Starting phenix.real_space_refine on Wed Jul 23 23:09:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ccw_45460/07_2025/9ccw_45460.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ccw_45460/07_2025/9ccw_45460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ccw_45460/07_2025/9ccw_45460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ccw_45460/07_2025/9ccw_45460.map" model { file = "/net/cci-nas-00/data/ceres_data/9ccw_45460/07_2025/9ccw_45460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ccw_45460/07_2025/9ccw_45460.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 17 5.16 5 C 2868 2.51 5 N 760 2.21 5 O 912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4557 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1227 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 10, 'TRANS': 153} Chain: "B" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1645 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 205} Chain: "C" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1685 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 211} Time building chain proxies: 3.28, per 1000 atoms: 0.72 Number of scatterers: 4557 At special positions: 0 Unit cell: (78.144, 66.304, 111.296, 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 17 16.00 O 912 8.00 N 760 7.00 C 2868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.04 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 209 " 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: 1.10 Conformation dependent library (CDL) restraints added in 589.4 milliseconds 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1108 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 14 sheets defined 5.8% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 37 through 40 removed outlier: 3.533A pdb=" N THR A 40 " --> pdb=" O ASP A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 37 through 40' Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 127 through 132 removed outlier: 4.327A pdb=" N LYS B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'C' and resid 33 through 37 removed outlier: 3.542A pdb=" N SER C 36 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 199 through 205 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 21 removed outlier: 3.625A pdb=" N GLY A 16 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE A 142 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 133 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 127 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE A 126 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA A 63 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL A 128 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY A 61 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE A 130 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 10 Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 17 removed outlier: 3.730A pdb=" N GLU B 110 " --> pdb=" O MET B 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN B 42 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL B 51 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.619A pdb=" N SER B 119 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N TYR B 178 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 150 through 155 Processing sheet with id=AA9, first strand: chain 'C' and resid 8 through 12 removed outlier: 3.607A pdb=" N CYS C 27 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 83 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP C 78 " --> pdb=" O THR C 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 15 through 17 removed outlier: 4.146A pdb=" N GLY C 15 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR C 123 " --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N MET C 39 " --> pdb=" O TYR C 55 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TYR C 55 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP C 41 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 64 " --> pdb=" O TYR C 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 15 through 17 removed outlier: 4.146A pdb=" N GLY C 15 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR C 123 " --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL C 115 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 133 through 136 removed outlier: 5.980A pdb=" N TYR C 189 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB5, first strand: chain 'C' and resid 208 through 213 140 hydrogen bonds defined for protein. 