Starting phenix.real_space_refine on Mon Feb 10 22:10:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wkt_21708/02_2025/6wkt_21708.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wkt_21708/02_2025/6wkt_21708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wkt_21708/02_2025/6wkt_21708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wkt_21708/02_2025/6wkt_21708.map" model { file = "/net/cci-nas-00/data/ceres_data/6wkt_21708/02_2025/6wkt_21708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wkt_21708/02_2025/6wkt_21708.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 1884 2.51 5 N 556 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 3152 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Restraints were copied for chains: C, B, D Time building chain proxies: 1.71, per 1000 atoms: 0.54 Number of scatterers: 3152 At special positions: 0 Unit cell: (79.056, 63.504, 55.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 620 8.00 N 556 7.00 C 1884 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: 0.71 Conformation dependent library (CDL) restraints added in 426.6 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 58 Processing helix chain 'A' and resid 62 through 82 Processing helix chain 'A' and resid 86 through 107 Processing helix chain 'B' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 58 Processing helix chain 'B' and resid 62 through 82 Processing helix chain 'B' and resid 86 through 107 Processing helix chain 'C' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 58 Processing helix chain 'C' and resid 62 through 82 Processing helix chain 'C' and resid 86 through 107 Processing helix chain 'D' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU D 29 " --> pdb=" O LYS D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 58 Processing helix chain 'D' and resid 62 through 82 Processing helix chain 'D' and resid 86 through 107 296 hydrogen bonds defined for protein. 888 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: 0.85 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 884 1.34 - 1.46: 504 1.46 - 1.58: 1696 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 3192 Sorted by residual: bond pdb=" C ILE B 39 " pdb=" N ARG B 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C ILE A 39 " pdb=" N ARG A 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C ILE D 39 " pdb=" N ARG D 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C ILE C 39 " pdb=" N ARG C 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C THR C 24 " pdb=" O THR C 24 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.17e-02 7.31e+03 3.08e+00 ... (remaining 3187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 4116 1.62 - 3.23: 124 3.23 - 4.85: 24 4.85 - 6.47: 12 6.47 - 8.09: 8 Bond angle restraints: 4284 Sorted by residual: angle pdb=" C GLN D 32 " pdb=" N HIS D 33 " pdb=" CA HIS D 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLN B 32 " pdb=" N HIS B 33 " pdb=" CA HIS B 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLN A 32 " pdb=" N HIS A 33 " pdb=" CA HIS A 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLN C 32 " pdb=" N HIS C 33 " pdb=" CA HIS C 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" O ILE D 39 " pdb=" C ILE D 39 " pdb=" N ARG D 40 " ideal model delta sigma weight residual 121.90 118.01 3.89 1.04e+00 9.25e-01 1.40e+01 ... (remaining 4279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 1820 17.75 - 35.49: 136 35.49 - 53.23: 24 53.23 - 70.97: 0 70.97 - 88.72: 8 Dihedral angle restraints: 1988 sinusoidal: 740 harmonic: 1248 Sorted by residual: dihedral pdb=" CA SER A 36 " pdb=" C SER A 36 " pdb=" N GLY A 37 " pdb=" CA GLY A 37 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER B 36 " pdb=" C SER B 36 " pdb=" N GLY B 37 " pdb=" CA GLY B 37 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER D 36 " pdb=" C SER D 36 " pdb=" N GLY D 37 " pdb=" CA GLY D 37 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 1985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 280 0.034 - 0.068: 148 0.068 - 0.102: 36 0.102 - 0.136: 12 0.136 - 0.170: 4 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA THR D 24 " pdb=" N THR D 24 " pdb=" C THR D 24 " pdb=" CB THR D 24 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA THR C 24 " pdb=" N THR C 24 " pdb=" C THR C 24 " pdb=" CB THR C 24 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA THR B 24 " pdb=" N THR B 24 " pdb=" C THR B 24 " pdb=" CB THR B 24 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 477 not shown) Planarity restraints: 568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 84 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C HIS B 84 " 0.049 2.00e-02 2.50e+03 pdb=" O HIS B 84 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP B 85 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 84 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C HIS D 84 " -0.049 2.00e-02 2.50e+03 pdb=" O HIS D 84 