Starting phenix.real_space_refine on Wed Sep 17 02:58:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v49_31704/09_2025/7v49_31704.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v49_31704/09_2025/7v49_31704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v49_31704/09_2025/7v49_31704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v49_31704/09_2025/7v49_31704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v49_31704/09_2025/7v49_31704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v49_31704/09_2025/7v49_31704.map" } resolution = 3.4 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= 0.000 sd= 0.005 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 765 2.51 5 N 210 2.21 5 O 246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s 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: 1221 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 407 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Restraints were copied for chains: A, B Time building chain proxies: 0.28, per 1000 atoms: 0.23 Number of scatterers: 1221 At special positions: 0 Unit cell: (78.44, 65.72, 28.62, 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 246 8.00 N 210 7.00 C 765 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: 0.18 Conformation dependent library (CDL) restraints added in 41.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 300 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 1 sheets defined 0.0% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 88 through 89 removed outlier: 6.281A pdb=" N ILE C 88 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 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: 0.20 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: 213 1.29 - 1.35: 192 1.35 - 1.42: 54 1.42 - 1.48: 207 1.48 - 1.54: 561 Bond restraints: 1227 Sorted by residual: bond pdb=" CB VAL A 82 " pdb=" CG1 VAL A 82 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.11e+00 bond pdb=" CB VAL B 82 " pdb=" CG1 VAL B 82 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.11e+00 bond pdb=" CB VAL C 82 " pdb=" CG1 VAL C 82 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 bond pdb=" CB VAL C 37 " pdb=" CG1 VAL C 37 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.96e-01 bond pdb=" CB VAL B 37 " pdb=" CG1 VAL B 37 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.70e-01 ... (remaining 1222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 1467 1.54 - 3.08: 177 3.08 - 4.61: 18 4.61 - 6.15: 0 6.15 - 7.69: 3 Bond angle restraints: 1665 Sorted by residual: angle pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " pdb=" CG LEU C 38 " ideal model delta sigma weight residual 116.30 123.99 -7.69 3.50e+00 8.16e-02 4.83e+00 angle pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " pdb=" CG LEU A 38 " ideal model delta sigma weight residual 116.30 123.98 -7.68 3.50e+00 8.16e-02 4.81e+00 angle pdb=" CA LEU B 38 " pdb=" CB LEU B 38 " pdb=" CG LEU B 38 " ideal model delta sigma weight residual 116.30 123.97 -7.67 3.50e+00 8.16e-02 4.80e+00 angle pdb=" N ILE B 88 " pdb=" CA ILE B 88 " pdb=" C ILE B 88 " ideal model delta sigma weight residual 106.61 110.32 -3.71 1.78e+00 3.16e-01 4.34e+00 angle pdb=" N ILE C 88 " pdb=" CA ILE C 88 " pdb=" C ILE C 88 " ideal model delta sigma weight residual 106.61 110.28 -3.67 1.78e+00 3.16e-01 4.25e+00 ... (remaining 1660 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 9.48: 557 9.48 - 18.94: 91 18.94 - 28.41: 36 28.41 - 37.88: 3 37.88 - 47.34: 15 Dihedral angle restraints: 702 sinusoidal: 222 harmonic: 480 Sorted by residual: dihedral pdb=" CA THR B 81 " pdb=" C THR B 81 " pdb=" N VAL B 82 " pdb=" CA VAL B 82 " ideal model delta harmonic sigma weight residual 180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA THR A 81 " pdb=" C THR A 81 " pdb=" N VAL A 82 " pdb=" CA VAL A 82 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR C 81 " pdb=" C THR C 81 " pdb=" N VAL C 82 " pdb=" CA VAL C 82 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 68 0.028 - 0.055: 77 0.055 - 0.082: 43 0.082 - 0.109: 19 0.109 - 0.136: 15 Chirality restraints: 222 Sorted by residual: chirality pdb=" CA VAL C 40 " pdb=" N VAL C 40 " pdb=" C VAL C 40 " pdb=" CB VAL C 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL B 40 " pdb=" N VAL B 40 " pdb=" C VAL B 40 " pdb=" CB VAL B 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL A 40 " pdb=" N VAL A 40 " pdb=" C VAL A 40 " pdb=" CB VAL A 40 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 219 not shown) Planarity restraints: 207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 70 " -0.005 2.00e-02 2.50e+03 9.63e-03 9.27e-01 pdb=" C VAL B 70 " 0.017 2.00e-02 2.50e+03 pdb=" O VAL B 70 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL B 71 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 70 " -0.005 2.00e-02 2.50e+03 9.44e-03 8.90e-01 pdb=" C VAL A 70 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL A 70 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL A 71 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 70 " -0.005 2.00e-02 2.50e+03 9.16e-03 8.39e-01 pdb=" C VAL C 70 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL C 70 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL C 71 " -0.005 2.00e-02 2.50e+03 ... (remaining 204 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 356 2.80 - 3.33: 1111 3.33 - 3.85: 1702 3.85 - 4.38: 1838 4.38 - 4.90: 3934 Nonbonded interactions: 8941 Sorted by model distance: nonbonded pdb=" O SER A 42 " pdb=" OG SER A 42 " model vdw 2.279 3.040 nonbonded pdb=" O SER B 42 " pdb=" OG SER B 42 " model vdw 2.279 3.040 nonbonded pdb=" O SER C 42 " pdb=" OG SER C 42 " model vdw 2.280 3.040 nonbonded pdb=" O LYS B 80 " pdb=" OG1 THR B 81 " model vdw 2.498 3.040 nonbonded pdb=" O LYS C 80 " pdb=" OG1 THR C 81 " model vdw 2.499 3.040 ... (remaining 8936 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: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.170 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:0.