Starting phenix.real_space_refine on Mon Feb 10 21:01:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tik_25912/02_2025/7tik_25912.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tik_25912/02_2025/7tik_25912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tik_25912/02_2025/7tik_25912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tik_25912/02_2025/7tik_25912.map" model { file = "/net/cci-nas-00/data/ceres_data/7tik_25912/02_2025/7tik_25912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tik_25912/02_2025/7tik_25912.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 3 Type Number sf(0) Gaussians C 1584 2.51 5 N 450 2.21 5 O 531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2565 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "E" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Restraints were copied for chains: C, B, D, F Time building chain proxies: 1.80, per 1000 atoms: 0.70 Number of scatterers: 2565 At special positions: 0 Unit cell: (52, 42.25, 118.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 531 8.00 N 450 7.00 C 1584 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: 0.69 Conformation dependent library (CDL) restraints added in 318.5 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 removed outlier: 3.618A pdb=" N LEU D1197 " --> pdb=" O ASN D1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1194 through 1197' Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 removed outlier: 3.618A pdb=" N LEU E1197 " --> pdb=" O ASN E1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1194 through 1197' Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 removed outlier: 3.618A pdb=" N LEU F1197 " --> pdb=" O ASN F1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1194 through 1197' 232 hydrogen bonds defined for protein. 696 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: 0.73 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 480 1.29 - 1.35: 420 1.35 - 1.41: 89 1.41 - 1.48: 382 1.48 - 1.54: 1206 Bond restraints: 2577 Sorted by residual: bond pdb=" CA LEU C 966 " pdb=" C LEU C 966 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.29e-02 6.01e+03 8.44e-01 bond pdb=" CA LEU B 966 " pdb=" C LEU B 966 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.29e-02 6.01e+03 8.25e-01 bond pdb=" CB ASN C 955 " pdb=" CG ASN C 955 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 8.08e-01 bond pdb=" CA LEU A 966 " pdb=" C LEU A 966 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.29e-02 6.01e+03 8.00e-01 bond pdb=" CA LEU B 962 " pdb=" C LEU B 962 " ideal model delta sigma weight residual 1.524 1.512 0.011 1.29e-02 6.01e+03 7.82e-01 ... (remaining 2572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 3371 1.05 - 2.11: 81 2.11 - 3.16: 13 3.16 - 4.21: 6 4.21 - 5.26: 6 Bond angle restraints: 3477 Sorted by residual: angle pdb=" CA ILE B 980 " pdb=" CB ILE B 980 " pdb=" CG1 ILE B 980 " ideal model delta sigma weight residual 110.40 115.66 -5.26 1.70e+00 3.46e-01 9.59e+00 angle pdb=" CA ILE A 980 " pdb=" CB ILE A 980 " pdb=" CG1 ILE A 980 " ideal model delta sigma weight residual 110.40 115.66 -5.26 1.70e+00 3.46e-01 9.56e+00 angle pdb=" CA ILE C 980 " pdb=" CB ILE C 980 " pdb=" CG1 ILE C 980 " ideal model delta sigma weight residual 110.40 115.66 -5.26 1.70e+00 3.46e-01 9.56e+00 angle pdb=" C ASP C 979 " pdb=" N ILE C 980 " pdb=" CA ILE C 980 " ideal model delta sigma weight residual 120.64 115.62 5.02 1.64e+00 3.72e-01 9.39e+00 angle pdb=" C ASP B 979 " pdb=" N ILE B 980 " pdb=" CA ILE B 980 " ideal model delta sigma weight residual 120.64 115.64 5.00 1.64e+00 3.72e-01 9.29e+00 ... (remaining 3472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 1404 17.40 - 34.81: 159 34.81 - 52.21: 21 52.21 - 69.61: 12 69.61 - 87.02: 6 Dihedral angle restraints: 1602 sinusoidal: 621 harmonic: 981 Sorted by residual: dihedral pdb=" CA ASN F1192 " pdb=" CB ASN F1192 " pdb=" CG ASN F1192 " pdb=" OD1 ASN F1192 " ideal model delta sinusoidal sigma weight residual 120.00 -168.29 -71.71 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN D1192 " pdb=" CB ASN D1192 " pdb=" CG ASN D1192 " pdb=" OD1 ASN D1192 " ideal model delta sinusoidal sigma weight residual 120.00 -168.31 -71.69 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN E1192 " pdb=" CB ASN E1192 " pdb=" CG ASN E1192 " pdb=" OD1 ASN E1192 " ideal model delta sinusoidal sigma weight residual 120.00 -168.33 -71.67 2 2.00e+01 2.50e-03 1.08e+01 ... (remaining 1599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 210 0.028 - 0.056: 165 0.056 - 0.084: 33 0.084 - 0.112: 7 0.112 - 0.140: 17 Chirality restraints: 432 Sorted by residual: chirality pdb=" CB ILE B 980 " pdb=" CA ILE B 980 " pdb=" CG1 ILE B 980 " pdb=" CG2 ILE B 980 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CB ILE A 980 " pdb=" CA ILE A 980 " pdb=" CG1 ILE A 980 " pdb=" CG2 ILE A 980 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA VAL E1176 " pdb=" N VAL E1176 " pdb=" C VAL E1176 " pdb=" CB VAL