Starting phenix.real_space_refine on Fri Aug 22 15:00:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tth_41608/08_2025/8tth_41608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tth_41608/08_2025/8tth_41608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tth_41608/08_2025/8tth_41608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tth_41608/08_2025/8tth_41608.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tth_41608/08_2025/8tth_41608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tth_41608/08_2025/8tth_41608.map" } resolution = 3.54 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= 0.002 sd= 0.060 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 26 5.16 5 C 3031 2.51 5 N 729 2.21 5 O 834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s 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: 4620 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2842 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Chain: "C" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "D" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Time building chain proxies: 1.22, per 1000 atoms: 0.26 Number of scatterers: 4620 At special positions: 0 Unit cell: (60.225, 72.6, 106.425, 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 26 16.00 O 834 8.00 N 729 7.00 C 3031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 112 " distance=2.03 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: 0.24 Conformation dependent library (CDL) restraints added in 134.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 6 sheets defined 58.7% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 2 through 33 removed outlier: 3.715A pdb=" N PHE A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Proline residue: A 24 - end of helix Proline residue: A 27 - end of helix removed outlier: 3.917A pdb=" N LEU A 33 " --> pdb=" O TYR A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 66 removed outlier: 3.666A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 66 through 86 removed outlier: 3.837A pdb=" N ALA A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 120 Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 125 through 150 Proline residue: A 144 - end of helix removed outlier: 3.931A pdb=" N MET A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 177 removed outlier: 3.543A pdb=" N VAL A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 233 removed outlier: 4.009A pdb=" N SER A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 266 removed outlier: 4.022A pdb=" N ILE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 289 removed outlier: 3.996A pdb=" N LEU A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 322 removed outlier: 3.639A pdb=" N ILE A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 324 through 354 Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 356 through 382 Processing helix chain 'C' and resid 54 through 56 No H-bonds generated for 'chain 'C' and resid 54 through 56' Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 33 Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 37 removed outlier: 8.450A pdb=" N ASP C 144 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N SER C 126 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP C 146 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ARG C 124 " --> pdb=" O TRP C 146 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN C 148 " --> pdb=" O CYS C 122 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS C 122 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG C 64 " --> pdb=" O TRP C 73 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP C 73 " --> pdb=" O ARG C 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 31 Processing sheet with id=AA5, first strand: chain 'D' and resid 34 through 36 removed outlier: 3.663A pdb=" N LEU D 35 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP D 59 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 34 through 36 removed outlier: 3.663A pdb=" N LEU D 35 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN D 114 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR D 121 " --> pdb=" O GLN D 114 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 915 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: 0.69 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1398 1.34 - 1.46: 1212 1.46 - 1.58: 2078 1.58 - 1.70: 0 1.70 - 1.81: 47 Bond restraints: 4735 Sorted by residual: bond pdb=" CA MET A 150 " pdb=" CB MET A 150 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.35e-02 5.49e+03 1.60e+00 bond pdb=" C GLN D 103 " pdb=" O GLN D 103 " ideal model delta sigma weight residual 1.236 1.246 -0.010 8.90e-03 1.26e+04 