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 0.048 1227 Z= 0.293 Angle : 1.014 7.691 1665 Z= 0.570 Chirality : 0.057 0.136 222 Planarity : 0.004 0.010 207 Dihedral : 13.695 47.342 402 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 39.66 % Favored : 60.34 % Rotamer: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % 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: -7.67 (0.34), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.84 (0.26), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.004 TYR A 39 PHE 0.007 0.002 PHE A 94 HIS 0.005 0.003 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00691 ( 1227) covalent geometry : angle 1.01414 ( 1665) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.024 Fit side-chains REVERT: C 43 LYS cc_start: 0.7224 (mttt) cc_final: 0.5716 (tttt) REVERT: C 94 PHE cc_start: 0.7455 (t80) cc_final: 0.6889 (t80) REVERT: A 43 LYS cc_start: 0.7146 (mttt) cc_final: 0.5842 (tttt) REVERT: A 57 GLU cc_start: 0.7923 (tp30) cc_final: 0.7141 (tp30) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0262 time to fit residues: 0.7372 Evaluate side-chains 13 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.094969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.080300 restraints weight = 2055.784| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.30 r_work: 0.3627 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1227 Z= 0.137 Angle : 0.799 6.688 1665 Z= 0.435 Chirality : 0.058 0.135 222 Planarity : 0.003 0.012 207 Dihedral : 6.614 18.225 180 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.41 % Favored : 77.59 % Rotamer: Outliers : 2.44 % Allowed : 16.26 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -6.87 (0.37), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.23 (0.28), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 39 PHE 0.015 0.003 PHE B 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 1227) covalent geometry : angle 0.79933 ( 1665) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.025 Fit side-chains REVERT: C 43 LYS cc_start: 0.6902 (mttt) cc_final: 0.5337 (tttt) REVERT: C 94 PHE cc_start: 0.7530 (t80) cc_final: 0.6946 (t80) REVERT: A 43 LYS cc_start: 0.6826 (mttt) cc_final: 0.5612 (tttt) REVERT: A 77 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7918 (t) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.0307 time to fit residues: 0.8491 Evaluate side-chains 22 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.0270 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.1244 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.099072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.083335 restraints weight = 2146.305| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 3.34 r_work: 0.3682 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1227 Z= 0.113 Angle : 0.711 6.098 1665 Z= 0.385 Chirality : 0.056 0.128 222 Planarity : 0.003 0.016 207 Dihedral : 5.918 16.863 180 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.82 % Favored : 82.18 % Rotamer: Outliers : 6.50 % Allowed : 13.82 % Favored : 79.67 % 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: -6.53 (0.38), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.97 (0.29), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR A 39 PHE 0.012 0.003 PHE A 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 1227) covalent geometry : angle 0.71060 ( 1665) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.024 Fit side-chains REVERT: C 37 VAL cc_start: 0.8076 (p) cc_final: 0.7789 (t) REVERT: C 43 LYS cc_start: 0.6798 (mttt) cc_final: 0.5282 (tttt) REVERT: C 94 PHE cc_start: 0.7515 (t80) cc_final: 0.6993 (t80) REVERT: A 43 LYS cc_start: 0.6901 (mttt) cc_final: 0.5697 (tttt) REVERT: A 77 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7971 (t) REVERT: B 43 LYS cc_start: 0.7058 (mttt) cc_final: 0.6665 (mptt) outliers start: 8 outliers final: 5 residues processed: 29 average time/residue: 0.0258 time to fit residues: 0.8730 Evaluate side-chains 29 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 3 optimal weight: 0.0050 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.5400 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.096231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.080984 restraints weight = 2117.814| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 3.38 r_work: 0.3650 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1227 Z= 0.134 Angle : 0.723 6.910 1665 Z= 0.396 Chirality : 0.056 0.128 222 Planarity : 0.003 0.016 207 Dihedral : 6.074 16.502 180 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.11 % Favored : 79.89 % Rotamer: Outliers : 5.69 % Allowed : 17.07 % Favored : 77.24 % 