Starting phenix.real_space_refine on Wed Mar 5 14:17:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hxa_52458/03_2025/9hxa_52458.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hxa_52458/03_2025/9hxa_52458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hxa_52458/03_2025/9hxa_52458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hxa_52458/03_2025/9hxa_52458.map" model { file = "/net/cci-nas-00/data/ceres_data/9hxa_52458/03_2025/9hxa_52458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hxa_52458/03_2025/9hxa_52458.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 530 2.51 5 N 148 2.21 5 O 170 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-5624/modules/chem_data/mon_lib" Total number of atoms: 848 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 424 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Restraints were copied for chains: C Time building chain proxies: 0.98, per 1000 atoms: 1.16 Number of scatterers: 848 At special positions: 0 Unit cell: (98.44, 89.24, 20.24, 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 170 8.00 N 148 7.00 C 530 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: 0.22 Conformation dependent library (CDL) restraints added in 124.6 milliseconds 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 208 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 148 1.29 - 1.35: 136 1.35 - 1.42: 34 1.42 - 1.48: 130 1.48 - 1.54: 404 Bond restraints: 852 Sorted by residual: bond pdb=" N VAL A 82 " pdb=" CA VAL A 82 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.03e+01 bond pdb=" N VAL C 82 " pdb=" CA VAL C 82 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N VAL C 77 " pdb=" CA VAL C 77 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.28e-02 6.10e+03 7.35e+00 bond pdb=" N VAL A 77 " pdb=" CA VAL A 77 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.28e-02 6.10e+03 7.32e+00 bond pdb=" N GLN C 79 " pdb=" CA GLN C 79 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.26e-02 6.30e+03 6.61e+00 ... (remaining 847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 991 1.02 - 2.04: 125 2.04 - 3.06: 25 3.06 - 4.08: 9 4.08 - 5.10: 4 Bond angle restraints: 1154 Sorted by residual: angle pdb=" N GLU A 83 " pdb=" CA GLU A 83 " pdb=" C GLU A 83 " ideal model delta sigma weight residual 112.87 107.77 5.10 1.20e+00 6.94e-01 1.80e+01 angle pdb=" N GLU C 83 " pdb=" CA GLU C 83 " pdb=" C GLU C 83 " ideal model delta sigma weight residual 112.87 107.79 5.08 1.20e+00 6.94e-01 1.79e+01 angle pdb=" CA LYS C 80 " pdb=" C LYS C 80 " pdb=" O LYS C 80 " ideal model delta sigma weight residual 121.84 118.08 3.76 1.16e+00 7.43e-01 1.05e+01 angle pdb=" CA LYS A 80 " pdb=" C LYS A 80 " pdb=" O LYS A 80 " ideal model delta sigma weight residual 121.84 118.11 3.73 1.16e+00 7.43e-01 1.04e+01 angle pdb=" CA THR C 81 " pdb=" CB THR C 81 " pdb=" OG1 THR C 81 " ideal model delta sigma weight residual 109.60 105.10 4.50 1.50e+00 4.44e-01 8.99e+00 ... (remaining 1149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.90: 438 10.90 - 21.80: 38 21.80 - 32.70: 10 32.70 - 43.60: 4 43.60 - 54.50: 2 Dihedral angle restraints: 492 sinusoidal: 160 harmonic: 332 Sorted by residual: dihedral pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " pdb=" CD GLU C 83 " ideal model delta sinusoidal sigma weight residual -60.00 -99.40 39.40 3 1.50e+01 4.44e-03 6.98e+00 dihedral pdb=" CA GLU A 83 " pdb=" CB GLU A 83 " pdb=" CG GLU A 83 " pdb=" CD GLU A 83 " ideal model delta sinusoidal sigma weight residual -60.00 -99.39 39.39 3 1.50e+01 4.44e-03 6.98e+00 dihedral pdb=" CA GLU C 61 " pdb=" C GLU C 61 " pdb=" N GLN C 62 " pdb=" CA GLN C 62 " ideal model delta harmonic sigma weight residual -180.00 -170.29 -9.71 0 5.00e+00 4.00e-02 3.77e+00 ... (remaining 489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 87 0.038 - 0.075: 30 0.075 - 0.113: 29 0.113 - 0.150: 0 0.150 - 0.188: 6 Chirality restraints: 152 Sorted by residual: chirality pdb=" CB VAL A 82 " pdb=" CA VAL A 82 " pdb=" CG1 VAL A 82 " pdb=" CG2 VAL A 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CA VAL C 77 " pdb=" N VAL C 77 " pdb=" C VAL C 77 " pdb=" CB VAL C 77 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.67e-01 chirality pdb=" CB VAL C 82 " pdb=" CA VAL C 82 " pdb=" CG1 VAL C 82 " pdb=" CG2 VAL C 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.61e-01 ... (remaining 149 not shown) Planarity restraints: 144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 38 " -0.007 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C LEU A 38 " 0.022 2.00e-02 2.50e+03 pdb=" O LEU A 38 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR A 39 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 38 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C