Starting phenix.real_space_refine on Fri Aug 22 13:06:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wkt_21708/08_2025/6wkt_21708.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wkt_21708/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/6wkt_21708/08_2025/6wkt_21708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wkt_21708/08_2025/6wkt_21708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wkt_21708/08_2025/6wkt_21708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wkt_21708/08_2025/6wkt_21708.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D Time building chain proxies: 0.98, per 1000 atoms: 0.31 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: 0.27 Conformation dependent library (CDL) restraints added in 127.5 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.06 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: 0.45 Time building geometry restraints manager: 0.38 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.790 Find NCS groups from input model: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.260 ------------------------------------------------------------------------------- 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= 0.264 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG B 40 TYR 0.006 0.002 TYR A 4 PHE 0.016 0.003 PHE A 23 HIS 0.004 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 3192) covalent geometry : angle 0.80782 ( 4284) hydrogen bonds : bond 0.09048 ( 296) hydrogen bonds : angle 4.72730 ( 888) *********************** 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 : 0.120 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: 0.0976 time to fit residues: 8.4343 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 : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.4440 r_free = 0.4440 target = 0.224777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.193932 restraints weight = 3187.719| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.34 r_work: 0.3945 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1444 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= 0.116 Angle : 0.472 4.445 4284 Z= 0.262 Chirality : 0.033 0.099 480 Planarity : 0.003 0.022 568 Dihedral : 4.052 12.609 440 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.37), residues: 416 helix: 0.94 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -2.52 (0.66), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 104 TYR 0.004 0.001 TYR C 4 PHE 0.006 0.001 PHE B 62 HIS 0.002 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 3192) covalent geometry : angle 0.47156 ( 4284) hydrogen bonds : bond 0.04152 ( 296) hydrogen bonds : angle 3.05369 ( 888) *********************** 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 80 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.127 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0673 time to fit residues: 6.5165 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 : 0.115 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4487 r_free = 0.4487 target = 0.229688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.199022 restraints weight = 3135.568| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.29 r_work: 0.3997 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3192 Z= 0.122 Angle : 0.504 4.792 4284 Z= 0.280 Chirality : 0.033 0.105 480 Planarity : 0.003 0.020 568 Dihedral : 3.838 11.807 440 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.15 % Allowed : 12.64 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.38), residues: 416 helix: 1.97 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.73 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 104 TYR 0.004 0.001 TYR B 4 PHE 0.008 0.002 PHE C 23 HIS 0.002 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 3192) covalent geometry : angle 0.50371 ( 4284) hydrogen bonds : bond 0.04173 ( 296) hydrogen bonds : angle 3.05590 ( 888) *********************** 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 84 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.123 Fit side-chains REVERT: A 59 ASP cc_start: 0.8091 (t0) cc_final: 0.7450 (t70) REVERT: B 59 ASP cc_start: 0.8062 (t0) cc_final: 0.7419 (t70) REVERT: C 59 ASP cc_start: 0.8087 (t0) cc_final: 0.7448 (t70) REVERT: D 59 ASP cc_start: 0.8090 (t0) cc_final: 0.7445 (t70) outliers start: 4 outliers final: 0 residues processed: 80 average time/residue: 0.0510 time to fit residues: 5.0263 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 : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.227702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.198360 restraints weight = 3124.253| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.24 r_work: 0.4006 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3192 Z= 0.119 Angle : 0.472 4.590 4284 Z= 0.265 Chirality : 0.032 0.100 480 Planarity : 0.003 0.022 568 Dihedral : 3.598 11.184 440 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.72 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.07 (0.38), residues: 416 helix: 2.51 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.35 (0.75), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 104 TYR 0.004 0.001 TYR C 4 PHE 0.012 0.002 PHE A 23 HIS 0.002 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 3192) covalent geometry : angle 0.47179 ( 4284) hydrogen bonds : bond 0.04063 ( 296) hydrogen bonds : angle 2.85551 ( 888) *********************** 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 : 0.127 Fit side-chains REVERT: A 59 ASP cc_start: 0.8270 (t0) cc_final: 0.7718 (t70) REVERT: A 75 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7673 (mm-30) REVERT: B 59 ASP cc_start: 0.8282 (t0) cc_final: 0.7729 (t70) REVERT: B 75 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7678 (mm-30) REVERT: C 59 ASP cc_start: 0.8282 (t0) cc_final: 