Starting phenix.real_space_refine on Wed Mar 5 14:40:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sl0_40570/03_2025/8sl0_40570.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sl0_40570/03_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_40570/03_2025/8sl0_40570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sl0_40570/03_2025/8sl0_40570.map" model { file = "/net/cci-nas-00/data/ceres_data/8sl0_40570/03_2025/8sl0_40570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sl0_40570/03_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-5624/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: 8.13, per 1000 atoms: 4.68 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: 0.47 Conformation dependent library (CDL) restraints added in 224.2 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: 0.16 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: 0.34 Time building geometry restraints manager: 0.55 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: 12.510 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.970 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- 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= 0.209 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 *********************** 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 : 0.305 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.3851 time to fit residues: 3.2173 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 : 0.213 ------------------------------------------------------------------------------- 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: 4.42 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= 0.264 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 *********************** 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 : 0.217 Fit side-chains REVERT: A 76 ASN cc_start: 0.9283 (OUTLIER) cc_final: 0.8795 (p0) outliers start: 8 outliers final: 7 residues processed: 12 average time/residue: 0.2399 time to fit residues: 3.3867 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 = 0.046582 restraints weight = 8394.378| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.90 r_work: 0.3069 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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= 0.279 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 *********************** 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 : 0.218 Fit side-chains REVERT: A 162 ASN cc_start: 0.9096 (OUTLIER) cc_final: 0.8835 (p0) outliers start: 16 outliers final: 11 residues processed: 20 average time/residue: 0.1742 time to fit residues: 4.1232 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 : 0.222 ------------------------------------------------------------------------------- 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: 0.0170 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4018 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.056310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.047576 restraints weight = 8313.105| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.97 r_work: 0.3092 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1764 Z= 0.156 Angle : 0.622 12.638 2384 Z= 0.286 Chirality : 0.046 0.136 274 Planarity : 0.004 0.037 312 Dihedral : 4.084 16.893 242 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.82 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: -1.58 (0.56), residues: 226 helix: -0.44 (1.04), residues: 26 sheet: -0.15 (0.51), residues: 110 loop : -2.37 (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 *********************** 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 : 0.227 Fit side-chains REVERT: A 145 TYR cc_start: 0.9238 (m-80) cc_final: 0.9012 (m-80) outliers start: 8 outliers final: 7 residues processed: 14 average time/residue: 0.2203 time to fit residues: 3.6167 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 : 0.196 ------------------------------------------------------------------------------- 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: 0.8980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.055858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.047249 restraints weight = 8348.875| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.89 r_work: 0.3086 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1730 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= 0.213 Angle : 0.617 10.651 2384 Z= 0.289 Chirality : 0.046 0.137 274 Planarity : 0.004 0.036 312 Dihedral : 4.060 16.591 242 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.69 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: -1.58 (0.56), residues: 226 helix: -0.33 (1.03), residues: 26 sheet: -0.17 (0.51), residues: 110 loop : -2.38 (0.59), 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 *********************** 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 18 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 5 time to evaluate : 0.249 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 17 average time/residue: 0.2297 time to fit residues: 4.5080 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 : 0.221 ------------------------------------------------------------------------------- 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: 0.5980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.055232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.046719 restraints weight = 8494.635| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.89 r_work: 0.3071 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1764 Z= 0.236 Angle : 0.609 10.383 2384 Z= 0.291 Chirality : 0.046 0.140 274 Planarity : 0.004 0.035 312 Dihedral : 4.099 16.728 242 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.62 % Favored : 88.94 % Rotamer: Outliers : 6.95 % Allowed : 25.67 % Favored : 67.38 % 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: -1.56 (0.56), residues: 226 helix: -0.22 (1.04), residues: 26 sheet: -0.19 (0.51), residues: 110 loop : -2.36 (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 *********************** 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 : 0.197 Fit side-chains REVERT: A 104 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8051 (p0) REVERT: A 145 TYR cc_start: 0.9310 (m-80) cc_final: 0.9051 (m-80) outliers start: 13 outliers final: 12 residues processed: 18 average time/residue: 0.1754 time to fit residues: 3.7214 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 : 0.198 ------------------------------------------------------------------------------- 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: 0.7980 