LEU C 38 " 0.022 2.00e-02 2.50e+03 pdb=" O LEU C 38 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR C 39 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 81 " 0.002 2.00e-02 2.50e+03 4.70e-03 2.21e-01 pdb=" C THR C 81 " -0.008 2.00e-02 2.50e+03 pdb=" O THR C 81 " 0.003 2.00e-02 2.50e+03 pdb=" N VAL C 82 " 0.003 2.00e-02 2.50e+03 ... (remaining 141 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 506 3.05 - 3.51: 692 3.51 - 3.98: 934 3.98 - 4.44: 738 4.44 - 4.90: 1420 Nonbonded interactions: 4290 Sorted by model distance: nonbonded pdb=" OG SER A 42 " pdb=" OG1 THR A 75 " model vdw 2.589 3.040 nonbonded pdb=" OG SER C 42 " pdb=" OG1 THR C 75 " model vdw 2.589 3.040 nonbonded pdb=" N GLU C 83 " pdb=" N GLY C 84 " model vdw 2.628 2.560 nonbonded pdb=" N GLU A 83 " pdb=" N GLY A 84 " model vdw 2.628 2.560 nonbonded pdb=" O SER C 42 " pdb=" OG SER C 42 " model vdw 2.655 3.040 ... (remaining 4285 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 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.570 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 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 : 0.006 0.040 852 Z= 0.420 Angle : 0.810 5.097 1154 Z= 0.533 Chirality : 0.062 0.188 152 Planarity : 0.002 0.013 144 Dihedral : 10.524 54.503 284 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 15.12 % Favored : 84.88 % 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: -2.61 (0.70), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.002 HIS C 50 PHE 0.005 0.002 PHE A 94 TYR 0.004 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.106 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1153 time to fit residues: 4.7897 Evaluate side-chains 28 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.240687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.228929 restraints weight = 1065.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.232128 restraints weight = 464.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.234141 restraints weight = 259.769| |-----------------------------------------------------------------------------| r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 852 Z= 0.143 Angle : 0.546 5.080 1154 Z= 0.296 Chirality : 0.050 0.142 152 Planarity : 0.002 0.011 144 Dihedral : 4.201 10.815 124 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 9.30 % Allowed : 25.58 % Favored : 65.12 % 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: -2.55 (0.71), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.004 0.001 PHE C 94 TYR 0.003 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.099 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 30 average time/residue: 0.1060 time to fit residues: 3.5293 Evaluate side-chains 30 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 0 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4753 r_free = 0.4753 target = 0.238605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.227486 restraints weight = 1027.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.230327 restraints weight = 440.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.232069 restraints weight = 239.217| |-----------------------------------------------------------------------------| r_work (final): 0.4670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 852 Z= 0.143 Angle : 0.553 5.697 1154 Z= 0.291 Chirality : 0.050 0.140 152 Planarity : 0.002 0.009 144 Dihedral : 4.137 11.456 124 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 16.28 % Allowed : 24.42 % Favored : 59.30 % 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: -2.61 (0.71), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.003 0.001 PHE A 94 TYR 0.002 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.091 Fit side-chains REVERT: C 43 LYS cc_start: 0.8108 (ptmt) cc_final: 0.7283 (mmtt) REVERT: A 43 LYS cc_start: 0.8042 (ptmt) cc_final: 0.7106 (mmtt) outliers start: 14 outliers final: 10 residues processed: 30 average time/residue: 0.0985 time to fit residues: 3.2936 Evaluate side-chains 32 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 0.0030 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.0570 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.0114 ------------------------------------------------------------------------------- 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 = 0.4736 r_free = 0.4736 target = 0.234828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.222324 restraints weight = 1095.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.225626 restraints weight = 478.