Starting phenix.real_space_refine on Mon Feb 10 19:26:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4c_31707/02_2025/7v4c_31707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4c_31707/02_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_31707/02_2025/7v4c_31707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4c_31707/02_2025/7v4c_31707.map" model { file = "/net/cci-nas-00/data/ceres_data/7v4c_31707/02_2025/7v4c_31707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4c_31707/02_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-5592/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: 0.85, per 1000 atoms: 0.66 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 419.3 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: 0.11 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: 0.17 Time building geometry restraints manager: 0.29 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.640 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.470 ------------------------------------------------------------------------------- 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 : 0.132 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: 0.1272 time to fit residues: 4.8495 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 : 0.117 ------------------------------------------------------------------------------- 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: 3.9990 chunk 8 optimal weight: 3.9990 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: 0.8027 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 : 0.144 Fit side-chains REVERT: F 43 LYS cc_start: 0.8669 (mttp) cc_final: 0.8468 (mttm) REVERT: F 83 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8085 (mm-30) REVERT: A 71 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8839 (t) REVERT: B 80 LYS cc_start: 0.8699 (tttp) cc_final: 0.6754 (pttt) outliers start: 7 outliers final: 2 residues processed: 35 average time/residue: 0.1096 time to fit residues: 4.4301 Evaluate side-chains 32 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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: 0.3980 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.120990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.094921 restraints weight = 1593.987| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.01 r_work: 0.3327 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 1293 Z= 0.347 Angle : 0.599 4.082 1749 Z= 0.348 Chirality : 0.055 0.147 231 Planarity : 0.002 0.014 216 Dihedral : 4.711 13.269 186 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Rotamer: Outliers : 9.09 % Allowed : 18.94 % 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: -5.68 (0.40), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.004 0.001 PHE F 94 TYR 0.004 0.002 TYR A 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 42 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.149 Fit side-chains REVERT: F 43 LYS cc_start: 0.8723 (mttp) cc_final: 0.8508 (mttp) REVERT: F 45 LYS cc_start: 0.8442 (tttt) cc_final: 0.7814 (mttm) REVERT: F 83 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8053 (tt0) REVERT: A 61 GLU cc_start: 0.8643 (tt0) cc_final: 0.8347 (tt0) REVERT: B 45 LYS cc_start: 0.8519 (tttt) cc_final: 0.8237 (mtpp) outliers start: 12 outliers final: 10 residues processed: 40 average time/residue: 0.1289 time to fit residues: 5.7912 Evaluate side-chains 37 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.125498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.099636 restraints weight = 1625.969| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.97 r_work: 0.3388 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1881 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= 0.231 Angle : 0.529 3.771 1749 Z= 0.306 Chirality : 0.052 0.134 231 Planarity : 0.002 0.012 216 Dihedral : 4.470 12.792 186 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 9.09 % Allowed : 18.94 % 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: -5.36 (0.42), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.32), 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 0.002 0.001 TYR B 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 39 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.146 Fit side-chains REVERT: F 83 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8102 (mm-30) REVERT: A 71 VAL cc_start: 0.9044 (p) cc_final: 0.8761 (t) REVERT: B 83 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8452 (tt0) outliers start: 12 outliers final: 10 residues processed: 36 average time/residue: 0.0989 time to fit residues: 4.1780 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 : 0.111 ------------------------------------------------------------------------------- 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 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 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 2 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.127839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.101772 restraints weight = 1554.025| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.97 r_work: 0.3392 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2054 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= 0.182 Angle : 0.474 2.895 1749 Z= 0.277 Chirality : 0.050 0.120 231 Planarity : 0.002 0.010 216 Dihedral : 4.190 12.336 186 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % 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 (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 0.004 0.001 PHE F 94 TYR 0.002 0.001 TYR A 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 43 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.145 Fit side-chains REVERT: F 83 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8035 (mm-30) REVERT: A 58 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7591 (mtpp) REVERT: A 71 VAL cc_start: 0.9011 (p) cc_final: 0.8797 (t) REVERT: B 83 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8381 (tt0) outliers start: 15 outliers final: 13 residues processed: 40 average time/residue: 0.1107 time to fit residues: 5.1394 Evaluate side-chains 41 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 27 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 12 optimal weight: 0.0370 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 1.1862 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.133456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.106889 restraints weight = 1518.167| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.96 r_work: 0.3408 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2314 