345 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: 1.12 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1456 1.34 - 1.47: 1190 1.47 - 1.59: 1993 1.59 - 1.71: 0 1.71 - 1.83: 22 Bond restraints: 4661 Sorted by residual: bond pdb=" CA CYS B 199 " pdb=" CB CYS B 199 " ideal model delta sigma weight residual 1.528 1.581 -0.053 2.61e-02 1.47e+03 4.15e+00 bond pdb=" C PHE A 84 " pdb=" N PRO A 85 " ideal model delta sigma weight residual 1.334 1.367 -0.034 2.34e-02 1.83e+03 2.06e+00 bond pdb=" CA ASN C 210 " pdb=" CB ASN C 210 " ideal model delta sigma weight residual 1.532 1.550 -0.019 1.74e-02 3.30e+03 1.17e+00 bond pdb=" CB ASN C 210 " pdb=" CG ASN C 210 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CA LYS C 214 " pdb=" C LYS C 214 " ideal model delta sigma weight residual 1.521 1.532 -0.012 1.14e-02 7.69e+03 1.04e+00 ... (remaining 4656 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 6281 2.87 - 5.75: 62 5.75 - 8.62: 6 8.62 - 11.50: 1 11.50 - 14.37: 1 Bond angle restraints: 6351 Sorted by residual: angle pdb=" CB MET B 9 " pdb=" CG MET B 9 " pdb=" SD MET B 9 " ideal model delta sigma weight residual 112.70 127.07 -14.37 3.00e+00 1.11e-01 2.30e+01 angle pdb=" N MET B 9 " pdb=" CA MET B 9 " pdb=" C MET B 9 " ideal model delta sigma weight residual 109.71 104.38 5.33 1.41e+00 5.03e-01 1.43e+01 angle pdb=" CA LEU B 101 " pdb=" CB LEU B 101 " pdb=" CG LEU B 101 " ideal model delta sigma weight residual 116.30 127.72 -11.42 3.50e+00 8.16e-02 1.06e+01 angle pdb=" C PRO B 124 " pdb=" N PRO B 125 " pdb=" CA PRO B 125 " ideal model delta sigma weight residual 121.65 118.43 3.22 1.01e+00 9.80e-01 1.02e+01 angle pdb=" N VAL C 182 " pdb=" CA VAL C 182 " pdb=" C VAL C 182 " ideal model delta sigma weight residual 109.34 115.52 -6.18 2.08e+00 2.31e-01 8.82e+00 ... (remaining 6346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 2357 17.60 - 35.20: 310 35.20 - 52.80: 82 52.80 - 70.40: 10 70.40 - 88.00: 7 Dihedral angle restraints: 2766 sinusoidal: 1029 harmonic: 1737 Sorted by residual: dihedral pdb=" CA PHE A 84 " pdb=" C PHE A 84 " pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta harmonic sigma weight residual -180.00 -129.74 -50.26 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA GLU C 161 " pdb=" C GLU C 161 " pdb=" N PRO C 162 " pdb=" CA PRO C 162 " ideal model delta harmonic sigma weight residual 180.00 155.67 24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA VAL C 163 " pdb=" C VAL C 163 " pdb=" N THR C 164 " pdb=" CA THR C 164 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 2763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 519 0.049 - 0.098: 148 0.098 - 0.146: 51 0.146 - 0.195: 6 0.195 - 0.244: 2 Chirality restraints: 726 Sorted by residual: chirality pdb=" CB ILE C 63 " pdb=" CA ILE C 63 " pdb=" CG1 ILE C 63 " pdb=" CG2 ILE C 63 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB VAL C 165 " pdb=" CA VAL C 165 " pdb=" CG1 VAL C 165 " pdb=" CG2 VAL C 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL C 109 " pdb=" N VAL C 109 " pdb=" C VAL C 109 " pdb=" CB VAL C 109 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.58e-01 ... (remaining 723 not shown) Planarity restraints: 813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 84 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO A 85 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 101 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO A 102 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 156 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.77e+00 pdb=" N PRO A 157 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " -0.036 5.00e-02 4.00e+02 ... (remaining 810 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 88 2.64 - 3.21: 4086 3.21 - 3.77: 7000 3.77 - 4.34: 9423 4.34 - 4.90: 15338 Nonbonded interactions: 35935 Sorted by model distance: nonbonded pdb=" OG1 THR C 105 " pdb=" O SER C 110 " model vdw 2.078 3.040 nonbonded pdb=" OD1 ASP C 95 " pdb=" OH TYR C 99 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR B 41 " pdb=" O TYR C 112 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR C 100 " pdb=" O GLY C 117 " model vdw 2.223 3.040 nonbonded pdb=" O TYR B 191 " pdb=" OH TYR B 197 " model vdw 2.231 3.040 ... (remaining 35930 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 group one per residue 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.130 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5783 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 : 0.004 0.053 4666 Z= 0.173 Angle : 0.811 14.374 6361 Z= 0.438 Chirality : 0.051 0.244 726 Planarity : 0.007 0.072 813 Dihedral : 17.064 87.996 1643 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.43 % Favored : 88.24 % Rotamer: Outliers : 0.00 % Allowed : 26.16 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -3.02 (0.32), residues: 595 helix: -1.31 (1.92), residues: 6 sheet: -1.41 (0.36), residues: 191 loop : -2.47 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 40 HIS 0.003 0.001 HIS B 94 PHE 0.027 0.002 PHE B 67 TYR 0.013 0.001 TYR C 189 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.15090 ( 135) hydrogen bonds : angle 9.79470 ( 345) SS BOND : bond 0.00492 ( 5) SS BOND : angle 1.55047 ( 10) covalent geometry : bond 0.00359 ( 4661) covalent geometry : angle 0.80978 ( 6351) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.480 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1517 time to fit residues: 14.9343 Evaluate side-chains 74 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.0870 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.190087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.173000 restraints weight = 7294.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.177133 restraints weight = 4263.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.179970 restraints weight = 2732.007| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4666 Z= 0.205 Angle : 0.716 9.082 6361 Z= 0.385 Chirality : 0.048 0.168 726 Planarity : 0.007 0.071 813 Dihedral : 6.310 44.512 647 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.11 % Favored : 86.55 % Rotamer: Outliers : 5.62 % Allowed : 22.29 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -3.24 (0.32), residues: 595 helix: -1.72 (1.34), residues: 12 sheet: -1.75 (0.34), residues: 211 loop : -2.52 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 116 HIS 0.004 0.001 HIS C 213 PHE 0.022 0.002 PHE C 159 TYR 0.016 0.002 TYR B 54 ARG 0.004 0.001 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 135) hydrogen bonds : angle 9.00467 ( 345) SS BOND : bond 0.00428 ( 5) SS BOND : angle 1.52304 ( 10) covalent geometry : bond 0.00439 ( 4661) covalent geometry : angle 0.71381 ( 6351) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.462 Fit side-chains REVERT: A 151 ASN cc_start: 0.6574 (t0) cc_final: 0.6241 (t0) REVERT: C 100 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.7306 (t80) REVERT: C 113 PHE cc_start: 0.6922 (m-80) cc_final: 0.6528 (m-80) outliers start: 29 outliers final: 21 residues processed: 95 average time/residue: 0.1415 time to fit residues: 17.7534 Evaluate side-chains 100 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 212 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 4 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.190086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.172902 restraints weight = 7287.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.177094 restraints weight = 4254.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.179959 restraints weight = 2727.279| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4666 Z= 0.180 Angle : 0.688 8.568 6361 Z= 0.369 Chirality : 0.048 0.182 726 Planarity : 0.007 0.071 813 Dihedral : 6.226 46.358 647 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.77 % Favored : 86.89 % Rotamer: Outliers : 6.20 % Allowed : 24.03 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -3.30 (0.32), residues: 595 helix: -1.84 (1.36), residues: 12 sheet: -1.78 (0.33), residues: 215 loop : -2.57 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 116 HIS 0.003 0.001 HIS C 213 PHE 0.015 0.002 PHE C 159 TYR 0.013 0.002 TYR B 54 ARG 0.003 0.000 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 135) hydrogen bonds : angle 8.71609 ( 345) SS BOND : bond 0.00390 ( 5) SS BOND : angle 1.41519 ( 10) covalent geometry : bond 0.00388 ( 4661) covalent geometry : angle 0.68624 ( 6351) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.502 Fit side-chains REVERT: A 151 ASN cc_start: 0.6723 (t0) cc_final: 0.6195 (t0) REVERT: B 172 ASP cc_start: 0.6481 (OUTLIER) cc_final: 0.6246 (t70) REVERT: C 100 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.7103 (t80) REVERT: C 113 PHE cc_start: 0.6908 (m-80) cc_final: 0.6513 (m-80) outliers start: 32 outliers final: 19 residues processed: 101 average time/residue: 0.1493 time to fit residues: 19.6917 Evaluate side-chains 103 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 212 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 51 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.188968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.171626 restraints weight = 7333.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.175863 restraints weight = 4278.