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP D 85 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 84 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C HIS C 84 " 0.049 2.00e-02 2.50e+03 pdb=" O HIS C 84 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP C 85 " -0.016 2.00e-02 2.50e+03 ... (remaining 565 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1012 2.84 - 3.36: 3094 3.36 - 3.87: 5334 3.87 - 4.39: 5872 4.39 - 4.90: 10766 Nonbonded interactions: 26078 Sorted by model distance: nonbonded pdb=" O LYS D 54 " pdb=" OG1 THR D 58 " model vdw 2.329 3.040 nonbonded pdb=" O LYS B 54 " pdb=" OG1 THR B 58 " model vdw 2.329 3.040 nonbonded pdb=" O LYS A 54 " pdb=" OG1 THR A 58 " model vdw 2.329 3.040 nonbonded pdb=" O LYS C 54 " pdb=" OG1 THR C 58 " model vdw 2.329 3.040 nonbonded pdb=" O GLU B 75 " pdb=" OG1 THR B 79 " model vdw 2.426 3.040 ... (remaining 26073 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 0.040 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.200 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.004 0.037 3192 Z= 0.298 Angle : 0.808 8.085 4284 Z= 0.490 Chirality : 0.046 0.170 480 Planarity : 0.006 0.029 568 Dihedral : 13.975 88.716 1164 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % 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: -3.42 (0.29), residues: 416 helix: -1.91 (0.19), residues: 368 sheet: None (None), residues: 0 loop : -3.11 (0.74), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 34 PHE 0.016 0.003 PHE A 23 TYR 0.006 0.002 TYR A 4 ARG 0.001 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.326 Fit side-chains REVERT: A 16 MET cc_start: 0.7205 (mtp) cc_final: 0.6914 (mtm) REVERT: A 80 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6400 (mm-30) REVERT: A 90 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8491 (mm-40) REVERT: B 16 MET cc_start: 0.7189 (mtp) cc_final: 0.6892 (mtm) REVERT: B 80 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6403 (mm-30) REVERT: B 90 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8495 (mm-40) REVERT: C 16 MET cc_start: 0.7198 (mtp) cc_final: 0.6894 (mtm) REVERT: C 80 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6407 (mm-30) REVERT: C 90 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8494 (mm-40) REVERT: D 16 MET cc_start: 0.7207 (mtp) cc_final: 0.6907 (mtm) REVERT: D 80 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6408 (mm-30) REVERT: D 90 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8496 (mm-40) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2462 time to fit residues: 21.2712 Evaluate side-chains 64 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- 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 = 0.4445 r_free = 0.4445 target = 0.225212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.194220 restraints weight = 3193.416| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.34 r_work: 0.3954 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3192 Z= 0.132 Angle : 0.470 4.485 4284 Z= 0.261 Chirality : 0.032 0.098 480 Planarity : 0.003 0.022 568 Dihedral : 4.059 12.818 440 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.37), residues: 416 helix: 0.95 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -2.55 (0.66), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 88 PHE 0.006 0.001 PHE A 23 TYR 0.004 0.001 TYR A 4 ARG 0.006 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.339 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1546 time to fit residues: 15.6384 Evaluate side-chains 80 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.228994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.199257 restraints weight = 3117.643| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.27 r_work: 0.3999 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3192 Z= 0.141 Angle : 0.484 4.928 4284 Z= 0.271 Chirality : 0.032 0.104 480 Planarity : 0.003 0.018 568 Dihedral : 3.689 11.872 440 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.38), residues: 416 helix: 2.09 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.71 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 34 PHE 0.011 0.002 PHE A 23 TYR 0.003 0.001 TYR B 4 ARG 0.006 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.357 Fit side-chains REVERT: A 59 ASP cc_start: 0.8230 (t0) cc_final: 0.7628 (t70) REVERT: B 59 ASP cc_start: 0.8245 (t0) cc_final: 0.7645 (t70) REVERT: C 59 ASP cc_start: 0.8212 (t0) cc_final: 0.7608 (t70) REVERT: D 59 ASP cc_start: 0.8274 (t0) cc_final: 0.7678 (t70) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1642 time to fit residues: 14.9632 Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4466 r_free = 0.4466 target = 0.227100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.198009 restraints weight = 3074.611| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.20 r_work: 0.3965 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3192 Z= 0.202 Angle : 0.503 4.414 4284 