1.22e+00 bond pdb=" CA PHE C 134 " pdb=" CB PHE C 134 " ideal model delta sigma weight residual 1.535 1.548 -0.013 1.37e-02 5.33e+03 8.91e-01 bond pdb=" C LEU D 102 " pdb=" N GLN D 103 " ideal model delta sigma weight residual 1.326 1.335 -0.009 1.12e-02 7.97e+03 7.17e-01 bond pdb=" CB ASN C 110 " pdb=" CG ASN C 110 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.96e-01 ... (remaining 4730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 6287 1.94 - 3.87: 106 3.87 - 5.81: 21 5.81 - 7.74: 5 7.74 - 9.68: 3 Bond angle restraints: 6422 Sorted by residual: angle pdb=" N VAL D 53 " pdb=" CA VAL D 53 " pdb=" C VAL D 53 " ideal model delta sigma weight residual 113.53 108.33 5.20 9.80e-01 1.04e+00 2.82e+01 angle pdb=" C TYR C 133 " pdb=" N PHE C 134 " pdb=" CA PHE C 134 " ideal model delta sigma weight residual 125.02 130.27 -5.25 1.76e+00 3.23e-01 8.89e+00 angle pdb=" CA LEU A 42 " pdb=" CB LEU A 42 " pdb=" CG LEU A 42 " ideal model delta sigma weight residual 116.30 125.98 -9.68 3.50e+00 8.16e-02 7.64e+00 angle pdb=" CB MET A 150 " pdb=" CG MET A 150 " pdb=" SD MET A 150 " ideal model delta sigma weight residual 112.70 120.88 -8.18 3.00e+00 1.11e-01 7.43e+00 angle pdb=" N LEU D 35 " pdb=" CA LEU D 35 " pdb=" C LEU D 35 " ideal model delta sigma weight residual 107.23 111.65 -4.42 1.67e+00 3.59e-01 7.00e+00 ... (remaining 6417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 2339 17.62 - 35.23: 314 35.23 - 52.84: 67 52.84 - 70.46: 19 70.46 - 88.07: 1 Dihedral angle restraints: 2740 sinusoidal: 1021 harmonic: 1719 Sorted by residual: dihedral pdb=" CB CYS D 47 " pdb=" SG CYS D 47 " pdb=" SG CYS D 112 " pdb=" CB CYS D 112 " ideal model delta sinusoidal sigma weight residual -86.00 -32.52 -53.48 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CA TRP C 131 " pdb=" C TRP C 131 " pdb=" N TYR C 132 " pdb=" CA TYR C 132 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA MET A 150 " pdb=" C MET A 150 " pdb=" N ALA A 151 " pdb=" CA ALA A 151 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 2737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 520 0.040 - 0.079: 156 0.079 - 0.119: 49 0.119 - 0.158: 6 0.158 - 0.198: 3 Chirality restraints: 734 Sorted by residual: chirality pdb=" CG LEU A 49 " pdb=" CB LEU A 49 " pdb=" CD1 LEU A 49 " pdb=" CD2 LEU A 49 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CA PHE C 134 " pdb=" N PHE C 134 " pdb=" C PHE C 134 " pdb=" CB PHE C 134 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CB VAL C 90 " pdb=" CA VAL C 90 " pdb=" CG1 VAL C 90 " pdb=" CG2 VAL C 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 731 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 103 " 0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO D 104 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 104 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 104 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 236 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO A 237 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 157 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO A 158 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 158 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 158 " 0.019 5.00e-02 4.00e+02 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 179 2.72 - 3.26: 4770 3.26 - 3.81: 7840 3.81 - 4.35: 8833 4.35 - 4.90: 15676 Nonbonded interactions: 37298 Sorted by model distance: nonbonded pdb=" OE1 GLN D 30 " pdb=" OG1 THR D 126 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR D 60 " pdb=" OE1 GLN D 113 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR A 278 " pdb=" O VAL A 301 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR A 29 " pdb=" O HIS A 155 " model vdw 2.296 3.040 nonbonded pdb=" O PHE C 55 " pdb=" OG SER C 79 " model vdw 2.311 3.040 ... (remaining 37293 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.600 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.770 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 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 : 0.003 0.024 4737 Z= 0.138 Angle : 0.689 9.675 6426 Z= 0.370 Chirality : 0.043 0.198 734 Planarity : 0.004 0.040 792 Dihedral : 16.672 88.074 1642 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.20 % Allowed : 31.00 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.88 (0.36), residues: 595 helix: 1.66 (0.30), residues: 323 sheet: 0.34 (0.51), residues: 109 loop : -1.40 (0.51), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 42 TYR 0.012 0.001 TYR D 73 PHE 0.018 0.002 PHE C 134 TRP 0.017 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4735) covalent geometry : angle 0.68677 ( 6422) SS BOND : bond 0.00306 ( 2) SS BOND : angle 2.09287 ( 4) hydrogen bonds : bond 0.15720 ( 320) hydrogen bonds : angle 6.64724 ( 915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: C 61 HIS cc_start: 0.8230 (m170) cc_final: 0.7925 (m170) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.0482 time to fit residues: 8.3599 Evaluate side-chains 125 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.0270 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.186716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.160606 restraints weight = 6202.