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.178835 restraints weight = 2744.880| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4666 Z= 0.188 Angle : 0.692 8.657 6361 Z= 0.370 Chirality : 0.048 0.221 726 Planarity : 0.007 0.071 813 Dihedral : 6.281 45.995 647 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.45 % Favored : 85.21 % Rotamer: Outliers : 5.81 % Allowed : 26.16 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -3.36 (0.32), residues: 595 helix: -2.05 (1.37), residues: 12 sheet: -1.81 (0.33), residues: 215 loop : -2.61 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 116 HIS 0.004 0.001 HIS C 213 PHE 0.022 0.002 PHE B 123 TYR 0.012 0.002 TYR B 54 ARG 0.003 0.000 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 135) hydrogen bonds : angle 8.54387 ( 345) SS BOND : bond 0.00254 ( 5) SS BOND : angle 1.24560 ( 10) covalent geometry : bond 0.00407 ( 4661) covalent geometry : angle 0.69046 ( 6351) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.503 Fit side-chains REVERT: A 151 ASN cc_start: 0.6969 (t0) cc_final: 0.6440 (t0) REVERT: C 61 ASP cc_start: 0.6142 (p0) cc_final: 0.5741 (p0) REVERT: C 100 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7148 (t80) REVERT: C 113 PHE cc_start: 0.6957 (m-80) cc_final: 0.6566 (m-80) outliers start: 30 outliers final: 23 residues processed: 107 average time/residue: 0.1447 time to fit residues: 20.0541 Evaluate side-chains 110 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 212 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.188337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.171358 restraints weight = 7379.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.175523 restraints weight = 4349.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.178384 restraints weight = 2793.723| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4666 Z= 0.201 Angle : 0.704 10.724 6361 Z= 0.379 Chirality : 0.050 0.248 726 Planarity : 0.007 0.071 813 Dihedral : 6.406 46.650 647 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.61 % Favored : 86.05 % Rotamer: Outliers : 6.98 % Allowed : 27.13 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -3.31 (0.33), residues: 595 helix: -2.16 (1.38), residues: 12 sheet: -1.81 (0.34), residues: 208 loop : -2.54 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 116 HIS 0.004 0.001 HIS C 213 PHE 0.009 0.002 PHE C 73 TYR 0.015 0.002 TYR C 112 ARG 0.006 0.000 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 135) hydrogen bonds : angle 8.57771 ( 345) SS BOND : bond 0.00330 ( 5) SS BOND : angle 1.29255 ( 10) covalent geometry : bond 0.00433 ( 4661) covalent geometry : angle 0.70272 ( 6351) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.441 Fit side-chains REVERT: A 151 ASN cc_start: 0.7119 (t0) cc_final: 0.6544 (t0) REVERT: B 172 ASP cc_start: 0.6497 (OUTLIER) cc_final: 0.6264 (t70) REVERT: C 61 ASP cc_start: 0.6312 (p0) cc_final: 0.5863 (p0) REVERT: C 100 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.7118 (t80) REVERT: C 109 VAL cc_start: 0.1042 (OUTLIER) cc_final: 0.0822 (t) REVERT: C 113 PHE cc_start: 0.6817 (m-80) cc_final: 0.6463 (m-80) outliers start: 36 outliers final: 25 residues processed: 110 average time/residue: 0.1363 time to fit residues: 19.7864 Evaluate side-chains 112 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 212 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 56 optimal weight: 0.0370 chunk 50 optimal weight: 0.0770 chunk 53 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.0170 overall best weight: 0.2254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.193851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.176401 restraints weight = 7222.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.180743 restraints weight = 4272.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.183703 restraints weight = 2738.662| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4666 Z= 0.118 Angle : 0.639 11.132 6361 Z= 0.340 Chirality : 0.047 0.193 726 Planarity : 0.006 0.066 813 Dihedral : 5.841 46.664 647 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.92 % Favored : 88.57 % Rotamer: Outliers : 5.04 % Allowed : 28.29 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -3.06 (0.33), residues: 595 helix: -1.94 (1.37), residues: 12 sheet: -1.58 (0.33), residues: 209 loop : -2.41 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 52 HIS 0.001 0.001 HIS C 213 PHE 0.009 0.001 PHE B 67 TYR 0.010 0.001 TYR C 189 ARG 0.007 0.001 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.02831 ( 135) hydrogen bonds : angle 7.66402 ( 345) SS BOND : bond 0.00188 ( 5) SS BOND : angle 0.94601 ( 10) covalent geometry : bond 0.00264 ( 4661) covalent