E1176 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 429 not shown) Planarity restraints: 456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 981 " 0.007 2.00e-02 2.50e+03 9.97e-03 1.74e+00 pdb=" CG PHE A 981 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 981 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 981 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 981 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 981 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 981 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 981 " -0.007 2.00e-02 2.50e+03 9.81e-03 1.68e+00 pdb=" CG PHE B 981 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 981 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 981 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 981 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 981 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 981 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 981 " -0.007 2.00e-02 2.50e+03 9.74e-03 1.66e+00 pdb=" CG PHE C 981 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE C 981 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 981 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 981 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 981 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 981 " -0.000 2.00e-02 2.50e+03 ... (remaining 453 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 463 2.75 - 3.29: 2698 3.29 - 3.83: 4418 3.83 - 4.36: 4841 4.36 - 4.90: 8357 Nonbonded interactions: 20777 Sorted by model distance: nonbonded pdb=" OG SER A 943 " pdb=" OE2 GLU F1182 " model vdw 2.218 3.040 nonbonded pdb=" OD2 ASP A 936 " pdb=" NH2 ARG F1185 " model vdw 2.259 3.120 nonbonded pdb=" O LYS B 964 " pdb=" OG SER B 967 " model vdw 2.283 3.040 nonbonded pdb=" O LYS A 964 " pdb=" OG SER A 967 " model vdw 2.283 3.040 nonbonded pdb=" O LYS C 964 " pdb=" OG SER C 967 " model vdw 2.283 3.040 ... (remaining 20772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 0.850 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.680 Find NCS groups from input model: 0.040 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.007 0.027 2577 Z= 0.418 Angle : 0.491 5.265 3477 Z= 0.283 Chirality : 0.042 0.140 432 Planarity : 0.003 0.016 456 Dihedral : 16.305 87.018 954 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % 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 (0.41), residues: 327 helix: 1.84 (0.28), residues: 252 sheet: None (None), residues: 0 loop : -2.67 (0.54), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 954 PHE 0.023 0.003 PHE A 981 ARG 0.006 0.002 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.273 Fit side-chains REVERT: C 969 LYS cc_start: 0.8670 (mmtp) cc_final: 0.8456 (mmtp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.5931 time to fit residues: 33.6056 Evaluate side-chains 53 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 ASN B 960 ASN C 960 ASN D1192 ASN E1192 ASN F1192 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.143226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.121653 restraints weight = 3559.550| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.09 r_work: 0.3946 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2577 Z= 0.211 Angle : 0.412 5.990 3477 Z= 0.223 Chirality : 0.039 0.136 432 Planarity : 0.002 0.009 456 Dihedral : 3.322 13.036 339 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.02 % Allowed : 14.81 % Favored : 83.16 % 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: 4.32 (0.43), residues: 327 helix: 3.83 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.90 (0.70), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 954 PHE 0.015 0.002 PHE A 981 ARG 0.003 0.001 ARG F1185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.310 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.5906 time to fit residues: 34.1296 Evaluate side-chains 56 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain E residue 1176 VAL Chi-restraints excluded: chain F residue 1176 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 21 optimal weight: 0.0670 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 28 optimal weight: 0.0070 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.149080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.128506 restraints weight = 3473.155| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.96 r_work: 0.3984 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2577 Z= 0.168 Angle : 0.362 3.941 3477 Z= 0.201 Chirality : 0.037 0.131 432 Planarity : 0.002 0.012 456 Dihedral : 3.099 12.287 339 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 15.49 % Favored : 83.16 % 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: 5.13 (0.44), residues: 327 helix: 4.38 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.52 (0.75), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 954 PHE 0.010 0.001 PHE B 981 ARG 0.002 0.001 ARG