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= 0.129 Angle : 0.432 2.875 1749 Z= 0.253 Chirality : 0.049 0.119 231 Planarity : 0.002 0.010 216 Dihedral : 3.990 11.786 186 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 10.61 % Allowed : 16.67 % 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: -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 40 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.114 Fit side-chains REVERT: F 83 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7974 (mm-30) REVERT: A 58 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7593 (mtpp) REVERT: B 43 LYS cc_start: 0.8883 (mttp) cc_final: 0.8648 (mttt) outliers start: 14 outliers final: 11 residues processed: 37 average time/residue: 0.1053 time to fit residues: 4.4918 Evaluate side-chains 35 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.129867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.103237 restraints weight = 1579.683| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.00 r_work: 0.3463 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1293 Z= 0.184 Angle : 0.458 3.130 1749 Z= 0.268 Chirality : 0.050 0.119 231 Planarity : 0.002 0.010 216 Dihedral : 4.028 11.551 186 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 9.85 % Allowed : 14.39 % Favored : 75.76 % 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 (0.45), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.34), 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 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 39 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.147 Fit side-chains REVERT: F 83 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8073 (mm-30) REVERT: A 58 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7576 (mtpp) outliers start: 13 outliers final: 13 residues processed: 37 average time/residue: 0.1084 time to fit residues: 4.6194 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 : 0.141 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 79 GLN 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: 9.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.122729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.096276 restraints weight = 1588.518| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.94 r_work: 0.3352 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 1293 Z= 0.354 Angle : 0.579 4.530 1749 Z= 0.337 Chirality : 0.054 0.152 231 Planarity : 0.002 0.012 216 Dihedral : 4.471 12.555 186 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.11 % Favored : 83.89 % Rotamer: Outliers : 9.85 % Allowed : 12.88 % Favored : 77.27 % 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 0.001 0.001 HIS A 50 PHE 0.003 0.001 PHE F 94 TYR 0.005 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 41 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.143 Fit side-chains REVERT: F 45 LYS cc_start: 0.8423 (tttt) cc_final: 0.7715 (mttm) REVERT: F 83 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8102 (mm-30) REVERT: A 58 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7353 (mtpp) REVERT: A 61 GLU cc_start: 0.8658 (tt0) cc_final: 0.8323 (tt0) REVERT: B 45 LYS cc_start: 0.8352 (tttt) cc_final: 0.8132 (mtpp) outliers start: 13 outliers final: 13 residues processed: 40 average time/residue: 0.1331 time to fit residues: 5.9956 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 : 0.144 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.130390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.103803 restraints weight = 1547.298| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.97 r_work: 0.3468 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2418 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= 0.157 Angle : 0.493 4.761 1749 Z= 0.286 Chirality : 0.051 0.124 231 Planarity : 0.002 0.010 216 Dihedral : 4.188 12.093 186 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 9.85 % Allowed : 13.64 % Favored : 76.52 % 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 B 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 38 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.139 Fit side-chains REVERT: F 83 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8032 (mm-30) REVERT: A 58 LYS cc_start: 0.7965 (mtpt) cc_final: 0.7533 (mtpp) outliers start: 13 outliers final: 12 residues processed: 37 average time/residue: 0.1060 time to fit residues: 4.5196 Evaluate side-chains 37 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 7 optimal weight: 8.9990 chunk 9 optimal weight: 0.3980 chunk 11 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.134207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.108664 restraints weight = 1563.750| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.79 r_work: 0.3412 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2497 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= 0.154 Angle : 0.454 3.306 1749 Z= 0.265 Chirality : 0.050 0.118 231 Planarity : 0.002 0.010 216 Dihedral : 4.039 11.582 186 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 9.09 % Allowed : 15.15 % Favored : 75.76 % 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: -4.50 (0.47), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.36), 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 0.002 0.001 TYR A 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 37 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.155 Fit side-chains REVERT: A 58 LYS cc_start: 0.8021 (mtpt) cc_final: 0.7599 (mtpp) outliers start: 12 outliers final: 12 residues processed: 36 average time/residue: 0.1112 time to fit residues: 4.7465 Evaluate side-chains 37 residues out of total 132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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: 10.0000 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.126104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.100121 restraints weight = 1600.363| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.87 r_work: 0.3361 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2423 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= 0.244 Angle : 0.536 5.149 1749 Z= 0.310 Chirality : 0.052 0.143 231 Planarity : 0.002 0.010 216 Dihedral : 4.296 11.602 186 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 9.85 % Allowed : 14.39 % Favored : 75.76 % 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: -4.60 (0.47), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.36), 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 0.003 0.001 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1110.38 seconds wall clock time: 21 minutes 6.47 seconds (1266.47 seconds total)