geometry : angle 0.63791 ( 6351) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.491 Fit side-chains REVERT: A 137 TYR cc_start: 0.7436 (t80) cc_final: 0.7003 (t80) REVERT: A 151 ASN cc_start: 0.7184 (t0) cc_final: 0.6572 (t0) REVERT: B 88 LEU cc_start: 0.7304 (mp) cc_final: 0.6955 (mp) REVERT: C 61 ASP cc_start: 0.6305 (p0) cc_final: 0.5830 (p0) REVERT: C 100 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.7043 (t80) REVERT: C 113 PHE cc_start: 0.6667 (m-80) cc_final: 0.6341 (m-80) outliers start: 26 outliers final: 17 residues processed: 99 average time/residue: 0.1502 time to fit residues: 19.3180 Evaluate side-chains 97 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 212 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.190653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.173631 restraints weight = 7304.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.177829 restraints weight = 4314.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.180772 restraints weight = 2775.571| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4666 Z= 0.170 Angle : 0.685 11.714 6361 Z= 0.365 Chirality : 0.048 0.176 726 Planarity : 0.006 0.067 813 Dihedral : 6.038 45.245 647 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.45 % Favored : 86.22 % Rotamer: Outliers : 5.23 % Allowed : 28.49 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -3.27 (0.32), residues: 595 helix: -1.69 (1.35), residues: 12 sheet: -1.71 (0.33), residues: 221 loop : -2.59 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 116 HIS 0.003 0.001 HIS C 213 PHE 0.012 0.002 PHE B 67 TYR 0.013 0.002 TYR B 54 ARG 0.006 0.001 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 135) hydrogen bonds : angle 8.03756 ( 345) SS BOND : bond 0.00643 ( 5) SS BOND : angle 2.56420 ( 10) covalent geometry : bond 0.00371 ( 4661) covalent geometry : angle 0.67806 ( 6351) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.442 Fit side-chains REVERT: A 23 ASN cc_start: 0.7898 (t0) cc_final: 0.7400 (t0) REVERT: A 137 TYR cc_start: 0.7514 (t80) cc_final: 0.7057 (t80) REVERT: A 151 ASN cc_start: 0.7210 (t0) cc_final: 0.6788 (t0) REVERT: C 100 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7133 (t80) REVERT: C 113 PHE cc_start: 0.6747 (m-80) cc_final: 0.6399 (m-80) outliers start: 27 outliers final: 23 residues processed: 98 average time/residue: 0.1415 time to fit residues: 18.2318 Evaluate side-chains 104 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 212 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.190073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.173088 restraints weight = 7292.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.177221 restraints weight = 4307.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.180162 restraints weight = 2785.711| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4666 Z= 0.174 Angle : 0.690 11.762 6361 Z= 0.368 Chirality : 0.049 0.179 726 Planarity : 0.006 0.067 813 Dihedral : 6.144 46.765 647 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.61 % Favored : 86.05 % Rotamer: Outliers : 5.43 % Allowed : 29.65 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -3.21 (0.33), residues: 595 helix: -1.39 (1.39), residues: 12 sheet: -1.70 (0.33), residues: 206 loop : -2.53 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 116 HIS 0.003 0.001 HIS C 213 PHE 0.013 0.001 PHE B 67 TYR 0.013 0.002 TYR B 197 ARG 0.008 0.001 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 135) hydrogen bonds : angle 8.10805 ( 345) SS BOND : bond 0.00548 ( 5) SS BOND : angle 2.41933 ( 10) covalent geometry : bond 0.00379 ( 4661) covalent geometry : angle 0.68433 ( 6351) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.484 Fit side-chains REVERT: A 136 ASN cc_start: 0.6185 (p0) cc_final: 0.5980 (p0) REVERT: A 137 TYR cc_start: 0.7561 (t80) cc_final: 0.7123 (t80) REVERT: A 151 ASN cc_start: 0.7221 (t0) cc_final: 0.6741 (t0) REVERT: C 100 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7205 (t80) REVERT: C 113 PHE cc_start: 0.6840 (m-80) cc_final: 0.6415 (m-80) outliers start: 28 outliers final: 25 residues processed: 96 average time/residue: 0.1457 time to fit residues: 18.2936 Evaluate side-chains 104 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 212 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 3 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.188757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.171905 restraints weight = 7268.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.176038 restraints weight = 4269.