Starting phenix.real_space_refine on Fri May 9 13:06:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sl0_40570/05_2025/8sl0_40570.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sl0_40570/05_2025/8sl0_40570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sl0_40570/05_2025/8sl0_40570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sl0_40570/05_2025/8sl0_40570.map" model { file = "/net/cci-nas-00/data/ceres_data/8sl0_40570/05_2025/8sl0_40570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sl0_40570/05_2025/8sl0_40570.cif" } resolution = 3.3 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= 0.034 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 2 5.16 5 C 1107 2.51 5 N 297 2.21 5 O 331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 1737 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 10, 'TRANS': 217} Time building chain proxies: 6.71, per 1000 atoms: 3.86 Number of scatterers: 1737 At special positions: 0 Unit cell: (90.153, 64.395, 70.119, 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 2 16.00 O 331 8.00 N 297 7.00 C 1107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.41 Conformation dependent library (CDL) restraints added in 222.5 milliseconds 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 410 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 13.2% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'A' and resid 139 through 147 removed outlier: 3.593A pdb=" N GLN A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 24 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 18 through 24 current: chain 'A' and resid 39 through 42 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 39 through 42 current: chain 'A' and resid 97 through 120 removed outlier: 7.586A pdb=" N ALA A 97 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 180 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 99 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU A 178 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA A 101 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 176 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR A 103 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY A 174 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 105 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY A 172 " --> pdb=" O GLN A 105 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG A 107 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS A 170 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 109 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA A 168 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 111 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 166 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE A 113 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE A 164 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ASN A 115 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN A 162 " --> pdb=" O ASN A 115 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 189 through 205 current: chain 'A' and resid 228 through 231 35 hydrogen bonds defined for protein. 96 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: 0.35 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: 579 1.34 - 1.46: 309 1.46 - 1.57: 873 1.57 - 1.69: 0 1.69 - 1.81: 3 Bond restraints: 1764 Sorted by residual: bond pdb=" C GLU A 219 " pdb=" N ILE A 220 " ideal model delta sigma weight residual 1.330 1.305 0.025 1.97e-02 2.58e+03 1.63e+00 bond pdb=" N SER A 55 " pdb=" CA SER A 55 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.82e-01 bond pdb=" N GLU A 182 " pdb=" CA GLU A 182 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.80e-01 bond pdb=" CA VAL A 89 " pdb=" CB VAL A 89 " ideal model delta sigma weight residual 1.540 1.550 -0.009 1.36e-02 5.41e+03 4.79e-01 bond pdb=" CA ASP A 6 " pdb=" C ASP A 6 " ideal model delta sigma weight residual 1.525 1.538 -0.013 2.10e-02 2.27e+03 4.09e-01 ... (remaining 1759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 2342 1.80 - 3.61: 35 3.61 - 5.41: 2 5.41 - 7.21: 3 7.21 - 9.01: 2 Bond angle restraints: 2384 Sorted by residual: angle pdb=" C GLU A 182 " pdb=" CA GLU A 182 " pdb=" CB GLU A 182 " ideal model delta sigma weight residual 110.42 115.84 -5.42 1.99e+00 2.53e-01 7.41e+00 angle pdb=" C SER A 55 " pdb=" CA SER A 55 " pdb=" CB SER A 55 " ideal model delta sigma weight residual 110.42 115.74 -5.32 1.99e+00 