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.054706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.046171 restraints weight = 8492.954| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.90 r_work: 0.3065 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2074 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= 0.299 Angle : 0.642 10.071 2384 Z= 0.306 Chirality : 0.046 0.141 274 Planarity : 0.004 0.034 312 Dihedral : 4.210 16.904 242 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.62 % Favored : 88.94 % Rotamer: Outliers : 8.02 % Allowed : 25.67 % 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: -1.59 (0.56), residues: 226 helix: -0.23 (1.03), residues: 26 sheet: -0.25 (0.52), residues: 110 loop : -2.32 (0.59), 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 110 *********************** 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 20 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 5 time to evaluate : 0.217 Fit side-chains REVERT: A 104 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8095 (p0) outliers start: 15 outliers final: 12 residues processed: 19 average time/residue: 0.1982 time to fit residues: 4.3732 Evaluate side-chains 18 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 5 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 104 ASN 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 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: 0.9980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.055900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.047394 restraints weight = 8473.703| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.93 r_work: 0.3087 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1764 Z= 0.164 Angle : 0.590 9.918 2384 Z= 0.278 Chirality : 0.046 0.142 274 Planarity : 0.004 0.036 312 Dihedral : 3.970 16.148 242 Min Nonbonded Distance : 2.607 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: 0.03 (1.07), residues: 26 sheet: -0.13 (0.52), residues: 110 loop : -2.13 (0.62), 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 *********************** 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 : 0.226 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 17 average time/residue: 0.2014 time to fit residues: 4.0040 Evaluate side-chains 17 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 6 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 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: 0.0980 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.055515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.046939 restraints weight = 8677.137| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 4.00 r_work: 0.3079 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2251 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= 0.200 Angle : 0.589 9.807 2384 Z= 0.281 Chirality : 0.046 0.142 274 Planarity : 0.004 0.035 312 Dihedral : 3.961 15.818 242 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.06 % Favored : 88.50 % Rotamer: Outliers : 7.49 % Allowed : 25.13 % Favored : 67.38 % 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: -0.14 (1.03), residues: 26 sheet: -0.08 (0.53), residues: 110 loop : -2.08 (0.63), 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 42 ARG 0.003 0.000 ARG A 110 *********************** 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 20 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 6 time to evaluate : 0.237 Fit side-chains REVERT: A 104 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8045 (p0) outliers start: 14 outliers final: 13 residues processed: 19 average time/residue: 0.2050 time to fit residues: 4.5340 Evaluate side-chains 20 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 6 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 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 192 LYS 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 Chi-restraints excluded: chain A residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.054321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.045793 restraints weight = 8792.033| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.96 r_work: 0.3056 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1764 Z= 0.291 Angle : 0.612 9.746 2384 Z= 0.297 Chirality : 0.047 0.145 274 Planarity : 0.004 0.034 312 Dihedral : 4.176 16.427 242 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.50 % Favored : 88.05 % Rotamer: Outliers : 8.02 % Allowed : 24.60 % Favored : 67.38 % 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: -1.40 (0.57), residues: 226 helix: -0.04 (1.03), residues: 26 sheet: -0.20 (0.53), residues: 110 loop : -2.09 (0.63), 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 0.012 0.002 TYR A 145 ARG 0.003 0.000 ARG A 110 ********************** 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 21 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 6 time to evaluate : 0.229 Fit side-chains REVERT: A 104 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8084 (p0) REVERT: A 145 TYR cc_start: 0.9056 (m-80) cc_final: 0.8645 (m-80) outliers start: 15 outliers final: 14 residues processed: 20 average time/residue: 0.1889 time to fit residues: 4.3981 Evaluate side-chains 21 residues out of total 187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 6 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 104 ASN 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 166 VAL Chi-restraints excluded: chain A residue 192 LYS 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 Chi-restraints excluded: chain A residue 222 VAL 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: 3.9990 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.054681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.046320 restraints weight = 8641.666| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.93 r_work: 0.3069 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2434 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= 0.224 Angle : 0.594 9.726 2384 Z= 0.284 Chirality : 0.046 0.144 274 Planarity : 0.004 0.035 312 Dihedral : 4.059 16.445 242 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.06 % Favored : 88.50 % Rotamer: Outliers : 7.49 % Allowed : 25.13 % Favored : 67.38 % 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: -1.33 (0.58), residues: 226 helix: -0.00 (1.04), residues: 26 sheet: -0.19 (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 0.009 0.001 TYR A 145 ARG 0.002 0.000 ARG A 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2033.29 seconds wall clock time: 35 minutes 47.20 seconds (2147.20 seconds total)