chains REVERT: A 261 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.7574 (p90) REVERT: A 389 ASN cc_start: 0.9249 (t0) cc_final: 0.8802 (t0) REVERT: B 91 GLU cc_start: 0.8452 (mp0) cc_final: 0.7668 (mp0) REVERT: C 80 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8683 (tptm) REVERT: C 102 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8355 (mt-10) outliers start: 17 outliers final: 13 residues processed: 56 average time/residue: 0.0582 time to fit residues: 4.4136 Evaluate side-chains 58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 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 36 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 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 = 0.3243 r_free = 0.3243 target = 0.080231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.068871 restraints weight = 10765.584| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.09 r_work: 0.2910 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4178 Z= 0.156 Angle : 0.504 4.192 5691 Z= 0.260 Chirality : 0.041 0.138 642 Planarity : 0.003 0.026 726 Dihedral : 4.482 48.392 575 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.39 % Allowed : 27.85 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.37), residues: 519 helix: 1.31 (0.52), residues: 94 sheet: -0.11 (0.41), residues: 173 loop : -0.13 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 96 TYR 0.015 0.001 TYR C 79 PHE 0.004 0.001 PHE A 329 TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 4177) covalent geometry : angle 0.50391 ( 5689) SS BOND : bond 0.00171 ( 1) SS BOND : angle 0.51686 ( 2) hydrogen bonds : bond 0.03013 ( 153) hydrogen bonds : angle 4.73706 ( 399) *********************** 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 58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.160 Fit side-chains REVERT: A 389 ASN cc_start: 0.9228 (t0) cc_final: 0.8776 (t0) REVERT: B 91 GLU cc_start: 0.8435 (mp0) cc_final: 0.7656 (mp0) REVERT: C 80 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8683 (tptm) outliers start: 14 outliers final: 13 residues processed: 55 average time/residue: 0.0620 time to fit residues: 4.5273 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 : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain C residue 80 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 0.0670 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.079991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.068524 restraints weight = 11034.302| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.14 r_work: 0.2905 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0993 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= 0.173 Angle : 0.515 4.117 5691 Z= 0.267 Chirality : 0.042 0.149 642 Planarity : 0.003 0.026 726 Dihedral : 4.546 48.204 575 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.12 % Allowed : 27.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.37), residues: 519 helix: 1.33 (0.52), residues: 94 sheet: -0.14 (0.40), residues: 173 loop : -0.15 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 242 TYR 0.017 0.001 TYR C 79 PHE 0.004 0.001 PHE B 4 TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 4177) covalent geometry : angle 0.51473 ( 5689) SS BOND : bond 0.00191 ( 1) SS BOND : angle 0.52467 ( 2) hydrogen bonds : bond 0.03061 ( 153) hydrogen bonds : angle 4.76196 ( 399) *********************** 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 61 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.171 Fit side-chains REVERT: A 261 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.7587 (p90) REVERT: A 389 ASN cc_start: 0.9233 (t0) cc_final: 0.8782 (t0) REVERT: B 91 GLU cc_start: 0.8444 (mp0) cc_final: 0.7654 (mp0) REVERT: C 80 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8681 (tptm) outliers start: 17 outliers final: 14 residues processed: 58 average time/residue: 0.0564 time to fit residues: 4.4347 Evaluate side-chains 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 226 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 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 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 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 = 0.3229 r_free = 0.3229 target = 0.079473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.068037 restraints weight = 10767.207| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.10 r_work: 0.2897 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4178 Z= 0.200 Angle : 0.534 4.716 5691 Z= 0.276 Chirality : 0.042 0.134 642 Planarity : 0.003 0.026 726 Dihedral : 4.628 49.149 575 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.36 % Allowed : 26.88 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.37), residues: 519 helix: 1.31 (0.52), residues: 94 sheet: -0.18 (0.40), residues: 173 loop : -0.18 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 262 TYR 0.019 0.001 TYR C 79 PHE 0.005 0.001 PHE B 4 TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 4177) covalent geometry : angle 0.53432 ( 5689) SS BOND : bond 0.00227 ( 1) SS BOND : angle 0.56038 ( 2) hydrogen bonds : bond 0.03216 ( 153) hydrogen bonds : angle 4.81249 ( 399) ********************** 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 63 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.7776 (m-30) cc_final: 0.7440 (p0) REVERT: A 237 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8852 (tp) REVERT: A 261 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.7584 (p90) REVERT: A 389 ASN cc_start: 0.9255 (t0) cc_final: 0.8805 (t0) REVERT: B 91 GLU cc_start: 0.8458 (mp0) cc_final: 0.7654 (mp0) REVERT: C 80 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8665 (tptm) outliers start: 18 outliers final: 15 residues processed: 60 average time/residue: 0.0597 time to fit residues: 4.7595 Evaluate side-chains 62 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 226 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.0570 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.080556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.069094 restraints weight = 10813.800| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.12 r_work: 0.2914 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0975 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= 0.143 Angle : 0.507 5.947 5691 Z= 0.262 Chirality : 0.041 0.137 642 Planarity : 0.003 0.026 726 Dihedral : 4.469 46.546 575 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.63 % Allowed : 27.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.37), residues: 519 helix: 1.32 (0.52), residues: 94 sheet: -0.15 (0.40), residues: 173 loop : -0.13 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 96 TYR 0.014 0.001 TYR C 79 PHE 0.004 0.001 PHE A 329 TRP 0.006 0.001 TRP A 353 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4177) covalent geometry : angle 0.50731 ( 5689) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.51951 ( 2) hydrogen bonds : bond 0.02944 ( 153) hydrogen bonds : angle 4.73315 ( 399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1006.10 seconds wall clock time: 18 minutes 3.20 seconds (1083.20 seconds total)