Starting phenix.real_space_refine on Wed Mar 5 17:06:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wkt_21708/03_2025/6wkt_21708.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wkt_21708/03_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_21708/03_2025/6wkt_21708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wkt_21708/03_2025/6wkt_21708.map" model { file = "/net/cci-nas-00/data/ceres_data/6wkt_21708/03_2025/6wkt_21708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wkt_21708/03_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-5624/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: 1.80, per 1000 atoms: 0.57 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: 0.72 Conformation dependent library (CDL) restraints added in 381.7 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: 0.25 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: 0.88 Time building geometry restraints manager: 0.88 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: 0.080 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.600 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.880 ------------------------------------------------------------------------------- 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 : 0.375 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: 0.2538 time to fit residues: 21.8995 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 : 0.361 ------------------------------------------------------------------------------- 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 = 0.225401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.194596 restraints weight = 3196.932| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.35 r_work: 0.3953 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- 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 : 0.347 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1503 time to fit residues: 15.3110 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 : 0.348 ------------------------------------------------------------------------------- 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: 6.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4475 r_free = 0.4475 target = 0.228307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.198465 restraints weight = 3114.876| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.27 r_work: 0.3985 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2080 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= 0.144 Angle : 0.485 4.892 4284 Z= 0.271 Chirality : 0.032 0.105 480 Planarity : 0.003 0.018 568 Dihedral : 3.699 11.818 440 Min Nonbonded Distance : 2.576 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: 2.39 (0.38), residues: 416 helix: 2.06 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.70 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 34 PHE 0.011 0.002 PHE B 23 TYR 0.004 0.001 TYR B 4 ARG 0.006 0.001 ARG A 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 : 0.371 Fit side-chains REVERT: A 59 ASP cc_start: 0.8230 (t0) cc_final: 0.7611 (t70) REVERT: B 59 ASP cc_start: 0.8240 (t0) cc_final: 0.7623 (t70) REVERT: C 59 ASP cc_start: 0.8218 (t0) cc_final: 0.7599 (t70) REVERT: D 59 ASP cc_start: 0.8283 (t0) cc_final: 0.7674 (t70) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1629 time to fit residues: 14.9036 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 : 0.343 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4447 r_free = 0.4447 target = 0.225242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.196020 restraints weight = 3081.576| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.19 r_work: 0.3983 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2142 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= 0.185 Angle : 0.493 4.469 4284 Z= 0.276 Chirality : 0.034 0.103 480 Planarity : 0.003 0.015 568 Dihedral : 3.637 10.597 440 Min Nonbonded Distance : 2.552 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: 2.82 (0.38), residues: 416 helix: 2.34 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.38 (0.75), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 34 PHE 0.011 0.002 PHE C 62 TYR 0.004 0.001 TYR C 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 : 0.350 Fit side-chains REVERT: A 59 ASP cc_start: 0.8286 (t0) cc_final: 0.7743 (t70) REVERT: B 59 ASP cc_start: 0.8285 (t0) cc_final: 0.7746 (t70) REVERT: C 59 ASP cc_start: 0.8287 (t0) cc_final: 0.7743 (t70) REVERT: D 59 ASP cc_start: 0.8312 (t0) cc_final: 0.7779 (t70) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1565 time to fit residues: 14.4261 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 : 0.340 ------------------------------------------------------------------------------- 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: 1.9990 chunk 7 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.221926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.193033 restraints weight = 3133.517| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 2.21 r_work: 0.3949 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3192 Z= 0.214 Angle : 0.523 4.331 4284 Z= 0.290 Chirality : 0.035 0.109 480 Planarity : 0.003 0.012 568 Dihedral : 3.730 10.795 440 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.85 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: 2.90 (0.37), residues: 416 helix: 2.36 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -1.13 (0.79), 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 A 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 72 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.356 Fit side-chains REVERT: A 59 ASP cc_start: 0.8263 (t0) cc_final: 0.7912 (t70) REVERT: B 59 ASP cc_start: 0.8263 (t0) cc_final: 0.7912 (t70) REVERT: C 59 ASP cc_start: 0.8254 (t0) cc_final: 0.7897 (t70) REVERT: D 59 ASP cc_start: 0.8287 (t0) cc_final: 0.7939 (t70) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1703 time to fit residues: 14.8395 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 : 0.336 ------------------------------------------------------------------------------- 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: 0.9980 chunk 19 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4480 r_free = 0.4480 target = 0.228667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.200674 restraints weight = 3146.379| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.17 r_work: 0.4003 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2327 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= 0.156 Angle : 0.479 4.590 4284 Z= 0.269 Chirality : 0.033 0.104 480 Planarity : 0.003 0.018 568 Dihedral : 3.609 10.837 440 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 14.66 % Favored : 85.34 % 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: 3.52 (0.38), residues: 416 helix: 2.76 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.76 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 34 PHE 0.010 0.002 PHE D 23 TYR 0.004 0.001 TYR B 4 ARG 0.006 0.001 ARG A 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 : 0.317 Fit side-chains REVERT: A 59 ASP cc_start: 0.8384 (t0) cc_final: 0.7924 (t70) REVERT: B 59 ASP cc_start: 0.8390 (t0) cc_final: 0.7932 (t70) REVERT: C 59 ASP cc_start: 0.8383 (t0) cc_final: 0.7919 (t70) REVERT: D 59 ASP cc_start: 0.8401 (t0) cc_final: 0.7943 (t70) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1573 time to fit residues: 14.4126 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 : 0.365 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.223012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.195050 