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: -6.43 (0.38), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.90 (0.29), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR A 39 PHE 0.012 0.003 PHE A 94 HIS 0.003 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 1227) covalent geometry : angle 0.72269 ( 1665) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.048 Fit side-chains REVERT: C 43 LYS cc_start: 0.6850 (mttt) cc_final: 0.5326 (tttt) REVERT: C 94 PHE cc_start: 0.7637 (t80) cc_final: 0.7017 (t80) REVERT: A 43 LYS cc_start: 0.6879 (mttt) cc_final: 0.5586 (tttt) REVERT: B 43 LYS cc_start: 0.6999 (mttt) cc_final: 0.6599 (mptt) outliers start: 7 outliers final: 7 residues processed: 28 average time/residue: 0.0496 time to fit residues: 1.6113 Evaluate side-chains 25 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 0.0060 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.101464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.085108 restraints weight = 2074.705| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.37 r_work: 0.3710 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1227 Z= 0.103 Angle : 0.642 4.998 1665 Z= 0.352 Chirality : 0.054 0.130 222 Planarity : 0.003 0.015 207 Dihedral : 5.544 15.685 180 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Rotamer: Outliers : 6.50 % Allowed : 15.45 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -6.30 (0.37), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.80 (0.29), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR A 39 PHE 0.014 0.003 PHE A 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 1227) covalent geometry : angle 0.64168 ( 1665) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.045 Fit side-chains REVERT: C 43 LYS cc_start: 0.6745 (mttt) cc_final: 0.5346 (tttt) REVERT: C 94 PHE cc_start: 0.7502 (t80) cc_final: 0.6922 (t80) REVERT: A 43 LYS cc_start: 0.6906 (mttt) cc_final: 0.5685 (tttt) REVERT: A 77 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7954 (t) REVERT: B 43 LYS cc_start: 0.7002 (mttt) cc_final: 0.6645 (mptt) outliers start: 8 outliers final: 7 residues processed: 24 average time/residue: 0.0524 time to fit residues: 1.4514 Evaluate side-chains 22 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 14 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 0.0070 chunk 4 optimal weight: 0.0000 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 overall best weight: 0.7604 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.104613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.087329 restraints weight = 2041.327| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 3.54 r_work: 0.3760 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1227 Z= 0.092 Angle : 0.593 4.722 1665 Z= 0.327 Chirality : 0.053 0.129 222 Planarity : 0.002 0.013 207 Dihedral : 5.126 14.545 180 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Rotamer: Outliers : 6.50 % Allowed : 16.26 % Favored : 77.24 % 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: -6.13 (0.38), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.67 (0.29), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 39 PHE 0.011 0.002 PHE A 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 1227) covalent geometry : angle 0.59318 ( 1665) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.047 Fit side-chains REVERT: C 43 LYS cc_start: 0.6539 (mttt) cc_final: 0.5129 (tttt) REVERT: C 94 PHE cc_start: 0.7393 (t80) cc_final: 0.6876 (t80) REVERT: A 43 LYS cc_start: 0.6840 (mttt) cc_final: 0.5502 (tttt) REVERT: A 77 VAL cc_start: 0.7969 (OUTLIER) cc_final: 0.7698 (t) REVERT: B 43 LYS cc_start: 0.6941 (mttt) cc_final: 0.6602 (mptt) outliers start: 8 outliers final: 7 residues processed: 24 average time/residue: 0.0545 time to fit residues: 1.5100 Evaluate side-chains 21 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 13 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.104775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.087441 restraints weight = 2059.818| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.58 r_work: 0.3751 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1227 Z= 0.096 Angle : 0.600 5.181 1665 Z= 0.333 Chirality : 0.053 0.137 222 Planarity : 0.002 0.010 207 Dihedral : 5.129 14.079 180 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % Rotamer: Outliers : 5.69 % Allowed : 19.51 % Favored : 74.80 % 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: -5.98 (0.40), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.30), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 39 PHE 0.009 0.002 PHE A 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 1227) covalent geometry : angle 0.60016 ( 1665) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 14 time to evaluate : 0.045 Fit side-chains REVERT: C 43 LYS cc_start: 0.6561 (mttt) cc_final: 0.5165 (tttt) REVERT: C 94 PHE cc_start: 0.7446 (t80) cc_final: 0.6936 (t80) REVERT: A 43 LYS cc_start: 0.6900 (mttt) cc_final: 0.5531 (tttt) REVERT: A 77 VAL cc_start: 0.8034 (OUTLIER) cc_final: 0.7751 (t) REVERT: B 43 LYS cc_start: 0.6951 (mttt) cc_final: 0.6659 (mptt) outliers start: 7 outliers final: 6 residues processed: 21 average time/residue: 0.0541 time to fit residues: 1.3149 Evaluate side-chains 20 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.101288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.083826 