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.165210 restraints weight = 3552.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.168315 restraints weight = 2457.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.170491 restraints weight = 1899.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.171998 restraints weight = 1572.071| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4737 Z= 0.139 Angle : 0.619 6.796 6426 Z= 0.320 Chirality : 0.044 0.212 734 Planarity : 0.004 0.041 792 Dihedral : 5.110 64.624 643 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.40 % Allowed : 27.60 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.15 (0.37), residues: 595 helix: 1.78 (0.30), residues: 327 sheet: 0.36 (0.51), residues: 112 loop : -1.08 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 45 TYR 0.016 0.001 TYR C 133 PHE 0.020 0.002 PHE C 134 TRP 0.007 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4735) covalent geometry : angle 0.61608 ( 6422) SS BOND : bond 0.00570 ( 2) SS BOND : angle 2.48554 ( 4) hydrogen bonds : bond 0.03949 ( 320) hydrogen bonds : angle 4.70040 ( 915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 74 SER cc_start: 0.7656 (p) cc_final: 0.7408 (p) outliers start: 22 outliers final: 12 residues processed: 145 average time/residue: 0.0499 time to fit residues: 9.9032 Evaluate side-chains 135 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain D residue 112 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.179052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.152297 restraints weight = 6177.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.156729 restraints weight = 3605.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.159803 restraints weight = 2524.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.161703 restraints weight = 1965.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.163254 restraints weight = 1657.356| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4737 Z= 0.203 Angle : 0.665 8.709 6426 Z= 0.346 Chirality : 0.046 0.221 734 Planarity : 0.005 0.054 792 Dihedral : 5.283 56.375 643 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.60 % Allowed : 28.00 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.80 (0.36), residues: 595 helix: 1.46 (0.29), residues: 327 sheet: 0.29 (0.50), residues: 109 loop : -1.18 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 380 TYR 0.020 0.002 TYR C 133 PHE 0.021 0.002 PHE C 134 TRP 0.011 0.001 TRP C 62 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 4735) covalent geometry : angle 0.66265 ( 6422) SS BOND : bond 0.00989 ( 2) SS BOND : angle 2.19953 ( 4) hydrogen bonds : bond 0.04297 ( 320) hydrogen bonds : angle 4.60031 ( 915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8683 (mm) cc_final: 0.8457 (mm) REVERT: C 94 PHE cc_start: 0.7816 (m-10) cc_final: 0.7303 (m-10) REVERT: C 109 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6596 (mmt) REVERT: D 73 TYR cc_start: 0.7870 (p90) cc_final: 0.7440 (p90) outliers start: 28 outliers final: 20 residues processed: 155 average time/residue: 0.0479 time to fit residues: 10.2228 Evaluate side-chains 150 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 18 optimal weight: 0.0370 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS C 129 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.183112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.155850 restraints weight = 6099.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.160651 restraints weight = 3435.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.163826 restraints weight = 2344.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.166003 restraints weight = 1805.