Starting phenix.real_space_refine on Tue Mar 3 10:48:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4c_31707/03_2026/7v4c_31707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4c_31707/03_2026/7v4c_31707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v4c_31707/03_2026/7v4c_31707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4c_31707/03_2026/7v4c_31707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v4c_31707/03_2026/7v4c_31707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4c_31707/03_2026/7v4c_31707.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 807 2.51 5 N 222 2.21 5 O 258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1287 Number of models: 1 Model: "" Number of chains: 1 Chain: "F" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 429 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Restraints were copied for chains: A, B Time building chain proxies: 0.20, per 1000 atoms: 0.16 Number of scatterers: 1287 At special positions: 0 Unit cell: (75.26, 66.78, 33.92, 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 258 8.00 N 222 7.00 C 807 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: 0.05 Conformation dependent library (CDL) restraints added in 30.9 milliseconds 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 318 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 11.3% 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 'F' and resid 68 through 71 removed outlier: 6.792A pdb=" N ALA F 69 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA A 69 " --> pdb=" O VAL B 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 74 through 76 removed outlier: 6.774A pdb=" N VAL F 74 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 74 " --> pdb=" O THR B 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 91 through 92 Processing sheet with id=AA4, first strand: chain 'F' and resid 95 through 96 4 hydrogen bonds defined for protein. 12 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.07 Time building geometry restraints manager: 0.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 225 1.28 - 1.35: 198 1.35 - 1.41: 54 1.41 - 1.48: 210 1.48 - 1.54: 606 Bond restraints: 1293 Sorted by residual: bond pdb=" C SER A 87 " pdb=" N ILE A 88 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.42e-02 4.96e+03 2.61e+00 bond pdb=" C SER B 87 " pdb=" N ILE B 88 " ideal model delta sigma weight residual 1.330 1.308 0.023 1.42e-02 4.96e+03 2.55e+00 bond pdb=" C SER F 87 " pdb=" N ILE F 88 " ideal model delta sigma weight residual 1.330 1.308 0.023 1.42e-02 4.96e+03 2.54e+00 bond pdb=" CB VAL A 48 " pdb=" CG1 VAL A 48 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.71e+00 bond pdb=" CB VAL F 48 " pdb=" CG1 VAL F 48 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.69e+00 ... (remaining 1288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 1456 0.88 - 1.76: 207 1.76 - 2.63: 77 2.63 - 3.51: 6 3.51 - 4.39: 3 Bond angle restraints: 1749 Sorted by residual: angle pdb=" CA GLY A 93 " pdb=" C GLY A 93 " pdb=" N PHE A 94 " ideal model delta sigma weight residual 114.86 117.14 -2.28 1.01e+00 9.80e-01 5.07e+00 angle pdb=" C ASN A 65 " pdb=" N VAL A 66 " pdb=" CA VAL A 66 " ideal model delta sigma weight residual 122.36 119.75 2.61 1.16e+00 7.43e-01 5.07e+00 angle pdb=" CA GLY B 93 " pdb=" C GLY B 93 " pdb=" N PHE B 94 " ideal model delta sigma weight residual 114.86 117.13 -2.27 1.01e+00 9.80e-01 5.06e+00 angle pdb=" C VAL B 66 " pdb=" N GLY B 67 " pdb=" CA GLY B 67 " ideal model delta sigma weight residual 121.41 117.02 4.39 1.96e+00 2.60e-01 5.01e+00 angle pdb=" CA GLY F 93 " pdb=" C GLY F 93 " pdb=" N PHE F 94 " ideal model delta sigma weight residual 114.86 117.11 -2.25 1.01e+00 9.80e-01 4.98e+00 ... (remaining 1744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.06: 594 10.06 - 20.12: 111 20.12 - 30.18: 39 30.18 - 40.24: 9 40.24 - 50.30: 3 Dihedral angle restraints: 756 sinusoidal: 252 harmonic: 504 Sorted by residual: dihedral pdb=" CA GLU B 57 " pdb=" CB GLU B 57 " pdb=" CG GLU B 57 " pdb=" CD GLU B 57 " ideal model delta sinusoidal sigma weight residual -60.00 -110.30 50.30 3 1.50e+01 4.44e-03 8.88e+00 dihedral pdb=" CA GLU F 57 " pdb=" CB GLU F 57 " pdb=" CG GLU F 57 " pdb=" CD GLU F 57 " ideal model delta sinusoidal sigma weight residual -60.00 -110.29 50.29 3 1.50e+01 4.44e-03 8.88e+00 dihedral pdb=" CA GLU A 57 " pdb=" CB GLU A 57 " pdb=" CG GLU A 57 " pdb=" CD GLU A 57 " ideal model delta sinusoidal sigma weight residual -60.00 -110.26 50.26 3 1.50e+01 4.44e-03 8.88e+00 ... (remaining 753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 