2.53e-01 7.13e+00 angle pdb=" CA LEU A 30 " pdb=" CB LEU A 30 " pdb=" CG LEU A 30 " ideal model delta sigma weight residual 116.30 125.31 -9.01 3.50e+00 8.16e-02 6.63e+00 angle pdb=" CA LEU A 90 " pdb=" CB LEU A 90 " pdb=" CG LEU A 90 " ideal model delta sigma weight residual 116.30 124.68 -8.38 3.50e+00 8.16e-02 5.74e+00 angle pdb=" C SER A 88 " pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta sigma weight residual 121.97 126.07 -4.10 1.80e+00 3.09e-01 5.18e+00 ... (remaining 2379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 943 17.60 - 35.20: 94 35.20 - 52.80: 23 52.80 - 70.40: 6 70.40 - 88.00: 4 Dihedral angle restraints: 1070 sinusoidal: 426 harmonic: 644 Sorted by residual: dihedral pdb=" CA ASN A 115 " pdb=" CB ASN A 115 " pdb=" CG ASN A 115 " pdb=" OD1 ASN A 115 " ideal model delta sinusoidal sigma weight residual 120.00 -168.87 -71.13 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ARG A 14 " pdb=" C ARG A 14 " pdb=" N LEU A 15 " pdb=" CA LEU A 15 " ideal model delta harmonic sigma weight residual 180.00 163.99 16.01 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA GLN A 28 " pdb=" CB GLN A 28 " pdb=" CG GLN A 28 " pdb=" CD GLN A 28 " ideal model delta sinusoidal sigma weight residual 180.00 120.32 59.68 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 158 0.028 - 0.056: 61 0.056 - 0.083: 26 0.083 - 0.111: 22 0.111 - 0.139: 7 Chirality restraints: 274 Sorted by residual: chirality pdb=" CB VAL A 89 " pdb=" CA VAL A 89 " pdb=" CG1 VAL A 89 " pdb=" CG2 VAL A 89 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE A 99 " pdb=" N ILE A 99 " pdb=" C ILE A 99 " pdb=" CB ILE A 99 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE A 27 " pdb=" N ILE A 27 " pdb=" C ILE A 27 " pdb=" CB ILE A 27 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 271 not shown) Planarity restraints: 312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 180 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.26e+00 pdb=" N PRO A 181 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 28 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 29 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 187 " -0.004 2.00e-02 2.50e+03 7.79e-03 6.07e-01 pdb=" C VAL A 187 " 0.013 2.00e-02 2.50e+03 pdb=" O VAL A 187 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY A 188 " -0.005 2.00e-02 2.50e+03 ... (remaining 309 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 140 2.74 - 3.28: 1782 3.28 - 3.82: 2699 3.82 - 4.36: 3065 4.36 - 4.90: 5315 Nonbonded interactions: 13001 Sorted by model distance: nonbonded pdb=" O CYS A 217 " pdb=" OG SER A 232 " model vdw 2.201 3.040 nonbonded pdb=" NH2 ARG A 151 " pdb=" OE1 GLU A 219 " model vdw 2.344 3.120 nonbonded pdb=" ND1 HIS A 31 " pdb=" OH TYR A 42 " model vdw 2.391 3.120 nonbonded pdb=" OH TYR A 103 " pdb=" OE1 GLN A 105 " model vdw 2.418 3.040 nonbonded pdb=" O SER A 201 " pdb=" OG SER A 201 " model vdw 2.477 3.040 ... (remaining 12996 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 12.490 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 14.730 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 0.025 1764 Z= 0.152 Angle : 0.622 9.015 2384 Z= 0.316 Chirality : 0.046 0.139 274 Planarity : 0.004 0.038 312 Dihedral : 15.999 87.997 660 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.41 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 29.95 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.56), residues: 226 helix: -0.33 (1.25), residues: 22 sheet: -0.31 (0.52), residues: 110 loop : -2.27 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 31 PHE 0.003 0.001 PHE A 164 TYR 0.007 0.001 TYR A 42 ARG 0.001 0.000 ARG A 110 Details of bonding type rmsd hydrogen bonds : bond 0.17267 ( 35) hydrogen bonds : angle 5.21109 ( 96) covalent geometry : bond 0.00312 ( 1764) covalent geometry : angle 0.62249 ( 2384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.3967 time to fit residues: 3.2156 Evaluate side-chains 5 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.055255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.046468 restraints weight = 8461.647| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.95 r_work: 0.3071 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1764 Z= 0.175 Angle : 0.603 8.055 2384 Z= 0.295 Chirality : 0.047 0.140 274 Planarity : 0.004 0.037 312 Dihedral : 4.257 16.199 242 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % Rotamer: Outliers : 4.28 % Allowed : 27.81 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.56), residues: 226 helix: -0.73 (1.03), residues: 26 sheet: -0.40 (0.51), residues: 110 loop : -2.40 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 31 PHE 0.003 0.001 PHE A 129 TYR 0.008 0.001 TYR A 11 ARG 0.008 0.001 ARG A 110 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 35) hydrogen bonds : angle 4.96324 ( 96) covalent geometry : bond 0.00387 ( 1764) covalent geometry : angle 0.60336 ( 2384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 5 time to evaluate : 0.210 Fit side-chains REVERT: A 76 ASN cc_start: 0.9283 (OUTLIER) cc_final: 0.8794 (p0) outliers start: 8 outliers final: 7 residues processed: 12 average time/residue: 0.2396 time to fit residues: 3.3807 Evaluate side-chains 13 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 5 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 162 ASN A 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.055198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.046583 restraints weight = 8394.378| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.90 r_work: 0.3073 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1764 Z= 0.185 Angle : 0.607 7.671 2384 Z= 0.298 Chirality : 0.047 0.139 274 Planarity : 0.004 0.034 312 Dihedral : 4.305 17.684 242 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 8.56 % Allowed : 25.13 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.56), residues: 226 helix: -0.71 (1.02), residues: 26 sheet: -0.34 (0.51), residues: 110 loop : -2.42 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 31 PHE 0.005 0.001 PHE A 129 TYR 0.008 0.001 TYR A 11 ARG 0.002 0.000 ARG A 110 Details of bonding type rmsd hydrogen bonds : bond 0.02919 ( 35) hydrogen bonds : angle 4.84647 ( 96) covalent geometry : bond 0.00408 ( 1764) covalent geometry : angle 0.60693 ( 2384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 5 time to evaluate : 0.214 Fit side-chains REVERT: A 162 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8828 (p0) outliers start: 16 outliers final: 11 residues processed: 20 average time/residue: 0.1706 time to fit residues: 4.0526 Evaluate side-chains 17 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 5 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 9 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.0370 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.056229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.047528 restraints weight = 8323.009| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.94 r_work: 0.3095 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1764 Z= 0.114 Angle : 0.621 12.594 2384 Z= 0.286 Chirality : 0.046 0.140 274 Planarity : 0.004 0.037 312 Dihedral : 4.108 16.968 242 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 4.28 % Allowed : 28.88 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.56), residues: 226 helix: -0.45 (1.03), residues: 26 sheet: -0.17 (0.51), residues: 110 loop : -2.39 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 31 PHE 0.005 0.001 PHE A 129 TYR 0.009 0.001 TYR A 11 ARG 0.001 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.02379 ( 35) hydrogen bonds : angle 4.73088 ( 96) covalent geometry : bond 0.00248 ( 1764) covalent geometry : angle 0.62114 ( 2384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 7 time to evaluate : 0.212 Fit side-chains REVERT: A 145 TYR cc_start: 0.9248 (m-80) cc_final: 0.8963 (m-80) outliers start: 8 outliers final: 7 residues processed: 14 average time/residue: 0.2108 time to fit residues: 3.4541 Evaluate side-chains 13 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 6 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.0050 chunk 4 optimal weight: 0.0050 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.056546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.047942 restraints weight = 8304.272| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.90 r_work: 0.3106 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1764 Z= 0.114 Angle : 0.612 10.660 2384 Z= 0.284 Chirality : 0.046 0.134 274 Planarity : 0.004 0.037 312 Dihedral : 3.965 16.271 242 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.18 % Favored : 89.38 % Rotamer: Outliers : 6.95 % Allowed : 26.20 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.56), residues: 226 helix: -0.28 (1.04), residues: 26 