Starting phenix.real_space_refine on Wed Sep 17 03:10:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tik_25912/09_2025/7tik_25912.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tik_25912/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tik_25912/09_2025/7tik_25912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tik_25912/09_2025/7tik_25912.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tik_25912/09_2025/7tik_25912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tik_25912/09_2025/7tik_25912.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: "D" 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: B, C, E, F Time building chain proxies: 0.68, per 1000 atoms: 0.27 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: 0.23 Conformation dependent library (CDL) restraints added in 104.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.06 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: 0.36 Time building geometry restraints manager: 0.32 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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: 1.110 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.370 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.000 ------------------------------------------------------------------------------- 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= 0.315 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.006 0.002 ARG D1185 PHE 0.023 0.003 PHE A 981 HIS 0.001 0.000 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00653 ( 2577) covalent geometry : angle 0.49124 ( 3477) hydrogen bonds : bond 0.03888 ( 232) hydrogen bonds : angle 3.11130 ( 696) *********************** 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 : 0.099 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: 0.3091 time to fit residues: 17.4176 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 : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.4399 r_free = 0.4399 target = 0.142869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.121386 restraints weight = 3549.134| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.08 r_work: 0.3929 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2577 Z= 0.169 Angle : 0.414 5.570 3477 Z= 0.225 Chirality : 0.039 0.135 432 Planarity : 0.002 0.009 456 Dihedral : 3.340 13.168 339 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.04 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.28 (0.43), residues: 327 helix: 3.79 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.90 (0.70), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F1185 PHE 0.015 0.002 PHE A 981 HIS 0.001 0.000 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 2577) covalent geometry : angle 0.41370 ( 3477) hydrogen bonds : bond 0.03355 ( 232) hydrogen bonds : angle 2.60444 ( 696) *********************** 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 56 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.114 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.2765 time to fit residues: 15.6215 Evaluate side-chains 53 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.079 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4402 r_free = 0.4402 target = 0.143204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.121570 restraints weight = 3557.260| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.10 r_work: 0.3943 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2577 Z= 0.170 Angle : 0.385 3.964 3477 Z= 0.214 Chirality : 0.038 0.132 432 Planarity : 0.002 0.013 456 Dihedral : 3.212 12.283 339 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.02 % Allowed : 14.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.87 (0.44), residues: 327 helix: 4.19 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.60 (0.75), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D1185 PHE 0.010 0.001 PHE A 981 HIS 0.001 0.000 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 2577) covalent geometry : angle 0.38511 ( 3477) hydrogen bonds : bond 0.03447 ( 232) hydrogen bonds : angle 2.55429 ( 696) *********************** 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 54 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.067 Fit side-chains REVERT: B 981 PHE cc_start: 0.7528 (m-10) cc_final: 0.7306 (m-80) outliers start: 6 outliers final: 2 residues processed: 52 average time/residue: 0.2735 time to fit residues: 14.8187 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 : 0.077 ------------------------------------------------------------------------------- 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: 0.4980 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4402 r_free = 0.4402 target = 0.143301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.121556 restraints weight = 3557.660| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.10 r_work: 0.3944 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2005 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= 0.166 Angle : 0.402 6.140 3477 Z= 0.218 Chirality : 0.038 0.138 432 Planarity : 0.002 0.009 456 Dihedral : 3.173 12.272 339 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 2.02 % Allowed : 13.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.17 (0.44), residues: 327 helix: 4.39 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.43 (0.76), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 983 PHE 0.008 0.001 PHE A 981 HIS 0.001 0.000 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 2577) covalent geometry : angle 0.40244 ( 3477) hydrogen bonds : bond 0.03411 ( 232) hydrogen bonds : angle 2.56225 ( 696) *********************** 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 54 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.121 Fit side-chains REVERT: C 983 ARG cc_start: 0.7820 (mtp180) cc_final: 0.7524 (ttp-170) outliers start: 6 outliers final: 2 residues processed: 50 average time/residue: 0.3063 time to fit residues: 16.0051 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 : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain B residue 963 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.4402 r_free = 0.4402 target = 0.143415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.121643 restraints weight = 3541.958| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.10 r_work: 0.3945 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2135 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= 0.140 Angle : 0.390 6.041 3477 Z= 0.212 Chirality : 0.038 0.138 432 Planarity : 0.002 0.015 456 Dihedral : 3.048 11.450 339 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.35 % Allowed : 15.15 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.40 (0.45), residues: 327 helix: 4.52 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.19 (0.79), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 983 PHE 0.035 0.002 PHE B 981 HIS 0.000 0.000 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 2577) covalent geometry : angle 0.38999 ( 3477) hydrogen bonds : bond 0.03354 ( 232) hydrogen bonds : angle 2.55068 ( 696) *********************** 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 53 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.112 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.3242 time to fit residues: 16.9130 Evaluate side-chains 51 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU 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 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.4399 r_free = 0.4399 target = 0.143158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.121409 restraints weight = 3568.101| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.11 r_work: 0.3941 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2577 Z= 0.141 Angle : 0.396 5.420 3477 Z= 0.221 Chirality : 0.038 0.131 432 Planarity : 0.002 0.023 456 