94 0.032 - 0.065: 83 0.065 - 0.097: 33 0.097 - 0.130: 12 0.130 - 0.162: 9 Chirality restraints: 231 Sorted by residual: chirality pdb=" CB VAL F 77 " pdb=" CA VAL F 77 " pdb=" CG1 VAL F 77 " pdb=" CG2 VAL F 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CB VAL B 77 " pdb=" CA VAL B 77 " pdb=" CG1 VAL B 77 " pdb=" CG2 VAL B 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CB VAL A 77 " pdb=" CA VAL A 77 " pdb=" CG1 VAL A 77 " pdb=" CG2 VAL A 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 228 not shown) Planarity restraints: 216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 67 " -0.003 2.00e-02 2.50e+03 6.98e-03 4.87e-01 pdb=" C GLY B 67 " 0.012 2.00e-02 2.50e+03 pdb=" O GLY B 67 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY B 68 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 67 " -0.003 2.00e-02 2.50e+03 6.64e-03 4.41e-01 pdb=" C GLY A 67 " 0.011 2.00e-02 2.50e+03 pdb=" O GLY A 67 " -0.004 2.00e-02 2.50e+03 pdb=" N GLY A 68 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 67 " -0.003 2.00e-02 2.50e+03 6.61e-03 4.37e-01 pdb=" C GLY F 67 " 0.011 2.00e-02 2.50e+03 pdb=" O GLY F 67 " -0.004 2.00e-02 2.50e+03 pdb=" N GLY F 68 " -0.004 2.00e-02 2.50e+03 ... (remaining 213 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 417 2.82 - 3.34: 1087 3.34 - 3.86: 1957 3.86 - 4.38: 2068 4.38 - 4.90: 3876 Nonbonded interactions: 9405 Sorted by model distance: nonbonded pdb=" OG1 THR A 81 " pdb=" O LYS B 80 " model vdw 2.305 3.040 nonbonded pdb=" OG1 THR F 81 " pdb=" O LYS A 80 " model vdw 2.340 3.040 nonbonded pdb=" OG1 THR B 72 " pdb=" N GLY B 73 " model vdw 2.622 3.120 nonbonded pdb=" OG1 THR A 72 " pdb=" N GLY A 73 " model vdw 2.622 3.120 nonbonded pdb=" OG1 THR F 72 " pdb=" N GLY F 73 " model vdw 2.623 3.120 ... (remaining 9400 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 'F' 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: 0.140 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: 0.010 Process input model: 1.880 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:0.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 2.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.008 0.043 1293 Z= 0.358 Angle : 0.745 4.388 1749 Z= 0.456 Chirality : 0.058 0.162 231 Planarity : 0.002 0.007 216 Dihedral : 12.467 50.301 438 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 0.00 % Allowed : 20.45 % Favored : 79.55 % 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 are not related in a simple way. whole: -6.54 (0.37), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.98 (0.28), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR F 39 PHE 0.003 0.001 PHE B 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00808 ( 1293) covalent geometry : angle 0.74512 ( 1749) hydrogen bonds : bond 0.11306 ( 4) hydrogen bonds : angle 2.98519 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.025 Fit side-chains REVERT: F 45 LYS cc_start: 0.8437 (tttt) cc_final: 0.7847 (mttm) REVERT: F 83 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7929 (mm-30) REVERT: B 43 LYS cc_start: 0.8913 (mttt) cc_final: 0.8663 (mttt) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0368 time to fit residues: 1.3731 Evaluate side-chains 24 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.025 ------------------------------------------------------------------------------- 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: 4.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS A 50 HIS B 50 HIS B 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.122120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.096546 restraints weight = 1613.595| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.94 r_work: 0.3278 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1293 Z= 0.197 Angle : 0.596 3.616 1749 Z= 0.342 Chirality : 0.055 0.149 231 Planarity : 0.002 0.008 216 Dihedral : 4.891 13.989 186 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.44 % Favored : 85.56 % Rotamer: Outliers : 8.33 % Allowed : 19.70 % Favored : 71.97 % 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 are not related in a simple way. whole: -6.04 (0.38), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.60 (0.29), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 39 PHE 0.004 0.001 PHE F 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 1293) covalent geometry : angle 0.59616 ( 1749) hydrogen bonds : bond 0.03261 ( 4) hydrogen bonds : angle 4.02976 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.025 Fit side-chains REVERT: F 43 LYS