Starting phenix.real_space_refine on Wed Mar 5 14:17:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4c_31707/03_2025/7v4c_31707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4c_31707/03_2025/7v4c_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7v4c_31707/03_2025/7v4c_31707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4c_31707/03_2025/7v4c_31707.map" model { file = "/net/cci-nas-00/data/ceres_data/7v4c_31707/03_2025/7v4c_31707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4c_31707/03_2025/7v4c_31707.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1287 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: B, F Time building chain proxies: 1.84, per 1000 atoms: 1.43 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: 0.23 Conformation dependent library (CDL) restraints added in 381.9 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: 0.12 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: 0.19 Time building geometry restraints manager: 0.28 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 8.220 Find NCS groups from input model: 0.020 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:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.770 ------------------------------------------------------------------------------- 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= 0.534 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.001 HIS A 50 PHE 0.003 0.001 PHE B 94 TYR 0.007 0.002 TYR F 39 *********************** 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 : 0.139 Fit side-chains REVERT: F 45 LYS cc_start: 0.8437 (tttt) cc_final: 0.7848 (mttp) 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: 0.8664 (mttt) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1195 time to fit residues: 4.5152 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 : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 0.0370 chunk 11 optimal weight: 5.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.126709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.101320 restraints weight = 1612.565| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.95 r_work: 0.3372 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1293 Z= 0.162 Angle : 0.518 3.560 1749 Z= 0.298 Chirality : 0.052 0.127 231 Planarity : 0.002 0.008 216 Dihedral : 4.512 13.183 186 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 5.30 % Allowed : 21.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.91 (0.38), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.50 (0.29), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.003 0.001 PHE F 94 TYR 0.003 0.001 TYR B 39 *********************** 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 39 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.145 Fit side-chains REVERT: F 83 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8087 (mm-30) REVERT: A 71 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8839 (t) REVERT: B 80 LYS cc_start: 0.8702 (tttp) cc_final: 0.6758 (pttt) outliers start: 7 outliers final: 2 residues processed: 35 average time/residue: 0.1216 time to fit residues: 4.8619 Evaluate side-chains 31 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain A 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 7 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.0470 chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.9684 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.126660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100992 restraints weight = 1571.804| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.95 r_work: 0.3410 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1770 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= 0.190 Angle : 0.496 2.969 1749 Z= 0.289 Chirality : 0.052 0.121 231 Planarity : 0.002 0.013 216 Dihedral : 4.289 11.869 186 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 9.09 % Allowed : 17.42 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.51 (0.40), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.30), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.004 0.001 PHE F 94 TYR 0.002 0.001 TYR B 39 *********************** 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 41 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.202 Fit side-chains REVERT: F 83 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7849 (tt0) REVERT: A 71 VAL cc_start: 0.9110 (OUTLIER) cc_final: 0.8786 (t) REVERT: B 83 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8472 (tt0) outliers start: 12 outliers final: 9 residues processed: 38 average time/residue: 0.1122 time to fit residues: 4.9889 Evaluate side-chains 36 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.123844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097559 restraints weight = 1621.023| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.99 r_work: 0.3321 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1293 Z= 0.268 Angle : 0.531 4.131 1749 Z= 0.309 Chirality : 0.053 0.139 231 Planarity : 0.002 0.013 216 Dihedral : 4.436 12.630 186 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.31 (0.42), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.32), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.003 0.001 PHE F 94 TYR 0.003 0.001 TYR F 39 *********************** 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 40 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.132 Fit side-chains REVERT: F 83 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8027 (mm-30) REVERT: A 71 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8750 (t) REVERT: B 45 LYS cc_start: 0.8370 (tttt) cc_final: 0.8095 (mtpp) outliers start: 14 outliers final: 13 residues processed: 37 average time/residue: 0.0973 time to fit residues: 4.2145 Evaluate side-chains 39 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 40 VAL Chi-restraints excluded: chain A residue 66 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.125211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.098967 restraints weight = 1552.079| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.95 r_work: 0.3350 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1966 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= 0.253 Angle : 0.518 3.527 1749 Z= 0.302 Chirality : 0.052 0.132 231 Planarity : 0.002 0.011 216 Dihedral : 4.369 12.739 186 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (0.43), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.33), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.004 0.001 PHE F 94 TYR 0.003 0.001 TYR F 39 *********************** 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 46 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.140 Fit side-chains REVERT: F 83 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8158 (tt0) REVERT: A 58 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7525 (mtpp) REVERT: A 71 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8840 (t) REVERT: B 43 LYS cc_start: 0.8847 (mttp) cc_final: 0.8629 (mttm) REVERT: B 45 LYS cc_start: 0.8411 (tttt) cc_final: 0.8208 (mtpp) REVERT: B 83 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8419 (tt0) outliers start: 17 outliers final: 15 residues processed: 41 average time/residue: 0.1137 time to fit residues: 5.3117 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 : 0.143 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 chunk 13 optimal