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.167532 restraints weight = 1490.284| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4737 Z= 0.140 Angle : 0.618 8.109 6426 Z= 0.318 Chirality : 0.044 0.224 734 Planarity : 0.004 0.049 792 Dihedral : 5.250 57.971 643 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.60 % Allowed : 30.20 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.95 (0.36), residues: 595 helix: 1.57 (0.30), residues: 328 sheet: 0.25 (0.50), residues: 110 loop : -1.05 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 45 TYR 0.015 0.002 TYR C 133 PHE 0.021 0.002 PHE C 134 TRP 0.011 0.001 TRP A 293 HIS 0.010 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4735) covalent geometry : angle 0.61712 ( 6422) SS BOND : bond 0.00697 ( 2) SS BOND : angle 1.71867 ( 4) hydrogen bonds : bond 0.03723 ( 320) hydrogen bonds : angle 4.40142 ( 915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8590 (mm) cc_final: 0.8358 (mm) REVERT: A 68 LYS cc_start: 0.7935 (pttt) cc_final: 0.7634 (pttt) REVERT: A 174 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.6843 (mm) REVERT: A 323 GLU cc_start: 0.7723 (pm20) cc_final: 0.7043 (tt0) REVERT: C 94 PHE cc_start: 0.7761 (m-10) cc_final: 0.7181 (m-10) REVERT: C 109 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6407 (mmt) REVERT: D 73 TYR cc_start: 0.7901 (p90) cc_final: 0.7470 (p90) outliers start: 23 outliers final: 13 residues processed: 150 average time/residue: 0.0410 time to fit residues: 8.5182 Evaluate side-chains 148 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.181761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.154437 restraints weight = 6189.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.159274 restraints weight = 3476.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.162582 restraints weight = 2373.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.164559 restraints weight = 1818.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.166236 restraints weight = 1522.198| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4737 Z= 0.148 Angle : 0.617 7.443 6426 Z= 0.319 Chirality : 0.044 0.225 734 Planarity : 0.004 0.049 792 Dihedral : 5.227 58.077 643 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 7.00 % Allowed : 27.40 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.91 (0.36), residues: 595 helix: 1.59 (0.30), residues: 327 sheet: 0.23 (0.50), residues: 110 loop : -1.15 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.015 0.002 TYR C 133 PHE 0.020 0.002 PHE C 134 TRP 0.009 0.001 TRP A 293 HIS 0.002 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4735) covalent geometry : angle 0.61585 ( 6422) SS BOND : bond 0.00767 ( 2) SS BOND : angle 1.79004 ( 4) hydrogen bonds : bond 0.03728 ( 320) hydrogen bonds : angle 4.34737 ( 915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7811 (pttt) cc_final: 0.7562 (pttm) REVERT: C 94 PHE cc_start: 0.7755 (m-10) cc_final: 0.7292 (m-10) REVERT: C 109 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6457 (mmt) REVERT: D 61 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7364 (tt0) REVERT: D 73 TYR cc_start: 0.7950 (p90) cc_final: 0.7515 (p90) outliers start: 35 outliers final: 23 residues processed: 160 average time/residue: 0.0436 time to fit residues: 9.6590 Evaluate side-chains 158 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 53 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.181732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.154221 restraints weight = 6291.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.159042 restraints weight = 3527.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.162379 restraints weight = 2401.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.164530 restraints weight = 1836.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.166112 restraints weight = 1525.308| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4737 Z= 0.142 Angle : 0.618 7.751 6426 Z= 0.318 Chirality : 0.044 0.225 734 Planarity : 0.004 0.049 792 Dihedral : 5.201 57.323 643 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 7.00 % Allowed : 28.40 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.06 (0.36), residues: 595 helix: 1.64 (0.30), residues: 327 sheet: 0.40 (0.51), residues: 106 loop : -0.97 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.018 0.002 TYR A 292 PHE 0.025 0.002 PHE A 161 TRP 0.014 0.001 TRP A 293 HIS 0.002 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4735) covalent geometry : angle 0.61664 ( 6422) SS BOND : bond 0.00677 ( 2) SS BOND : angle 1.62787 ( 4) hydrogen bonds : bond 0.03653 ( 320) hydrogen bonds : angle 4.30503 ( 915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7889 (pttt) cc_final: 0.7529 (pttt) REVERT: A 323 GLU cc_start: 0.7532 (pm20) cc_final: 0.6737 (tt0) REVERT: C 94 PHE cc_start: 0.7806 (m-10) cc_final: 0.7372 (m-10) REVERT: C 106 TYR cc_start: 0.7140 (m-80) cc_final: 0.6343 (m-80) REVERT: C 109 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6522 (mmt) REVERT: D 61 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: D 73 TYR cc_start: 0.7991 (p90) cc_final: 0.7498 (p90) outliers start: 35 outliers final: 23 residues processed: 162 average time/residue: 0.0451 time to fit residues: 10.1402 Evaluate side-chains 154 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.0070 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.181505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.154094 restraints weight = 6187.