Dihedral : 3.045 12.095 339 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.01 % Allowed : 15.49 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.42 (0.44), residues: 327 helix: 4.49 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.02 (0.81), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1185 PHE 0.054 0.002 PHE B 981 HIS 0.000 0.000 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 2577) covalent geometry : angle 0.39565 ( 3477) hydrogen bonds : bond 0.03356 ( 232) hydrogen bonds : angle 2.57556 ( 696) *********************** 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: 3 poor density : 49 time to evaluate : 0.125 Fit side-chains REVERT: A 981 PHE cc_start: 0.7888 (m-10) cc_final: 0.7640 (m-80) REVERT: B 977 LEU cc_start: 0.8180 (mt) cc_final: 0.7808 (mt) REVERT: C 983 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7472 (ttp-170) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.3051 time to fit residues: 15.9220 Evaluate side-chains 51 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain B residue 963 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 30.0000 chunk 25 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.142385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.120315 restraints weight = 3612.897| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.14 r_work: 0.3923 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2577 Z= 0.182 Angle : 0.425 5.806 3477 Z= 0.241 Chirality : 0.039 0.154 432 Planarity : 0.002 0.028 456 Dihedral : 3.137 11.705 339 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.20 (0.45), residues: 327 helix: 4.32 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.04 (0.81), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1185 PHE 0.064 0.003 PHE B 981 HIS 0.001 0.000 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 2577) covalent geometry : angle 0.42486 ( 3477) hydrogen bonds : bond 0.03478 ( 232) hydrogen bonds : angle 2.67780 ( 696) *********************** 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 52 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.108 Fit side-chains REVERT: A 981 PHE cc_start: 0.7746 (m-10) cc_final: 0.7472 (m-80) REVERT: C 983 ARG cc_start: 0.7647 (mtp180) cc_final: 0.7398 (ttp-170) outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 0.2946 time to fit residues: 15.0639 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 : 0.099 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 962 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.143313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.121031 restraints weight = 3601.928| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.14 r_work: 0.3928 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2387 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= 0.144 Angle : 0.413 6.222 3477 Z= 0.232 Chirality : 0.038 0.158 432 Planarity : 0.002 0.026 456 Dihedral : 3.083 11.951 339 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.35 % Allowed : 15.82 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.38 (0.45), residues: 327 helix: 4.45 (0.27), residues: 252 sheet: None (None), residues: 0 loop : 0.04 (0.82), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F1185 PHE 0.060 0.003 PHE B 981 HIS 0.001 0.000 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2577) covalent geometry : angle 0.41324 ( 3477) hydrogen bonds : bond 0.03375 ( 232) hydrogen bonds : angle 2.61449 ( 696) *********************** 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 51 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.094 Fit side-chains REVERT: A 981 PHE cc_start: 0.7709 (m-10) cc_final: 0.7433 (m-80) REVERT: C 983 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7384 (ttp-170) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.3006 time to fit residues: 15.3557 Evaluate side-chains 50 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.059 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN E1159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.142959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.120792 restraints weight = 3598.014| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.14 r_work: 0.3926 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2577 Z= 0.156 Angle : 0.411 6.299 3477 Z= 0.235 Chirality : 0.039 0.155 432 Planarity : 0.002 0.025 456 Dihedral : 3.104 13.114 339 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.35 % Allowed : 16.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.38 (0.45), residues: 327 helix: 4.45 (0.27), residues: 252 sheet: None (None), residues: 0 loop : 0.05 (0.82), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1185 PHE 0.059 0.003 PHE B 981 HIS 0.001 0.000 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2577) covalent geometry : angle 0.41113 ( 3477) hydrogen bonds : bond 0.03393 ( 232) hydrogen bonds : angle 2.61653 ( 696) *********************** 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: 4 poor density : 47 time to evaluate : 0.097 Fit side-chains REVERT: A 981 PHE cc_start: 0.7704 (m-10) cc_final: 0.7423 (m-80) REVERT: C 983 ARG cc_start: 0.7655 (mtp180) cc_final: 0.7398 (ttp-170) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.3092 time to fit residues: 15.4779 Evaluate side-chains 51 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 964 LYS 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 11 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.142621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.120663 restraints weight = 3626.701| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.12 r_work: 0.3919 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2577 Z= 0.171 Angle : 0.447 6.786 3477 Z= 0.246 Chirality : 0.039 0.150 432 Planarity : 0.002 0.027 456 Dihedral : 3.153 14.738 339 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 : 1.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.33 (0.45), residues: 327 helix: 4.41 (0.27), residues: 252 sheet: None (None), residues: 0 loop : 0.04 (0.82), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1185 PHE 0.062 0.003 PHE B 981 HIS 0.001 0.000 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 2577) covalent geometry : angle 0.44699 ( 3477) hydrogen bonds : bond 0.03438 ( 232) hydrogen bonds : angle 2.64979 ( 696) ********************** 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 52 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.083 Fit side-chains REVERT: A 981 PHE cc_start: 0.7903 (m-10) cc_final: 0.7590 (m-80) REVERT: C 983 ARG cc_start: 0.7793 (mtp180) cc_final: 0.7513 (ttp-170) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.3073 time to fit residues: 15.6958 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 : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 964 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.143576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.121735 restraints weight = 3596.022| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.13 r_work: 0.3937 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2577 Z= 0.126 Angle : 0.406 5.885 3477 Z= 0.234 Chirality : 0.038 0.180 432 Planarity : 0.002 0.030 456 Dihedral : 3.062 14.751 339 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 16.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.51 (0.45), residues: 327 helix: 4.54 (0.27), residues: 252 sheet: None (None), residues: 0 loop : 0.09 (0.81), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F1185 PHE 0.069 0.003 PHE B 981 HIS 0.001 0.000 HIS F1159 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2577) covalent geometry : angle 0.40588 ( 3477) hydrogen bonds : bond 0.03332 ( 232) hydrogen bonds : angle 2.56471 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1125.25 seconds wall clock time: 20 minutes 0.88 seconds (1200.88 seconds total)