weight: 0.8980 overall best weight: 1.1964 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.132576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.106265 restraints weight = 1514.097| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.94 r_work: 0.3496 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1293 Z= 0.130 Angle : 0.436 2.811 1749 Z= 0.256 Chirality : 0.049 0.121 231 Planarity : 0.002 0.010 216 Dihedral : 4.041 12.087 186 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 9.85 % Allowed : 20.45 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.46), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.35), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.004 0.001 PHE F 94 TYR 0.002 0.001 TYR A 39 *********************** 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 38 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.142 Fit side-chains REVERT: F 83 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7969 (mm-30) REVERT: A 58 LYS cc_start: 0.7938 (mtpt) cc_final: 0.7534 (mtpp) REVERT: B 43 LYS cc_start: 0.8828 (mttp) cc_final: 0.8602 (mttm) outliers start: 13 outliers final: 10 residues processed: 34 average time/residue: 0.0963 time to fit residues: 3.8642 Evaluate side-chains 33 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 79 GLN 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 B residue 40 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 0.0000 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.123188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.096939 restraints weight = 1604.537| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.92 r_work: 0.3311 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 1293 Z= 0.340 Angle : 0.564 4.035 1749 Z= 0.330 Chirality : 0.054 0.150 231 Planarity : 0.002 0.010 216 Dihedral : 4.443 12.471 186 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.22 % Favored : 82.78 % Rotamer: Outliers : 9.85 % Allowed : 15.15 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.43), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.33), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.003 0.001 PHE F 94 TYR 0.005 0.001 TYR A 39 *********************** 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 41 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.144 Fit side-chains REVERT: F 45 LYS cc_start: 0.8434 (tttt) cc_final: 0.7767 (mttm) REVERT: F 83 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8137 (mm-30) REVERT: A 58 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7394 (mtpp) REVERT: A 61 GLU cc_start: 0.8665 (tt0) cc_final: 0.8328 (tt0) REVERT: B 43 LYS cc_start: 0.8840 (mttp) cc_final: 0.8582 (mttt) REVERT: B 45 LYS cc_start: 0.8425 (tttt) cc_final: 0.8201 (mtpp) outliers start: 13 outliers final: 13 residues processed: 40 average time/residue: 0.1270 time to fit residues: 5.7786 Evaluate side-chains 40 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.125073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.098945 restraints weight = 1564.986| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.93 r_work: 0.3335 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1293 Z= 0.272 Angle : 0.560 4.888 1749 Z= 0.325 Chirality : 0.053 0.160 231 Planarity : 0.002 0.011 216 Dihedral : 4.407 12.470 186 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 9.85 % Allowed : 16.67 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.04 (0.44), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.33), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.004 0.001 PHE F 94 TYR 0.004 0.001 TYR A 39 *********************** 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 39 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.134 Fit side-chains REVERT: A 58 LYS cc_start: 0.7852 (mtpt) cc_final: 0.7411 (mtpp) REVERT: B 45 LYS cc_start: 0.8387 (tttt) cc_final: 0.8172 (mtpp) outliers start: 13 outliers final: 13 residues processed: 38 average time/residue: 0.1281 time to fit residues: 5.5611 Evaluate side-chains 38 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 10.0000 chunk 2 optimal weight: 0.4980 chunk 6 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.125453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.099531 restraints weight = 1554.396| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.90 r_work: 0.3321 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1293 Z= 0.282 Angle : 0.545 3.914 1749 Z= 0.318 Chirality : 0.053 0.135 231 Planarity : 0.002 0.010 216 Dihedral : 4.394 12.726 186 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 10.61 % Allowed : 15.91 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.44), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.33), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.003 0.001 PHE F 94 TYR 0.004 0.001 TYR A 39 *********************** 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 39 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.143 Fit side-chains REVERT: A 58 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7419 (mtpp) REVERT: A 61 GLU cc_start: 0.8640 (tt0) cc_final: 0.8309 (tt0) REVERT: B 45 LYS cc_start: 0.8406 (tttt) cc_final: 0.8191 (mtpp) outliers start: 14 outliers final: 13 residues processed: 38 average time/residue: 0.1205 time to fit residues: 5.2080 Evaluate side-chains 37 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.133391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.107796 restraints weight = 1556.775| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.84 r_work: 0.3465 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1293 Z= 0.140 Angle : 0.484 4.739 1749 Z= 0.282 Chirality : 0.050 0.118 231 Planarity : 0.002 0.010 216 Dihedral : 4.077 11.937 186 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 9.85 % Allowed : 16.67 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.71 (0.46), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.35), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.004 0.001 PHE F 94 TYR 0.002 0.001 TYR F 39 ********************** 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 38 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.176 Fit side-chains REVERT: A 58 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7543 (mtpp) REVERT: B 43 LYS cc_start: 0.8861 (mttp) cc_final: 0.8659 (mttt) outliers start: 13 outliers final: 12 residues processed: 37 average time/residue: 0.1210 time to fit residues: 5.1439 Evaluate side-chains 36 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain A residue 77 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 11 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.128544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.102532 restraints weight = 1635.764| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.88 r_work: 0.3365 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1293 Z= 0.236 Angle : 0.510 3.418 1749 Z= 0.297 Chirality : 0.052 0.142 231 Planarity : 0.002 0.010 216 Dihedral : 4.250 12.245 186 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 9.09 % Allowed : 15.91 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (0.46), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.35), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.004 0.001 PHE F 94 TYR 0.003 0.001 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1119.52 seconds wall clock time: 20 minutes 26.06 seconds (1226.06 seconds total)