restraints weight = 2164.425| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.69 r_work: 0.3679 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1227 Z= 0.122 Angle : 0.635 5.380 1665 Z= 0.354 Chirality : 0.053 0.153 222 Planarity : 0.002 0.009 207 Dihedral : 5.622 15.823 180 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.41 % Favored : 77.59 % Rotamer: Outliers : 5.69 % Allowed : 21.95 % Favored : 72.36 % 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: -5.93 (0.41), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.31), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.003 TYR A 39 PHE 0.009 0.002 PHE A 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 1227) covalent geometry : angle 0.63491 ( 1665) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.032 Fit side-chains REVERT: C 43 LYS cc_start: 0.6705 (mttt) cc_final: 0.5293 (tttt) REVERT: C 94 PHE cc_start: 0.7618 (t80) cc_final: 0.6998 (t80) REVERT: A 43 LYS cc_start: 0.6884 (mttt) cc_final: 0.5546 (tttt) REVERT: A 77 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7823 (t) REVERT: B 43 LYS cc_start: 0.7026 (mttt) cc_final: 0.6701 (mptt) outliers start: 7 outliers final: 6 residues processed: 20 average time/residue: 0.0599 time to fit residues: 1.3549 Evaluate side-chains 20 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.109927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.090689 restraints weight = 1991.965| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 3.65 r_work: 0.3802 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1227 Z= 0.092 Angle : 0.598 5.613 1665 Z= 0.333 Chirality : 0.052 0.159 222 Planarity : 0.002 0.008 207 Dihedral : 5.028 14.646 180 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 6.50 % Allowed : 21.95 % Favored : 71.54 % 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: -5.77 (0.43), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.39 (0.33), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR A 39 PHE 0.009 0.002 PHE A 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 1227) covalent geometry : angle 0.59788 ( 1665) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 15 time to evaluate : 0.048 Fit side-chains REVERT: C 43 LYS cc_start: 0.6624 (mttt) cc_final: 0.5261 (tttt) REVERT: C 94 PHE cc_start: 0.7453 (t80) cc_final: 0.6950 (t80) REVERT: A 43 LYS cc_start: 0.6936 (mttt) cc_final: 0.5595 (tttt) REVERT: A 77 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7779 (t) REVERT: B 43 LYS cc_start: 0.7060 (mttt) cc_final: 0.6733 (mptt) outliers start: 8 outliers final: 7 residues processed: 23 average time/residue: 0.0529 time to fit residues: 1.4099 Evaluate side-chains 22 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 14 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.113943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.094516 restraints weight = 1905.508| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 3.48 r_work: 0.3824 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1227 Z= 0.090 Angle : 0.589 5.653 1665 Z= 0.328 Chirality : 0.052 0.155 222 Planarity : 0.001 0.008 207 Dihedral : 4.830 13.921 180 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 7.32 % Allowed : 20.33 % Favored : 72.36 % 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: -5.61 (0.44), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.34), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR A 39 PHE 0.008 0.002 PHE A 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00184 ( 1227) covalent geometry : angle 0.58892 ( 1665) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 15 time to evaluate : 0.045 Fit side-chains REVERT: C 43 LYS cc_start: 0.6598 (mttt) cc_final: 0.5272 (tttt) REVERT: C 94 PHE cc_start: 0.7487 (t80) cc_final: 0.7018 (t80) REVERT: A 43 LYS cc_start: 0.6981 (mttt) cc_final: 0.5655 (tttt) REVERT: A 77 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7824 (t) REVERT: B 43 LYS cc_start: 0.7057 (mttt) cc_final: 0.6767 (mptt) outliers start: 9 outliers final: 7 residues processed: 23 average time/residue: 0.0523 time to fit residues: 1.3937 Evaluate side-chains 22 residues out of total 123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 14 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 0.0770 chunk 17 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 0.0030 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6550 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.114061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.094732 restraints weight = 1848.994| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 3.42 r_work: 0.3878 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1227 Z= 0.088 Angle : 0.576 5.667 1665 Z= 0.321 Chirality : 0.052 0.163 222 Planarity : 0.002 0.008 207 Dihedral : 4.767 13.618 180 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 5.69 % Allowed : 21.95 % Favored : 72.36 % 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: -5.50 (0.45), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.34), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR A 39 PHE 0.007 0.002 PHE A 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00178 ( 1227) covalent geometry : angle 0.57608 ( 1665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 613.07 seconds wall clock time: 11 minutes 16.32 seconds (676.32 seconds total)