Z= 0.280 Chirality : 0.034 0.103 480 Planarity : 0.003 0.014 568 Dihedral : 3.665 10.692 440 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.38), residues: 416 helix: 2.27 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.41 (0.75), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 34 PHE 0.011 0.002 PHE A 62 TYR 0.005 0.001 TYR A 4 ARG 0.006 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.347 Fit side-chains REVERT: A 59 ASP cc_start: 0.8303 (t0) cc_final: 0.7760 (t70) REVERT: B 59 ASP cc_start: 0.8330 (t0) cc_final: 0.7794 (t70) REVERT: C 59 ASP cc_start: 0.8315 (t0) cc_final: 0.7773 (t70) REVERT: D 59 ASP cc_start: 0.8346 (t0) cc_final: 0.7812 (t70) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1666 time to fit residues: 15.2260 Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.218771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.190351 restraints weight = 3118.777| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.17 r_work: 0.3910 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3192 Z= 0.279 Angle : 0.561 4.286 4284 Z= 0.310 Chirality : 0.037 0.112 480 Planarity : 0.003 0.013 568 Dihedral : 3.905 11.068 440 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.37), residues: 416 helix: 2.05 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -1.36 (0.77), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 88 PHE 0.014 0.003 PHE B 62 TYR 0.004 0.001 TYR A 4 ARG 0.006 0.001 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.376 Fit side-chains REVERT: A 59 ASP cc_start: 0.8270 (t0) cc_final: 0.7928 (t70) REVERT: B 59 ASP cc_start: 0.8280 (t0) cc_final: 0.7946 (t70) REVERT: C 59 ASP cc_start: 0.8271 (t0) cc_final: 0.7928 (t70) REVERT: D 59 ASP cc_start: 0.8296 (t0) cc_final: 0.7958 (t70) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1919 time to fit residues: 18.8522 Evaluate side-chains 84 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 9 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS B 86 HIS C 86 HIS D 86 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.229114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.198507 restraints weight = 3169.677| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.34 r_work: 0.4011 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3192 Z= 0.153 Angle : 0.503 4.588 4284 Z= 0.279 Chirality : 0.034 0.099 480 Planarity : 0.003 0.021 568 Dihedral : 3.857 11.417 440 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 15.80 % Favored : 84.20 % 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: 3.19 (0.38), residues: 416 helix: 2.54 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.93 (0.81), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 34 PHE 0.010 0.002 PHE A 23 TYR 0.004 0.001 TYR A 4 ARG 0.007 0.001 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.359 Fit side-chains REVERT: A 59 ASP cc_start: 0.8272 (t0) cc_final: 0.7860 (t70) REVERT: B 59 ASP cc_start: 0.8282 (t0) cc_final: 0.7870 (t70) REVERT: C 59 ASP cc_start: 0.8282 (t0) cc_final: 0.7868 (t70) REVERT: D 59 ASP cc_start: 0.8292 (t0) cc_final: 0.7878 (t70) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1643 time to fit residues: 15.1530 Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.221273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.191480 restraints weight = 3096.034| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.23 r_work: 0.3953 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3192 Z= 0.259 Angle : 0.558 4.236 4284 Z= 0.307 Chirality : 0.036 0.108 480 Planarity : 0.003 0.015 568 Dihedral : 3.993 11.413 440 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 16.09 % Favored : 83.91 % 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: 3.00 (0.38), residues: 416 helix: 2.38 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.73 (0.85), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 34 PHE 0.012 0.003 PHE D 62 TYR 0.006 0.002 TYR A 4 ARG 0.006 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.398 Fit side-chains REVERT: A 59 ASP cc_start: 0.8294 (t0) cc_final: 0.7990 (t70) REVERT: A 75 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7776 (mm-30) REVERT: B 59 ASP cc_start: 0.8272 (t0) cc_final: 0.7971 (t70) REVERT: B 75 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7770 (mm-30) REVERT: C 59 ASP cc_start: 0.8286 (t0) cc_final: 0.7980 (t70) REVERT: C 75 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7792 (mm-30) REVERT: D 59 ASP cc_start: 0.8298 (t0) cc_final: 0.7998 (t70) REVERT: D 75 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7772 (mm-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1938 time to fit residues: 17.3755 Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4486 r_free = 0.4486 target = 0.229076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.199376 restraints weight = 3104.380| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.26 r_work: 0.4027 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3192 