0.7727 (t70) REVERT: C 75 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7677 (mm-30) REVERT: D 59 ASP cc_start: 0.8304 (t0) cc_final: 0.7755 (t70) REVERT: D 75 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7672 (mm-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0566 time to fit residues: 5.2139 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 : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.225771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.195614 restraints weight = 3109.069| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.35 r_work: 0.3934 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3192 Z= 0.155 Angle : 0.509 4.308 4284 Z= 0.283 Chirality : 0.035 0.108 480 Planarity : 0.003 0.012 568 Dihedral : 3.678 10.678 440 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.52 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.37), residues: 416 helix: 2.46 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -1.18 (0.78), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 104 TYR 0.005 0.001 TYR A 4 PHE 0.011 0.002 PHE B 62 HIS 0.002 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3192) covalent geometry : angle 0.50930 ( 4284) hydrogen bonds : bond 0.04412 ( 296) hydrogen bonds : angle 3.03289 ( 888) *********************** 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 72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.128 Fit side-chains REVERT: A 59 ASP cc_start: 0.8137 (t0) cc_final: 0.7637 (t70) REVERT: B 59 ASP cc_start: 0.8127 (t0) cc_final: 0.7624 (t70) REVERT: C 59 ASP cc_start: 0.8135 (t0) cc_final: 0.7637 (t70) REVERT: D 59 ASP cc_start: 0.8134 (t0) cc_final: 0.7629 (t70) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0787 time to fit residues: 6.7653 Evaluate side-chains 72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4495 r_free = 0.4495 target = 0.230352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.200744 restraints weight = 3089.722| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.32 r_work: 0.4006 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2373 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= 0.116 Angle : 0.462 4.631 4284 Z= 0.261 Chirality : 0.033 0.101 480 Planarity : 0.003 0.019 568 Dihedral : 3.539 10.996 440 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.72 (0.37), residues: 416 helix: 2.91 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.86 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 104 TYR 0.004 0.001 TYR A 4 PHE 0.010 0.002 PHE D 23 HIS 0.002 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 3192) covalent geometry : angle 0.46224 ( 4284) hydrogen bonds : bond 0.04082 ( 296) hydrogen bonds : angle 2.83009 ( 888) *********************** 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 : 0.071 Fit side-chains REVERT: A 59 ASP cc_start: 0.8237 (t0) cc_final: 0.7720 (t70) REVERT: A 75 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7601 (mm-30) REVERT: B 59 ASP cc_start: 0.8245 (t0) cc_final: 0.7725 (t70) REVERT: B 75 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7594 (mm-30) REVERT: C 59 ASP cc_start: 0.8256 (t0) cc_final: 0.7740 (t70) REVERT: C 75 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7602 (mm-30) REVERT: D 59 ASP cc_start: 0.8260 (t0) cc_final: 0.7743 (t70) REVERT: D 75 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7585 (mm-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0643 time to fit residues: 5.8185 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 : 0.100 ------------------------------------------------------------------------------- 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: 8.9990 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4470 r_free = 0.4470 target = 0.227475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.199459 restraints weight = 3141.561| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.16 r_work: 0.4014 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3192 Z= 0.141 Angle : 0.494 4.255 4284 Z= 0.276 Chirality : 0.034 0.105 480 Planarity : 0.003 0.018 568 Dihedral : 3.596 10.691 440 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.37), residues: 416 helix: 2.85 (0.23), residues: 360 sheet: None (None), residues: 0 loop : -0.70 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 104 TYR 0.005 0.001 TYR D 4 PHE 0.012 0.002 PHE D 62 HIS 0.002 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3192) covalent geometry : angle 0.49359 ( 4284) hydrogen bonds : bond 0.04297 ( 296) hydrogen bonds : angle 2.94242 ( 888) *********************** 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 : 0.122 Fit side-chains REVERT: A 59 ASP cc_start: 0.8360 (t0) cc_final: 0.7910 (t70) REVERT: A 75 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 59 ASP cc_start: 0.8352 (t0) cc_final: 0.7903 (t70) REVERT: B 75 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7679 (mm-30) REVERT: C 59 ASP cc_start: 0.8341 (t0) cc_final: 0.7884 (t70) REVERT: C 75 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7685 (mm-30) REVERT: D 59 ASP cc_start: 0.8384 (t0) cc_final: 0.7944 (t70) REVERT: D 75 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7666 (mm-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0724 time to fit residues: 6.6520 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 : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4479 r_free = 0.4479 target = 0.229560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.200616 restraints weight = 3134.093| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.24 r_work: 0.4021 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2503 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= 0.114 Angle : 0.458 4.459 4284 Z= 0.259 Chirality : 0.033 0.105 480 Planarity : 0.003 0.023 568 Dihedral : 3.462 10.441 