F1185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.271 Fit side-chains REVERT: B 981 PHE cc_start: 0.7611 (m-10) cc_final: 0.7395 (m-80) outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.6506 time to fit residues: 32.7336 Evaluate side-chains 48 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 29 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.0670 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.144169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.122538 restraints weight = 3499.627| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 2.07 r_work: 0.3957 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2577 Z= 0.183 Angle : 0.383 5.208 3477 Z= 0.207 Chirality : 0.037 0.135 432 Planarity : 0.001 0.008 456 Dihedral : 3.049 12.310 339 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 14.81 % Favored : 84.18 % 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: 5.40 (0.45), residues: 327 helix: 4.55 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.34 (0.77), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 954 PHE 0.008 0.001 PHE A 981 ARG 0.002 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.268 Fit side-chains REVERT: B 977 LEU cc_start: 0.8109 (mt) cc_final: 0.7541 (mt) REVERT: B 981 PHE cc_start: 0.7781 (m-10) cc_final: 0.7581 (m-80) REVERT: C 983 ARG cc_start: 0.7794 (mtp180) cc_final: 0.7500 (ttp-170) outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 0.6471 time to fit residues: 33.8879 Evaluate side-chains 52 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.142480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.120930 restraints weight = 3560.859| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.09 r_work: 0.3937 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2577 Z= 0.258 Angle : 0.398 4.611 3477 Z= 0.223 Chirality : 0.038 0.132 432 Planarity : 0.002 0.009 456 Dihedral : 3.188 12.673 339 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.02 % Allowed : 13.47 % Favored : 84.51 % 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: 5.24 (0.45), residues: 327 helix: 4.40 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.24 (0.79), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 954 PHE 0.008 0.001 PHE B 981 ARG 0.002 0.001 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.276 Fit side-chains REVERT: A 981 PHE cc_start: 0.7857 (m-10) cc_final: 0.7652 (m-10) REVERT: B 977 LEU cc_start: 0.8148 (mt) cc_final: 0.7613 (mt) REVERT: C 983 ARG cc_start: 0.7740 (mtp180) cc_final: 0.7479 (ttp-170) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.6304 time to fit residues: 35.7814 Evaluate side-chains 54 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 963 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 28 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.144293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.122120 restraints weight = 3552.985| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.13 r_work: 0.3942 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2577 Z= 0.170 Angle : 0.392 6.299 3477 Z= 0.213 Chirality : 0.037 0.134 432 Planarity : 0.002 0.016 456 Dihedral : 3.031 12.387 339 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 14.81 % Favored : 83.84 % 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: 5.58 (0.45), residues: 327 helix: 4.65 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.10 (0.80), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.037 0.002 PHE B 981 ARG 0.001 0.000 ARG F1185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.274 Fit side-chains REVERT: A 981 PHE cc_start: 0.7714 (m-10) cc_final: 0.7493 (m-10) REVERT: B 977 LEU cc_start: 0.8076 (mt) cc_final: 0.7491 (mt) REVERT: C 983 ARG cc_start: 0.7652 (mtp180) cc_final: 0.7388 (ttp-170) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.6444 time to fit residues: 33.1454 Evaluate side-chains 51 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 963 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.0010 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN B 978 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.142933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.120971 restraints weight = 3596.593| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.12 r_work: 0.3939 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2577 Z= 0.216 Angle : 0.400 5.619 3477 Z= 0.228 Chirality : 0.038 0.134 432 Planarity : 0.002 0.026 456 Dihedral : 3.112 13.929 339 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.68 % Allowed : 14.48 % Favored : 83.84 % 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: 5.44 (0.44), residues: 327 helix: 4.50 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.00 (0.80), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.060 0.003 PHE B 981 ARG 0.002 0.000 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.287 Fit side-chains REVERT: A 981 PHE cc_start: 0.7710 (m-10) cc_final: 0.7498 (m-10) REVERT: B 977 LEU cc_start: 0.8123 (mt) cc_final: 