cc_start: 0.8630 (mttp) cc_final: 0.8390 (mttm) REVERT: F 83 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8066 (mm-30) REVERT: A 83 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7972 (mm-30) REVERT: B 45 LYS cc_start: 0.8432 (tttt) cc_final: 0.8175 (mtpp) REVERT: B 80 LYS cc_start: 0.8644 (tttp) cc_final: 0.6701 (pttt) outliers start: 11 outliers final: 7 residues processed: 37 average time/residue: 0.0320 time to fit residues: 1.3399 Evaluate side-chains 35 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 77 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 0.0870 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.121033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094932 restraints weight = 1627.680| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.04 r_work: 0.3284 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1293 Z= 0.197 Angle : 0.578 3.581 1749 Z= 0.334 Chirality : 0.054 0.144 231 Planarity : 0.002 0.009 216 Dihedral : 4.723 13.242 186 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.44 % Favored : 85.56 % Rotamer: Outliers : 9.09 % Allowed : 19.70 % Favored : 71.21 % 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 are not related in a simple way. whole: -5.67 (0.40), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.31 (0.30), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 39 PHE 0.004 0.001 PHE F 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 1293) covalent geometry : angle 0.57754 ( 1749) hydrogen bonds : bond 0.02947 ( 4) hydrogen bonds : angle 4.34191 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.048 Fit side-chains REVERT: F 83 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8074 (mm-30) REVERT: A 83 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7994 (mm-30) REVERT: B 43 LYS cc_start: 0.8937 (mttp) cc_final: 0.8616 (mttp) REVERT: B 45 LYS cc_start: 0.8467 (tttt) cc_final: 0.8183 (mtpp) outliers start: 12 outliers final: 12 residues processed: 38 average time/residue: 0.0545 time to fit residues: 2.3558 Evaluate side-chains 38 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 0.0670 chunk 3 optimal weight: 0.0000 chunk 11 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.2128 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.125627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099967 restraints weight = 1646.310| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.97 r_work: 0.3375 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1293 Z= 0.142 Angle : 0.512 3.556 1749 Z= 0.297 Chirality : 0.051 0.123 231 Planarity : 0.002 0.008 216 Dihedral : 4.508 13.210 186 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 12.88 % Allowed : 15.91 % Favored : 71.21 % 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 are not related in a simple way. whole: -5.28 (0.42), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.32), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 39 PHE 0.004 0.001 PHE F 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 1293) covalent geometry : angle 0.51214 ( 1749) hydrogen bonds : bond 0.02573 ( 4) hydrogen bonds : angle 4.27617 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.050 Fit side-chains REVERT: F 83 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7989 (mm-30) REVERT: A 71 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8789 (t) REVERT: A 83 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7915 (mm-30) REVERT: B 45 LYS cc_start: 0.8410 (tttt) cc_final: 0.8122 (mtpp) REVERT: B 83 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8415 (tt0) outliers start: 17 outliers final: 12 residues processed: 39 average time/residue: 0.0447 time to fit residues: 2.0123 Evaluate side-chains 38 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.127549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.101701 restraints weight = 1586.862| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.95 r_work: 0.3383 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1293 Z= 0.132 Angle : 0.502 3.719 1749 Z= 0.293 Chirality : 0.051 0.123 231 Planarity : 0.002 0.013 216 Dihedral : 4.387 12.936 186 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 12.88 % Allowed : 14.39 % Favored : 72.73 % 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 are not related in a simple way. whole: -5.05 (0.44), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.33), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR A 39 PHE 0.004 0.001 PHE F 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 1293) covalent geometry : angle 0.50207 ( 