440 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.18 (0.37), residues: 416 helix: 3.21 (0.23), residues: 360 sheet: None (None), residues: 0 loop : -0.67 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 104 TYR 0.004 0.001 TYR C 4 PHE 0.011 0.002 PHE C 23 HIS 0.002 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 3192) covalent geometry : angle 0.45782 ( 4284) hydrogen bonds : bond 0.04025 ( 296) hydrogen bonds : angle 2.79043 ( 888) *********************** 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 80 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.074 Fit side-chains REVERT: A 59 ASP cc_start: 0.8332 (t0) cc_final: 0.7920 (t70) REVERT: A 75 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7632 (mm-30) REVERT: A 80 GLU cc_start: 0.7480 (tp30) cc_final: 0.7086 (mm-30) REVERT: B 59 ASP cc_start: 0.8329 (t0) cc_final: 0.7918 (t70) REVERT: B 75 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7624 (mm-30) REVERT: B 80 GLU cc_start: 0.7501 (tp30) cc_final: 0.7109 (mm-30) REVERT: C 59 ASP cc_start: 0.8341 (t0) cc_final: 0.7932 (t70) REVERT: C 75 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7640 (mm-30) REVERT: C 80 GLU cc_start: 0.7486 (tp30) cc_final: 0.7094 (mm-30) REVERT: D 59 ASP cc_start: 0.8341 (t0) cc_final: 0.7932 (t70) REVERT: D 75 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7612 (mm-30) REVERT: D 80 GLU cc_start: 0.7487 (tp30) cc_final: 0.7093 (mm-30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0495 time to fit residues: 4.8197 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 : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4471 r_free = 0.4471 target = 0.227827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.198564 restraints weight = 3132.321| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.23 r_work: 0.4009 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3192 Z= 0.127 Angle : 0.465 4.184 4284 Z= 0.262 Chirality : 0.033 0.106 480 Planarity : 0.003 0.021 568 Dihedral : 3.431 10.074 440 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.16 (0.37), residues: 416 helix: 3.21 (0.23), residues: 360 sheet: None (None), residues: 0 loop : -0.77 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 104 TYR 0.004 0.001 TYR D 4 PHE 0.010 0.002 PHE D 23 HIS 0.002 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3192) covalent geometry : angle 0.46539 ( 4284) hydrogen bonds : bond 0.04127 ( 296) hydrogen bonds : angle 2.83911 ( 888) *********************** 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 72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.142 Fit side-chains REVERT: A 59 ASP cc_start: 0.8373 (t0) cc_final: 0.7978 (t70) REVERT: B 59 ASP cc_start: 0.8363 (t0) cc_final: 0.7967 (t70) REVERT: C 59 ASP cc_start: 0.8381 (t0) cc_final: 0.7987 (t70) REVERT: D 59 ASP cc_start: 0.8376 (t0) cc_final: 0.7983 (t70) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0492 time to fit residues: 4.4008 Evaluate side-chains 72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4507 r_free = 0.4507 target = 0.232272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.203422 restraints weight = 3051.008| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.22 r_work: 0.4063 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2709 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= 0.115 Angle : 0.455 4.329 4284 Z= 0.257 Chirality : 0.033 0.106 480 Planarity : 0.003 0.023 568 Dihedral : 3.354 9.765 440 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.46 (0.37), residues: 416 helix: 3.42 (0.23), residues: 360 sheet: None (None), residues: 0 loop : -0.70 (0.85), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 104 TYR 0.004 0.001 TYR C 4 PHE 0.011 0.002 PHE C 23 HIS 0.002 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 3192) covalent geometry : angle 0.45472 ( 4284) hydrogen bonds : bond 0.03985 ( 296) hydrogen bonds : angle 2.77476 ( 888) ********************** 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 72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.069 Fit side-chains REVERT: A 59 ASP cc_start: 0.8192 (t0) cc_final: 0.7799 (t70) REVERT: A 75 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7888 (mm-30) REVERT: B 59 ASP cc_start: 0.8189 (t0) cc_final: 0.7791 (t70) REVERT: B 75 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7893 (mm-30) REVERT: C 59 ASP cc_start: 0.8210 (t0) cc_final: 0.7811 (t70) REVERT: C 75 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7894 (mm-30) REVERT: D 59 ASP cc_start: 0.8195 (t0) cc_final: 0.7797 (t70) REVERT: D 75 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7878 (mm-30) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0467 time to fit residues: 4.1059 Evaluate side-chains 72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4465 r_free = 0.4465 target = 0.227757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.198975 restraints weight = 3118.773| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.21 r_work: 0.4005 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2621 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= 0.131 Angle : 0.472 4.257 4284 Z= 0.265 Chirality : 0.034 0.107 480 Planarity : 0.003 0.021 568 Dihedral : 3.358 8.891 440 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.29 (0.37), residues: 416 helix: 3.30 (0.23), residues: 360 sheet: None (None), residues: 0 loop : -0.71 (0.85), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 104 TYR 0.004 0.001 TYR A 4 PHE 0.010 0.002 PHE A 23 HIS 0.003 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3192) covalent geometry : angle 0.47219 ( 4284) hydrogen bonds : bond 0.04155 ( 296) hydrogen bonds : angle 2.84811 ( 888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 716.02 seconds wall clock time: 14 minutes 5.33 seconds (845.33 seconds total)