restraints weight = 3082.377| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.16 r_work: 0.3939 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3192 Z= 0.233 Angle : 0.526 4.248 4284 Z= 0.292 Chirality : 0.036 0.108 480 Planarity : 0.003 0.014 568 Dihedral : 3.739 10.835 440 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.85 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 (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: 3.26 (0.38), residues: 416 helix: 2.56 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.68 (0.85), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 88 PHE 0.011 0.002 PHE C 62 TYR 0.005 0.001 TYR D 4 ARG 0.006 0.001 ARG A 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 74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.319 Fit side-chains REVERT: A 59 ASP cc_start: 0.8403 (t0) cc_final: 0.8082 (t70) REVERT: A 75 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7735 (mm-30) REVERT: B 59 ASP cc_start: 0.8406 (t0) cc_final: 0.8095 (t70) REVERT: B 75 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7729 (mm-30) REVERT: C 59 ASP cc_start: 0.8391 (t0) cc_final: 0.8064 (t70) REVERT: C 75 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7741 (mm-30) REVERT: D 59 ASP cc_start: 0.8412 (t0) cc_final: 0.8100 (t70) REVERT: D 75 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7733 (mm-30) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1801 time to fit residues: 15.7392 Evaluate side-chains 74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 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 = 0.4486 r_free = 0.4486 target = 0.229805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.201128 restraints weight = 3083.579| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.27 r_work: 0.4002 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2478 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= 0.138 Angle : 0.467 4.568 4284 Z= 0.263 Chirality : 0.033 0.106 480 Planarity : 0.003 0.023 568 Dihedral : 3.554 10.662 440 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.50 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 (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: 3.97 (0.38), residues: 416 helix: 3.04 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.44 (0.88), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 34 PHE 0.010 0.002 PHE D 23 TYR 0.004 0.001 TYR D 4 ARG 0.006 0.001 ARG A 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 : 0.352 Fit side-chains REVERT: A 59 ASP cc_start: 0.8365 (t0) cc_final: 0.7959 (t70) REVERT: A 75 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 59 ASP cc_start: 0.8370 (t0) cc_final: 0.7966 (t70) REVERT: B 75 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7692 (mm-30) REVERT: C 59 ASP cc_start: 0.8386 (t0) cc_final: 0.7982 (t70) REVERT: C 75 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7713 (mm-30) REVERT: D 59 ASP cc_start: 0.8379 (t0) cc_final: 0.7974 (t70) REVERT: D 75 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7689 (mm-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1593 time to fit residues: 14.5883 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 : 0.349 ------------------------------------------------------------------------------- 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: 0.6980 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.228810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.200999 restraints weight = 3069.945| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.17 r_work: 0.4004 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3192 Z= 0.162 Angle : 0.477 4.236 4284 Z= 0.268 Chirality : 0.033 0.107 480 Planarity : 0.003 0.021 568 Dihedral : 3.523 10.633 440 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.02 (0.37), residues: 416 helix: 3.08 (0.23), residues: 360 sheet: None (None), residues: 0 loop : -0.51 (0.87), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 34 PHE 0.011 0.002 PHE D 62 TYR 0.004 0.001 TYR C 4 ARG 0.007 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 : 0.331 Fit side-chains REVERT: A 59 ASP cc_start: 0.8373 (t0) cc_final: 0.7989 (t70) REVERT: A 75 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 59 ASP cc_start: 0.8361 (t0) cc_final: 0.7977 (t70) REVERT: B 75 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7662 (mm-30) REVERT: C 59 ASP cc_start: 0.8369 (t0) cc_final: 0.7984 (t70) REVERT: C 75 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7674 (mm-30) REVERT: D 59 ASP cc_start: 0.8375 (t0) cc_final: 0.7994 (t70) REVERT: D 75 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7652 (mm-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1589 time to fit residues: 14.6385 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 : 0.317 ------------------------------------------------------------------------------- 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: 0.9980 chunk 3 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4409 r_free = 0.4409 target = 0.222581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.194413 restraints weight = 3045.723| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.15 r_work: 0.3959 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2416 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= 0.204 Angle : 0.507 4.273 4284 Z= 0.282 Chirality : 0.035 0.110 480 Planarity : 0.003 0.019 568 Dihedral : 3.655 10.878 440 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.85 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 (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: 3.75 (0.37), residues: 416 helix: 2.90 (0.23), residues: 360 sheet: None (None), residues: 0 loop : -0.57 (0.86), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 34 PHE 0.014 0.003 PHE C 62 TYR 0.005 0.001 TYR B 4 ARG 0.007 0.001 ARG B 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 : 0.362 Fit side-chains REVERT: A 59 ASP cc_start: 0.8408 (t0) cc_final: 0.8141 (t70) REVERT: A 75 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7686 (mm-30) REVERT: B 59 ASP cc_start: 0.8384 (t0) cc_final: 0.8115 (t70) REVERT: B 75 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7686 (mm-30) REVERT: C 59 ASP cc_start: 0.8398 (t0) cc_final: 0.8126 (t70) REVERT: C 75 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7695 (mm-30) REVERT: D 59 ASP cc_start: 0.8405 (t0) cc_final: 0.8145 (t70) REVERT: D 75 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7682 (mm-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1669 time to fit residues: 15.3965 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 : 0.330 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.221033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.193358 restraints weight = 3086.005| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.15 r_work: 0.3924 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3192 Z= 0.279 Angle : 0.562 4.334 4284 Z= 0.309 Chirality : 0.037 0.112 480 Planarity : 0.003 0.015 568 Dihedral : 3.933 11.623 440 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.52 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 (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 (0.37), residues: 416 helix: 2.51 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.69 (0.85), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 88 PHE 0.014 0.003 PHE C 62 TYR 0.005 0.001 TYR D 4 ARG 0.006 0.001 ARG B 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1614.13 seconds wall clock time: 30 minutes 17.87 seconds (1817.87 seconds total)