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.227698 restraints weight = 265.806| |-----------------------------------------------------------------------------| r_work (final): 0.4648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 852 Z= 0.142 Angle : 0.563 6.443 1154 Z= 0.291 Chirality : 0.049 0.134 152 Planarity : 0.002 0.009 144 Dihedral : 4.218 12.499 124 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 13.95 % Allowed : 30.23 % Favored : 55.81 % 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: -2.55 (0.72), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.003 0.001 PHE C 94 TYR 0.002 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.084 Fit side-chains REVERT: C 43 LYS cc_start: 0.8133 (ptmt) cc_final: 0.7234 (mmtt) REVERT: A 43 LYS cc_start: 0.8086 (ptmt) cc_final: 0.7169 (mmtt) outliers start: 12 outliers final: 8 residues processed: 30 average time/residue: 0.0965 time to fit residues: 3.2252 Evaluate side-chains 32 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4694 r_free = 0.4694 target = 0.230675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.218184 restraints weight = 1097.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.221529 restraints weight = 488.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.223469 restraints weight = 269.187| |-----------------------------------------------------------------------------| r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 852 Z= 0.218 Angle : 0.674 7.408 1154 Z= 0.348 Chirality : 0.052 0.175 152 Planarity : 0.002 0.007 144 Dihedral : 4.949 15.909 124 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 12.79 % Allowed : 29.07 % Favored : 58.14 % 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: -2.62 (0.72), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.002 HIS C 50 PHE 0.005 0.002 PHE C 94 TYR 0.004 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.088 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 38 average time/residue: 0.1120 time to fit residues: 4.6644 Evaluate side-chains 37 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 5 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.236298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.224181 restraints weight = 1084.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.227449 restraints weight = 465.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.229351 restraints weight = 250.597| |-----------------------------------------------------------------------------| r_work (final): 0.4648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 852 Z= 0.094 Angle : 0.572 7.917 1154 Z= 0.286 Chirality : 0.048 0.110 152 Planarity : 0.002 0.011 144 Dihedral : 3.843 11.289 124 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 10.47 % Allowed : 36.05 % Favored : 53.49 % 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: -2.32 (0.75), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS C 50 PHE 0.001 0.000 PHE A 94 TYR 0.001 0.000 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.087 Fit side-chains REVERT: C 43 LYS cc_start: 0.8151 (ptmt) cc_final: 0.7244 (mmtt) REVERT: A 43 LYS cc_start: 0.8156 (ptmt) cc_final: 0.7274 (mmtt) outliers start: 9 outliers final: 9 residues processed: 32 average time/residue: 0.1208 time to fit residues: 4.2014 Evaluate side-chains 36 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 0.0030 chunk 8 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.239531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.228442 restraints weight = 999.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.231044 restraints weight = 434.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.232716 restraints weight = 240.915| |-----------------------------------------------------------------------------| r_work (final): 0.4678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 852 Z= 0.094 Angle : 0.602 9.152 1154 Z= 0.286 Chirality : 0.049 0.113 152 Planarity : 0.002 0.011 144 Dihedral : 3.617 14.865 124 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 11.63 % Allowed : 36.05 % Favored : 52.33 % 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: -2.19 (0.77), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS C 50 PHE 0.002 0.001 PHE C 94 TYR 0.003 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.085 Fit side-chains REVERT: C 43 LYS cc_start: 0.8121 (ptmt) cc_final: 0.7225 (mmtt) REVERT: A 43 LYS cc_start: 0.8171 (ptmt) cc_final: 0.7316 (mmtt) outliers start: 10 outliers final: 8 residues processed: 38 average time/residue: 0.1047 time to fit residues: 4.3559 Evaluate side-chains 38 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.0030 chunk 3 optimal weight: 0.0770 chunk 2 optimal weight: 0.0970 chunk 11 optimal weight: 0.0980 chunk 7 optimal weight: 0.4980 chunk 9 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.1546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.247835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.235704 restraints weight = 993.