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.158884 restraints weight = 3492.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.162205 restraints weight = 2385.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164198 restraints weight = 1828.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.165887 restraints weight = 1530.076| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4737 Z= 0.152 Angle : 0.645 8.371 6426 Z= 0.331 Chirality : 0.045 0.224 734 Planarity : 0.005 0.048 792 Dihedral : 5.258 57.706 643 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.80 % Allowed : 28.20 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.00 (0.36), residues: 595 helix: 1.59 (0.30), residues: 327 sheet: 0.37 (0.50), residues: 106 loop : -1.01 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.023 0.002 TYR A 292 PHE 0.025 0.002 PHE A 161 TRP 0.014 0.001 TRP A 293 HIS 0.002 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4735) covalent geometry : angle 0.64360 ( 6422) SS BOND : bond 0.00670 ( 2) SS BOND : angle 1.62477 ( 4) hydrogen bonds : bond 0.03752 ( 320) hydrogen bonds : angle 4.32119 ( 915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7367 (tt) cc_final: 0.7155 (tt) REVERT: A 323 GLU cc_start: 0.7654 (pm20) cc_final: 0.6791 (tt0) REVERT: C 94 PHE cc_start: 0.7829 (m-10) cc_final: 0.7319 (m-10) REVERT: C 106 TYR cc_start: 0.7173 (m-80) cc_final: 0.6352 (m-80) REVERT: C 109 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6389 (mmt) REVERT: D 61 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: D 73 TYR cc_start: 0.8008 (p90) cc_final: 0.7516 (p90) outliers start: 34 outliers final: 28 residues processed: 158 average time/residue: 0.0499 time to fit residues: 10.7739 Evaluate side-chains 160 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 0.0040 chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.156151 restraints weight = 6236.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.161072 restraints weight = 3483.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164359 restraints weight = 2371.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.166396 restraints weight = 1828.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.168095 restraints weight = 1523.533| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4737 Z= 0.131 Angle : 0.621 8.320 6426 Z= 0.318 Chirality : 0.044 0.224 734 Planarity : 0.004 0.047 792 Dihedral : 5.213 57.902 643 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 7.00 % Allowed : 27.60 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.16 (0.37), residues: 595 helix: 1.69 (0.30), residues: 326 sheet: 0.46 (0.50), residues: 106 loop : -0.86 (0.54), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 113 TYR 0.020 0.001 TYR A 292 PHE 0.018 0.002 PHE C 134 TRP 0.018 0.001 TRP A 293 HIS 0.002 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4735) covalent geometry : angle 0.62025 ( 6422) SS BOND : bond 0.00593 ( 2) SS BOND : angle 1.31827 ( 4) hydrogen bonds : bond 0.03520 ( 320) hydrogen bonds : angle 4.26953 ( 915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7644 (pttm) cc_final: 0.7387 (pttt) REVERT: C 94 PHE cc_start: 0.7748 (m-10) cc_final: 0.7358 (m-10) REVERT: C 106 TYR cc_start: 0.7069 (m-80) cc_final: 0.6293 (m-80) REVERT: C 109 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.6470 (mmt) REVERT: D 61 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7339 (tt0) REVERT: D 73 TYR cc_start: 0.8005 (p90) cc_final: 0.7474 (p90) outliers start: 35 outliers final: 28 residues processed: 159 average time/residue: 0.0488 time to fit residues: 10.5668 Evaluate side-chains 160 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.180119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.152671 restraints weight = 6101.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.157409 restraints weight = 3478.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.160681 restraints weight = 2404.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.162921 restraints weight = 1853.