1749) hydrogen bonds : bond 0.02485 ( 4) hydrogen bonds : angle 4.40736 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 27 time to evaluate : 0.049 Fit side-chains REVERT: F 83 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7958 (mm-30) REVERT: A 58 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7556 (mtpp) REVERT: A 83 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7891 (mm-30) REVERT: B 45 LYS cc_start: 0.8366 (tttt) cc_final: 0.8143 (mtpp) REVERT: B 83 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8345 (tt0) outliers start: 17 outliers final: 14 residues processed: 40 average time/residue: 0.0457 time to fit residues: 2.1139 Evaluate side-chains 42 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.126531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.100652 restraints weight = 1598.220| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.95 r_work: 0.3414 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1293 Z= 0.161 Angle : 0.509 3.589 1749 Z= 0.298 Chirality : 0.052 0.123 231 Planarity : 0.002 0.012 216 Dihedral : 4.400 13.434 186 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 11.36 % Allowed : 15.91 % Favored : 72.73 % 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 are not related in a simple way. whole: -5.04 (0.44), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 39 PHE 0.004 0.001 PHE F 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 1293) covalent geometry : angle 0.50935 ( 1749) hydrogen bonds : bond 0.02640 ( 4) hydrogen bonds : angle 4.56995 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.029 Fit side-chains REVERT: F 83 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8070 (mm-30) REVERT: A 58 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7475 (mtpp) REVERT: A 83 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7919 (mm-30) REVERT: B 45 LYS cc_start: 0.8442 (tttt) cc_final: 0.8233 (mtpp) outliers start: 15 outliers final: 15 residues processed: 39 average time/residue: 0.0402 time to fit residues: 1.7854 Evaluate side-chains 39 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.127873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.101830 restraints weight = 1581.112| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.94 r_work: 0.3437 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1293 Z= 0.143 Angle : 0.510 4.461 1749 Z= 0.296 Chirality : 0.051 0.122 231 Planarity : 0.002 0.010 216 Dihedral : 4.334 13.549 186 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 13.64 % Allowed : 13.64 % Favored : 72.73 % 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 are not related in a simple way. whole: -4.92 (0.45), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR A 39 PHE 0.004 0.001 PHE F 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 1293) covalent geometry : angle 0.50953 ( 1749) hydrogen bonds : bond 0.02534 ( 4) hydrogen bonds : angle 4.69863 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 0.048 Fit side-chains REVERT: F 83 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8128 (mm-30) REVERT: A 58 LYS cc_start: 0.7883 (mtpt) cc_final: 0.7457 (mtpp) REVERT: A 83 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7997 (mm-30) REVERT: B 45 LYS cc_start: 0.8375 (tttt) cc_final: 0.8166 (mtpp) REVERT: B 83 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8401 (tt0) outliers start: 18 outliers final: 15 residues processed: 40 average time/residue: 0.0481 time to fit residues: 2.1943 Evaluate side-chains 41 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.123467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.097449 restraints weight = 1579.304| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.93 r_work: 0.3308 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 1293 Z= 0.248 Angle : 0.603 4.652 1749 Z= 0.351 Chirality : 0.055 0.153 231 Planarity : 0.002 0.012 216 Dihedral : 4.696 14.370 186 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 12.12 % Allowed : 15.15 % Favored : 72.73 % 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 are not related in a simple way. whole: -5.16 (0.44), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.002 TYR A 39 PHE 0.003 0.001 PHE F 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 1293) covalent geometry : angle 0.60279 ( 1749) hydrogen bonds : bond 0.02974 ( 4) hydrogen bonds : angle 5.13379 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 26 time to evaluate : 0.042 Fit side-chains REVERT: F 45 LYS cc_start: 0.8461 (tttt) cc_final: 0.7796 (mttm) REVERT: F 83 