Z= 0.144 Angle : 0.488 4.550 4284 Z= 0.272 Chirality : 0.033 0.107 480 Planarity : 0.003 0.021 568 Dihedral : 3.747 11.186 440 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 16.09 % Favored : 83.91 % 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: 3.72 (0.38), residues: 416 helix: 2.86 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.43 (0.89), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 34 PHE 0.010 0.002 PHE C 23 TYR 0.004 0.001 TYR C 4 ARG 0.007 0.001 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.355 Fit side-chains REVERT: A 59 ASP cc_start: 0.8423 (t0) cc_final: 0.8117 (t70) REVERT: B 59 ASP cc_start: 0.8403 (t0) cc_final: 0.8095 (t70) REVERT: C 59 ASP cc_start: 0.8419 (t0) cc_final: 0.8110 (t70) REVERT: D 59 ASP cc_start: 0.8397 (t0) cc_final: 0.8087 (t70) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1615 time to fit residues: 14.7553 Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.4455 r_free = 0.4455 target = 0.225952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.196035 restraints weight = 3086.108| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.27 r_work: 0.3991 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3192 Z= 0.189 Angle : 0.506 4.237 4284 Z= 0.280 Chirality : 0.034 0.108 480 Planarity : 0.003 0.024 568 Dihedral : 3.771 11.096 440 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 16.09 % Favored : 83.91 % 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: 3.67 (0.38), residues: 416 helix: 2.84 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.55 (0.87), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 34 PHE 0.012 0.002 PHE B 62 TYR 0.005 0.001 TYR A 4 ARG 0.008 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.371 Fit side-chains REVERT: A 59 ASP cc_start: 0.8397 (t0) cc_final: 0.8104 (t70) REVERT: A 75 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7817 (mm-30) REVERT: B 59 ASP cc_start: 0.8381 (t0) cc_final: 0.8086 (t70) REVERT: B 75 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7818 (mm-30) REVERT: C 59 ASP cc_start: 0.8390 (t0) cc_final: 0.8094 (t70) REVERT: C 75 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7824 (mm-30) REVERT: D 59 ASP cc_start: 0.8394 (t0) cc_final: 0.8102 (t70) REVERT: D 75 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7811 (mm-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1601 time to fit residues: 14.6350 Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.225925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.196208 restraints weight = 3073.413| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.25 r_work: 0.3994 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3192 Z= 0.184 Angle : 0.508 4.262 4284 Z= 0.282 Chirality : 0.034 0.109 480 Planarity : 0.003 0.016 568 Dihedral : 3.755 11.127 440 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 16.09 % Favored : 83.91 % 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: 3.69 (0.38), residues: 416 helix: 2.84 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.49 (0.87), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 34 PHE 0.012 0.002 PHE A 62 TYR 0.005 0.001 TYR A 4 ARG 0.006 0.001 ARG D 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.371 Fit side-chains REVERT: A 59 ASP cc_start: 0.8376 (t0) cc_final: 0.8090 (t70) REVERT: A 75 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7737 (mm-30) REVERT: B 59 ASP cc_start: 0.8364 (t0) cc_final: 0.8076 (t70) REVERT: B 75 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7732 (mm-30) REVERT: C 59 ASP cc_start: 0.8376 (t0) cc_final: 0.8086 (t70) REVERT: C 75 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7739 (mm-30) REVERT: D 59 ASP cc_start: 0.8377 (t0) cc_final: 0.8090 (t70) REVERT: D 75 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7732 (mm-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1602 time to fit residues: 14.6739 Evaluate side-chains 76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 7 optimal weight: 0.0370 overall best weight: 1.3864 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.226685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.196743 restraints weight = 3114.110| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.28 r_work: 0.3998 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3192 Z= 0.175 Angle : 0.500 4.225 4284 Z= 0.278 Chirality : 0.034 0.107 480 Planarity : 0.003 0.016 568 Dihedral : 3.719 11.161 440 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 16.09 % Favored : 83.91 % 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: 3.82 (0.38), residues: 416 helix: 2.94 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.48 (0.87), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 34 PHE 0.011 0.002 PHE D 62 TYR 0.005 0.001 TYR D 4 ARG 0.007 0.001 ARG C 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1612.30 seconds wall clock time: 30 minutes 54.59 seconds (1854.59 seconds total)