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.238638 restraints weight = 434.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.240297 restraints weight = 237.713| |-----------------------------------------------------------------------------| r_work (final): 0.4724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 852 Z= 0.095 Angle : 0.595 8.957 1154 Z= 0.284 Chirality : 0.047 0.110 152 Planarity : 0.003 0.014 144 Dihedral : 3.186 12.943 124 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 11.63 % Allowed : 36.05 % Favored : 52.33 % 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: -2.15 (0.79), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 50 PHE 0.002 0.000 PHE C 94 TYR 0.001 0.000 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.090 Fit side-chains REVERT: C 43 LYS cc_start: 0.8074 (ptmt) cc_final: 0.7168 (mmtt) REVERT: A 43 LYS cc_start: 0.8118 (ptmt) cc_final: 0.7252 (mmtt) outliers start: 10 outliers final: 6 residues processed: 34 average time/residue: 0.1229 time to fit residues: 4.5555 Evaluate side-chains 34 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN A 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.237853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.226108 restraints weight = 1048.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.229100 restraints weight = 463.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.230907 restraints weight = 252.438| |-----------------------------------------------------------------------------| r_work (final): 0.4650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 852 Z= 0.159 Angle : 0.677 9.520 1154 Z= 0.330 Chirality : 0.048 0.116 152 Planarity : 0.002 0.012 144 Dihedral : 4.276 16.514 124 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 8.14 % Allowed : 43.02 % Favored : 48.84 % 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: -2.24 (0.76), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.003 0.001 PHE A 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.083 Fit side-chains REVERT: C 43 LYS cc_start: 0.8140 (ptmt) cc_final: 0.7250 (mmtt) REVERT: A 43 LYS cc_start: 0.8087 (ptmt) cc_final: 0.7133 (mmtt) outliers start: 7 outliers final: 7 residues processed: 31 average time/residue: 0.1039 time to fit residues: 3.5628 Evaluate side-chains 36 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 = 0.4780 r_free = 0.4780 target = 0.242988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.231412 restraints weight = 1052.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.234097 restraints weight = 444.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.235966 restraints weight = 241.918| |-----------------------------------------------------------------------------| r_work (final): 0.4688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 852 Z= 0.095 Angle : 0.613 9.412 1154 Z= 0.293 Chirality : 0.047 0.109 152 Planarity : 0.002 0.014 144 Dihedral : 3.573 12.929 124 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 8.14 % Allowed : 39.53 % Favored : 52.33 % 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: -2.14 (0.76), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.001 0.000 PHE A 94 TYR 0.001 0.001 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.090 Fit side-chains REVERT: C 43 LYS cc_start: 0.8097 (ptmt) cc_final: 0.7176 (mmtt) REVERT: A 43 LYS cc_start: 0.8147 (ptmt) cc_final: 0.7278 (mmtt) outliers start: 7 outliers final: 7 residues processed: 30 average time/residue: 0.1037 time to fit residues: 3.4522 Evaluate side-chains 35 residues out of total 86 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4757 r_free = 0.4757 target = 0.236878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.224195 restraints weight = 1066.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.227346 restraints weight = 466.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.228945 restraints weight = 254.960| |-----------------------------------------------------------------------------| r_work (final): 0.4667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 852 Z= 0.123 Angle : 0.605 8.271 1154 Z= 0.300 Chirality : 0.047 0.111 152 Planarity : 0.002 0.013 144 Dihedral : 3.890 14.779 124 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 10.47 % Allowed : 36.05 % Favored : 53.49 % 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: -2.21 (0.75), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.003 0.001 PHE A 94 TYR 0.003 0.001 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 860.80 seconds wall clock time: 15 minutes 32.73 seconds (932.73 seconds total)