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8101 (mm-30) REVERT: A 83 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7949 (mm-30) REVERT: B 45 LYS cc_start: 0.8423 (tttt) cc_final: 0.8204 (mtpp) outliers start: 16 outliers final: 16 residues processed: 41 average time/residue: 0.0523 time to fit residues: 2.4249 Evaluate side-chains 41 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 0.0070 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.128164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.102107 restraints weight = 1581.537| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.95 r_work: 0.3437 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1293 Z= 0.136 Angle : 0.522 4.986 1749 Z= 0.303 Chirality : 0.051 0.130 231 Planarity : 0.002 0.010 216 Dihedral : 4.422 14.125 186 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 12.12 % Allowed : 15.15 % Favored : 72.73 % 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 are not related in a simple way. whole: -4.86 (0.46), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.35), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR A 39 PHE 0.004 0.001 PHE F 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 1293) covalent geometry : angle 0.52242 ( 1749) hydrogen bonds : bond 0.02528 ( 4) hydrogen bonds : angle 5.05271 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 22 time to evaluate : 0.029 Fit side-chains REVERT: F 83 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8100 (mm-30) REVERT: A 58 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7467 (mtpp) REVERT: A 83 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7983 (mm-30) REVERT: B 83 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8022 (mm-30) outliers start: 16 outliers final: 14 residues processed: 36 average time/residue: 0.0497 time to fit residues: 2.0429 Evaluate side-chains 37 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 22 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 8.9990 chunk 13 optimal weight: 0.0060 chunk 14 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.8200 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.124506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.098477 restraints weight = 1543.980| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.98 r_work: 0.3363 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1293 Z= 0.176 Angle : 0.533 3.739 1749 Z= 0.310 Chirality : 0.052 0.135 231 Planarity : 0.002 0.010 216 Dihedral : 4.495 14.325 186 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 11.36 % Allowed : 16.67 % Favored : 71.97 % 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 are not related in a simple way. whole: -4.93 (0.45), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.35), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 39 PHE 0.003 0.001 PHE F 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 1293) covalent geometry : angle 0.53250 ( 1749) hydrogen bonds : bond 0.02690 ( 4) hydrogen bonds : angle 5.13604 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 0.065 Fit side-chains REVERT: F 83 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8141 (mm-30) REVERT: A 58 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7461 (mtpp) REVERT: A 83 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7921 (mm-30) outliers start: 15 outliers final: 14 residues processed: 38 average time/residue: 0.0513 time to fit residues: 2.2745 Evaluate side-chains 37 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 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 = 0.3775 r_free = 0.3775 target = 0.122892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096788 restraints weight = 1596.177| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.99 r_work: 0.3356 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 1293 Z= 0.207 Angle : 0.590 5.488 1749 Z= 0.342 Chirality : 0.054 0.157 231 Planarity : 0.002 0.011 216 Dihedral : 4.610 14.681 186 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.44 % Favored : 85.56 % Rotamer: Outliers : 10.61 % Allowed : 17.42 % Favored : 71.97 % 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 are not related in a simple way. whole: -4.99 (0.45), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 39 PHE 0.004 0.001 PHE F 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 1293) covalent geometry : angle 0.59033 ( 1749) hydrogen bonds : bond 0.02852 ( 4) hydrogen bonds : angle 5.27217 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 577.13 seconds wall clock time: 11 minutes 5.41 seconds (665.41 seconds total)