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.178873 restraints weight = 2748.090| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4666 Z= 0.192 Angle : 0.708 11.874 6361 Z= 0.378 Chirality : 0.049 0.191 726 Planarity : 0.007 0.067 813 Dihedral : 6.312 45.245 647 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.62 % Favored : 85.04 % Rotamer: Outliers : 5.43 % Allowed : 30.04 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -3.30 (0.33), residues: 595 helix: -1.61 (1.11), residues: 18 sheet: -1.88 (0.33), residues: 208 loop : -2.50 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 116 HIS 0.006 0.001 HIS C 213 PHE 0.013 0.002 PHE B 67 TYR 0.014 0.002 TYR B 197 ARG 0.006 0.001 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 135) hydrogen bonds : angle 8.36210 ( 345) SS BOND : bond 0.00530 ( 5) SS BOND : angle 2.31125 ( 10) covalent geometry : bond 0.00416 ( 4661) covalent geometry : angle 0.70250 ( 6351) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.502 Fit side-chains REVERT: A 137 TYR cc_start: 0.7583 (t80) cc_final: 0.7073 (t80) REVERT: A 151 ASN cc_start: 0.7219 (t0) cc_final: 0.6777 (t0) REVERT: C 100 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.7119 (t80) REVERT: C 113 PHE cc_start: 0.6867 (m-80) cc_final: 0.6414 (m-80) outliers start: 28 outliers final: 24 residues processed: 96 average time/residue: 0.1494 time to fit residues: 18.9535 Evaluate side-chains 103 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 212 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 3 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 51 optimal weight: 0.0870 chunk 36 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.190654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.173516 restraints weight = 7163.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.177867 restraints weight = 4165.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.180801 restraints weight = 2647.727| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4666 Z= 0.159 Angle : 0.679 11.907 6361 Z= 0.362 Chirality : 0.048 0.184 726 Planarity : 0.006 0.067 813 Dihedral : 6.079 45.801 647 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.27 % Favored : 87.39 % Rotamer: Outliers : 5.04 % Allowed : 30.23 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -3.28 (0.32), residues: 595 helix: -1.46 (1.36), residues: 12 sheet: -1.86 (0.33), residues: 206 loop : -2.50 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 52 HIS 0.003 0.001 HIS C 213 PHE 0.011 0.001 PHE B 67 TYR 0.012 0.002 TYR B 54 ARG 0.007 0.000 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 135) hydrogen bonds : angle 8.03590 ( 345) SS BOND : bond 0.00482 ( 5) SS BOND : angle 2.02746 ( 10) covalent geometry : bond 0.00350 ( 4661) covalent geometry : angle 0.67504 ( 6351) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.455 Fit side-chains REVERT: A 137 TYR cc_start: 0.7484 (t80) cc_final: 0.7019 (t80) REVERT: A 151 ASN cc_start: 0.7255 (t0) cc_final: 0.6819 (t0) REVERT: C 100 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7022 (t80) REVERT: C 113 PHE cc_start: 0.6834 (m-80) cc_final: 0.6315 (m-80) outliers start: 26 outliers final: 24 residues processed: 98 average time/residue: 0.1623 time to fit residues: 20.9866 Evaluate side-chains 105 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 212 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.189941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.173072 restraints weight = 7147.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.177331 restraints weight = 4142.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.180231 restraints weight = 2635.420| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4666 Z= 0.177 Angle : 0.692 11.833 6361 Z= 0.373 Chirality : 0.048 0.190 726 Planarity : 0.007 0.101 813 Dihedral : 6.163 45.311 647 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.96 % Favored : 84.71 % Rotamer: Outliers : 4.84 % Allowed : 31.01 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -3.30 (0.33), residues: 595 helix: -1.47 (1.36), residues: 12 sheet: -1.87 (0.33), residues: 206 loop : -2.51 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 40 HIS 0.004 0.001 HIS C 213 PHE 0.012 0.002 PHE B 67 TYR 0.012 0.002 TYR C 158 ARG 0.006 0.000 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 135) hydrogen bonds : angle 8.12157 ( 345) SS BOND : bond 0.00505 ( 5) SS BOND : angle 2.10247 ( 10) covalent geometry : bond 0.00396 ( 4661) covalent geometry : angle 0.68705 ( 6351) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1823.66 seconds wall clock time: 32 minutes 24.86 seconds (1944.86 seconds total)