0.7788 (mt) REVERT: C 983 ARG cc_start: 0.7648 (mtp180) cc_final: 0.7403 (ttp-170) outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 0.6299 time to fit residues: 32.9998 Evaluate side-chains 50 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain B residue 963 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.143796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.121338 restraints weight = 3599.344| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.15 r_work: 0.3935 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2577 Z= 0.183 Angle : 0.414 6.810 3477 Z= 0.234 Chirality : 0.038 0.175 432 Planarity : 0.002 0.029 456 Dihedral : 3.020 13.002 339 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 16.50 % Favored : 82.49 % 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: 5.44 (0.45), residues: 327 helix: 4.48 (0.27), residues: 252 sheet: None (None), residues: 0 loop : 0.09 (0.81), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.067 0.003 PHE B 981 ARG 0.001 0.000 ARG F1185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.296 Fit side-chains REVERT: A 981 PHE cc_start: 0.7786 (m-10) cc_final: 0.7553 (m-10) REVERT: C 983 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7399 (ttp-170) outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.6448 time to fit residues: 31.7357 Evaluate side-chains 48 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain B residue 963 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN F1159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.143311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.121348 restraints weight = 3587.672| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.11 r_work: 0.3937 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2577 Z= 0.204 Angle : 0.411 5.336 3477 Z= 0.237 Chirality : 0.038 0.150 432 Planarity : 0.002 0.029 456 Dihedral : 3.093 14.057 339 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.01 % Allowed : 16.84 % Favored : 82.15 % 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: 5.31 (0.45), residues: 327 helix: 4.38 (0.27), residues: 252 sheet: None (None), residues: 0 loop : 0.10 (0.81), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.067 0.003 PHE B 981 ARG 0.001 0.000 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.293 Fit side-chains REVERT: A 981 PHE cc_start: 0.7960 (m-10) cc_final: 0.7716 (m-10) REVERT: C 983 ARG cc_start: 0.7783 (mtp180) cc_final: 0.7490 (ttp-170) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.6363 time to fit residues: 32.6825 Evaluate side-chains 50 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain B residue 963 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.0070 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.145119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.122921 restraints weight = 3562.653| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.15 r_work: 0.3956 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2577 Z= 0.135 Angle : 0.412 7.199 3477 Z= 0.231 Chirality : 0.037 0.164 432 Planarity : 0.002 0.030 456 Dihedral : 2.948 14.295 339 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 17.17 % Favored : 82.15 % 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: 5.57 (0.45), residues: 327 helix: 4.56 (0.27), residues: 252 sheet: None (None), residues: 0 loop : 0.24 (0.82), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.070 0.003 PHE B 981 ARG 0.001 0.000 ARG F1185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.301 Fit side-chains REVERT: A 981 PHE cc_start: 0.7786 (m-10) cc_final: 0.7550 (m-10) REVERT: C 983 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7390 (ttp-170) outliers start: 2 outliers final: 2 residues processed: 48 average time/residue: 0.6580 time to fit residues: 33.0784 Evaluate side-chains 49 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain B residue 963 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 0.0870 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 14 optimal weight: 0.0980 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 = 0.4421 r_free = 0.4421 target = 0.145048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.122864 restraints weight = 3553.800| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.11 r_work: 0.3954 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2577 Z= 0.152 Angle : 0.401 5.848 3477 Z= 0.232 Chirality : 0.037 0.162 432 Planarity : 0.002 0.030 456 Dihedral : 3.008 14.448 339 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.67 % Allowed : 17.17 % Favored : 82.15 % 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: 5.61 (0.45), residues: 327 helix: 4.58 (0.27), residues: 252 sheet: None (None), residues: 0 loop : 0.26 (0.83), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F1159 PHE 0.069 0.003 PHE B 981 ARG 0.001 0.000 ARG F1185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2140.31 seconds wall clock time: 38 minutes 31.06 seconds (2311.06 seconds total)