sheet: -0.14 (0.51), residues: 110 loop : -2.35 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 31 PHE 0.005 0.001 PHE A 129 TYR 0.008 0.001 TYR A 11 ARG 0.001 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.02317 ( 35) hydrogen bonds : angle 4.62569 ( 96) covalent geometry : bond 0.00248 ( 1764) covalent geometry : angle 0.61240 ( 2384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 6 time to evaluate : 0.214 Fit side-chains REVERT: A 145 TYR cc_start: 0.9275 (m-80) cc_final: 0.9075 (m-80) outliers start: 13 outliers final: 12 residues processed: 18 average time/residue: 0.2183 time to fit residues: 4.5259 Evaluate side-chains 18 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 6 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.0030 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.055413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.046836 restraints weight = 8458.751| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.92 r_work: 0.3073 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1764 Z= 0.145 Angle : 0.602 10.399 2384 Z= 0.286 Chirality : 0.046 0.138 274 Planarity : 0.004 0.036 312 Dihedral : 4.015 16.208 242 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.18 % Favored : 89.38 % Rotamer: Outliers : 6.95 % Allowed : 25.13 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.56), residues: 226 helix: -0.15 (1.04), residues: 26 sheet: -0.18 (0.52), residues: 110 loop : -2.33 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 31 PHE 0.005 0.001 PHE A 129 TYR 0.008 0.001 TYR A 11 ARG 0.001 0.000 ARG A 14 Details of bonding type rmsd hydrogen bonds : bond 0.02494 ( 35) hydrogen bonds : angle 4.63448 ( 96) covalent geometry : bond 0.00319 ( 1764) covalent geometry : angle 0.60242 ( 2384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 6 time to evaluate : 0.200 Fit side-chains REVERT: A 104 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8046 (p0) REVERT: A 145 TYR cc_start: 0.9297 (m-80) cc_final: 0.9062 (m-80) outliers start: 13 outliers final: 12 residues processed: 18 average time/residue: 0.1777 time to fit residues: 3.7728 Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 6 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.0170 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.056350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.047805 restraints weight = 8309.273| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.92 r_work: 0.3103 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1764 Z= 0.108 Angle : 0.608 10.126 2384 Z= 0.282 Chirality : 0.046 0.139 274 Planarity : 0.004 0.037 312 Dihedral : 3.871 15.723 242 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.18 % Favored : 89.38 % Rotamer: Outliers : 6.42 % Allowed : 26.74 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.57), residues: 226 helix: -0.04 (1.07), residues: 26 sheet: -0.08 (0.52), residues: 110 loop : -2.18 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 31 PHE 0.006 0.001 PHE A 129 TYR 0.008 0.001 TYR A 11 ARG 0.001 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.02183 ( 35) hydrogen bonds : angle 4.56517 ( 96) covalent geometry : bond 0.00237 ( 1764) covalent geometry : angle 0.60833 ( 2384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 6 time to evaluate : 0.217 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 17 average time/residue: 0.1893 time to fit residues: 3.8086 Evaluate side-chains 18 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 6 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.0020 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.055653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.047120 restraints weight = 8472.514| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.92 r_work: 0.3084 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1764 Z= 0.136 Angle : 0.584 9.983 2384 Z= 0.279 Chirality : 0.046 0.141 274 Planarity : 0.004 0.036 312 Dihedral : 3.902 15.590 242 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.06 % Favored : 88.50 % Rotamer: Outliers : 6.42 % Allowed : 26.74 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.57), residues: 226 helix: -0.07 (1.05), residues: 26 sheet: -0.09 (0.52), residues: 110 loop : -2.09 (0.62), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 31 PHE 0.004 0.001 PHE A 129 TYR 0.008 0.001 TYR A 11 ARG 0.001 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.02451 ( 35) hydrogen bonds : angle 4.55361 ( 96) covalent geometry : bond 0.00297 ( 1764) covalent geometry : angle 0.58401 ( 2384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 6 time to evaluate : 0.217 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 17 average time/residue: 0.1899 time to fit residues: 3.8201 Evaluate side-chains 18 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 6 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.055913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.047355 restraints weight = 8579.050| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.94 r_work: 0.3090 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1764 Z= 0.116 Angle : 0.577 9.848 2384 Z= 0.274 Chirality : 0.046 0.141 274 Planarity : 0.004 0.037 312 Dihedral : 3.841 15.465 242 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.62 % Favored : 88.94 % Rotamer: Outliers : 6.95 % Allowed : 26.20 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.58), residues: 226 helix: 0.02 (1.06), residues: 26 sheet: -0.04 (0.53), residues: 110 loop : -1.99 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 31 PHE 0.005 0.001 PHE A 129 TYR 0.011 0.001 TYR A 145 ARG 0.001 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.02240 ( 35) hydrogen bonds : angle 4.54411 ( 96) covalent geometry : bond 0.00252 ( 1764) covalent geometry : angle 0.57748 ( 2384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 6 time to evaluate : 0.225 Fit side-chains REVERT: A 104 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8003 (p0) REVERT: A 145 TYR cc_start: 0.9011 (m-80) cc_final: 0.8611 (m-80) outliers start: 13 outliers final: 12 residues processed: 18 average time/residue: 0.1831 time to fit residues: 3.8793 Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 6 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 5 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.056036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.047494 restraints weight = 8642.032| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.96 r_work: 0.3095 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1764 Z= 0.120 Angle : 0.575 9.788 2384 Z= 0.273 Chirality : 0.046 0.143 274 Planarity : 0.004 0.037 312 Dihedral : 3.819 15.467 242 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.06 % Favored : 88.50 % Rotamer: Outliers : 6.95 % Allowed : 26.20 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.58), residues: 226 helix: 0.07 (1.07), residues: 26 sheet: -0.03 (0.53), residues: 110 loop : -1.95 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 31 PHE 0.005 0.001 PHE A 129 TYR 0.008 0.001 TYR A 11 ARG 0.000 0.000 ARG A 14 Details of bonding type rmsd hydrogen bonds : bond 0.02312 ( 35) hydrogen bonds : angle 4.54263 ( 96) covalent geometry : bond 0.00261 ( 1764) covalent geometry : angle 0.57457 ( 2384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 6 time to evaluate : 0.218 Fit side-chains REVERT: A 104 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8000 (p0) REVERT: A 145 TYR cc_start: 0.9048 (m-80) cc_final: 0.8646 (m-80) outliers start: 13 outliers final: 12 residues processed: 18 average time/residue: 0.1814 time to fit residues: 3.8643 Evaluate side-chains 19 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 6 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.055106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.046560 restraints weight = 8619.284| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.93 r_work: 0.3067 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1764 Z= 0.164 Angle : 0.589 9.759 2384 Z= 0.285 Chirality : 0.046 0.144 274 Planarity : 0.004 0.035 312 Dihedral : 3.993 15.562 242 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.06 % Favored : 88.50 % Rotamer: Outliers : 7.49 % Allowed : 25.67 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.58), residues: 226 helix: 0.02 (1.06), residues: 26 sheet: -0.07 (0.53), residues: 110 loop : -1.96 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 31 PHE 0.005 0.001 PHE A 129 TYR 0.009 0.001 TYR A 145 ARG 0.001 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.02537 ( 35) hydrogen bonds : angle 4.64199 ( 96) covalent geometry : bond 0.00359 ( 1764) covalent geometry : angle 0.58941 ( 2384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1965.06 seconds wall clock time: 35 minutes 0.71 seconds (2100.71 seconds total)