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.164283 restraints weight = 1533.670| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4737 Z= 0.171 Angle : 0.672 9.476 6426 Z= 0.345 Chirality : 0.046 0.222 734 Planarity : 0.005 0.050 792 Dihedral : 5.345 57.534 643 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 6.40 % Allowed : 29.60 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.87 (0.36), residues: 595 helix: 1.47 (0.30), residues: 327 sheet: 0.28 (0.50), residues: 109 loop : -1.01 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 90 TYR 0.024 0.002 TYR A 292 PHE 0.025 0.002 PHE A 161 TRP 0.018 0.001 TRP A 293 HIS 0.014 0.002 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 4735) covalent geometry : angle 0.67122 ( 6422) SS BOND : bond 0.00684 ( 2) SS BOND : angle 1.69210 ( 4) hydrogen bonds : bond 0.03937 ( 320) hydrogen bonds : angle 4.37302 ( 915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7641 (pttm) cc_final: 0.7394 (pttt) REVERT: A 323 GLU cc_start: 0.7257 (pm20) cc_final: 0.6698 (tt0) REVERT: C 94 PHE cc_start: 0.7893 (m-10) cc_final: 0.7398 (m-10) REVERT: C 106 TYR cc_start: 0.7129 (m-80) cc_final: 0.6249 (m-80) REVERT: C 109 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6274 (mmt) REVERT: D 61 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: D 73 TYR cc_start: 0.8095 (p90) cc_final: 0.7600 (p90) outliers start: 32 outliers final: 25 residues processed: 157 average time/residue: 0.0478 time to fit residues: 10.2494 Evaluate side-chains 158 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 29 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.155679 restraints weight = 6205.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.160698 restraints weight = 3506.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164076 restraints weight = 2386.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.166190 restraints weight = 1825.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.167686 restraints weight = 1514.221| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4737 Z= 0.135 Angle : 0.655 8.703 6426 Z= 0.334 Chirality : 0.045 0.220 734 Planarity : 0.004 0.047 792 Dihedral : 5.292 57.683 643 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.60 % Allowed : 31.00 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.04 (0.37), residues: 595 helix: 1.57 (0.30), residues: 327 sheet: 0.34 (0.49), residues: 106 loop : -0.78 (0.55), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 156 TYR 0.025 0.002 TYR A 292 PHE 0.016 0.001 PHE C 134 TRP 0.025 0.002 TRP A 293 HIS 0.013 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4735) covalent geometry : angle 0.65449 ( 6422) SS BOND : bond 0.00577 ( 2) SS BOND : angle 1.30267 ( 4) hydrogen bonds : bond 0.03643 ( 320) hydrogen bonds : angle 4.31996 ( 915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7727 (pttm) cc_final: 0.7503 (pttt) REVERT: A 323 GLU cc_start: 0.7243 (pm20) cc_final: 0.6738 (tt0) REVERT: C 94 PHE cc_start: 0.7810 (m-10) cc_final: 0.7313 (m-10) REVERT: C 106 TYR cc_start: 0.7064 (m-80) cc_final: 0.6286 (m-80) REVERT: C 109 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6353 (mmt) REVERT: D 61 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: D 73 TYR cc_start: 0.8049 (p90) cc_final: 0.7633 (p90) outliers start: 28 outliers final: 24 residues processed: 152 average time/residue: 0.0475 time to fit residues: 9.9030 Evaluate side-chains 157 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 50 optimal weight: 0.0070 chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.183470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.156051 restraints weight = 6257.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.161017 restraints weight = 3495.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.164403 restraints weight = 2384.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.166601 restraints weight = 1822.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.168280 restraints weight = 1505.499| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4737 Z= 0.134 Angle : 0.650 9.018 6426 Z= 0.330 Chirality : 0.045 0.221 734 Planarity : 0.004 0.046 792 Dihedral : 5.238 58.106 643 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.60 % Allowed : 30.60 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.02 (0.37), residues: 595 helix: 1.56 (0.30), residues: 327 sheet: 0.33 (0.49), residues: 106 loop : -0.82 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 156 TYR 0.023 0.002 TYR D 79 PHE 0.025 0.002 PHE A 161 TRP 0.024 0.002 TRP A 293 HIS 0.011 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4735) covalent geometry : angle 0.64949 ( 6422) SS BOND : bond 0.00580 ( 2) SS BOND : angle 1.34754 ( 4) hydrogen bonds : bond 0.03629 ( 320) hydrogen bonds : angle 4.29728 ( 915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 847.75 seconds wall clock time: 15 minutes 17.65 seconds (917.65 seconds total)