Starting phenix.real_space_refine on Tue Feb 11 07:04:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tth_41608/02_2025/8tth_41608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tth_41608/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tth_41608/02_2025/8tth_41608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tth_41608/02_2025/8tth_41608.map" model { file = "/net/cci-nas-00/data/ceres_data/8tth_41608/02_2025/8tth_41608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tth_41608/02_2025/8tth_41608.cif" } resolution = 3.54 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= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.56, per 1000 atoms: 0.77 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: 1.15 Conformation dependent library (CDL) restraints added in 566.6 milliseconds 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: 0.47 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: 1.36 Time building geometry restraints manager: 1.34 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: 0.950 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.070 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.210 ------------------------------------------------------------------------------- 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 4735 Z= 0.171 Angle : 0.687 9.675 6422 Z= 0.369 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 : 12.41 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 (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: 0.88 (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 TRP 0.017 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.018 0.002 PHE C 134 TYR 0.012 0.001 TYR D 73 ARG 0.002 0.000 ARG D 42 *********************** 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 : 0.485 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: 0.1321 time to fit residues: 22.9012 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 : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 0.0770 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 GLN ** 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 = 0.4079 r_free = 0.4079 target = 0.187099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.160252 restraints weight = 6205.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.165136 restraints weight = 3451.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.168434 restraints weight = 2347.012| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4735 Z= 0.194 Angle : 0.617 6.754 6422 Z= 0.319 Chirality : 0.043 0.215 734 Planarity : 0.005 0.041 792 Dihedral : 5.109 64.691 643 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.20 % Allowed : 27.60 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.20 (0.37), residues: 595 helix: 1.85 (0.30), residues: 324 sheet: 0.36 (0.50), residues: 112 loop : -1.06 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.022 0.002 PHE C 134 TYR 0.016 0.001 TYR C 133 ARG 0.002 0.000 ARG A 324 *********************** 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 152 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 74 SER cc_start: 0.7661 (p) cc_final: 0.7405 (p) outliers start: 21 outliers final: 12 residues processed: 144 average time/residue: 0.1310 time to fit residues: 25.5138 Evaluate side-chains 137 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 12 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.184523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.158185 restraints weight = 6145.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.162736 restraints weight = 3577.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.165664 restraints weight = 2492.773| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4735 Z= 0.213 Angle : 0.610 8.722 6422 Z= 0.315 Chirality : 0.044 0.217 734 Planarity : 0.004 0.047 792 Dihedral : 5.063 59.315 643 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.00 % Allowed : 28.40 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.36), residues: 595 helix: 1.66 (0.30), residues: 328 sheet: 0.34 (0.51), residues: 110 loop : -1.06 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 62 HIS 0.003 0.001 HIS A 155 PHE 0.020 0.002 PHE C 134 TYR 0.015 0.002 TYR C 133 ARG 0.001 0.000 ARG A 324 *********************** 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 157 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7745 (pttm) cc_final: 0.7415 (pttt) REVERT: C 109 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6479 (mmt) REVERT: D 73 TYR cc_start: 0.7815 (p90) cc_final: 0.7403 (p90) outliers start: 25 outliers final: 18 residues processed: 148 average time/residue: 0.1354 time to fit residues: 26.5591 Evaluate side-chains 146 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 29 TYR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 153 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 51 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN D 61 GLN ** 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 = 0.3993 r_free = 0.3993 target = 0.178313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.151367 restraints weight = 6215.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155942 restraints weight = 3602.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158959 restraints weight = 2506.618| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4735 Z= 0.294 Angle : 0.653 6.917 6422 Z= 0.341 Chirality : 0.045 0.221 734 Planarity : 0.005 0.055 792 Dihedral : 5.317 57.111 643 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.20 % Allowed : 28.60 % 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 (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: 0.81 (0.36), residues: 595 helix: 1.48 (0.29), residues: 328 sheet: 0.19 (0.50), residues: 110 loop : -1.15 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 62 HIS 0.003 0.001 HIS A 155 PHE 0.020 0.002 PHE C 134 TYR 0.020 0.002 TYR C 133 ARG 0.001 0.000 ARG A 324 *********************** 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 164 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7696 (pttm) cc_final: 0.7312 (pttt) REVERT: A 174 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.6829 (mm) REVERT: A 378 GLN cc_start: 0.6666 (tt0) cc_final: 0.6257 (mt0) REVERT: C 94 PHE cc_start: 0.7871 (m-10) cc_final: 0.7245 (m-10) REVERT: C 109 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6596 (mmt) REVERT: D 61 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: D 73 TYR cc_start: 0.7953 (p90) cc_final: 0.7527 (p90) outliers start: 31 outliers final: 21 residues processed: 154 average time/residue: 0.1212 time to fit residues: 25.0774 Evaluate side-chains 154 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 25 VAL 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 297 LEU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 63 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 61 GLN 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 16 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.181633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.153923 restraints weight = 6281.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.158798 restraints weight = 3520.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.162099 restraints weight = 2413.253| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4735 Z= 0.217 Angle : 0.624 9.009 6422 Z= 0.321 Chirality : 0.044 0.224 734 Planarity : 0.004 0.050 792 Dihedral : 5.267 57.682 643 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.40 % Allowed : 28.60 % 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 (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: 0.91 (0.36), residues: 595 helix: 1.60 (0.30), residues: 327 sheet: 0.12 (0.49), residues: 110 loop : -1.08 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.020 0.002 PHE C 134 TYR 0.015 0.002 TYR C 133 ARG 0.001 0.000 ARG C 45 *********************** 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 167 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7622 (pttm) cc_final: 0.7279 (pttt) REVERT: A 323 GLU cc_start: 0.7762 (pm20) cc_final: 0.7076 (tt0) REVERT: A 378 GLN cc_start: 0.6565 (tt0) cc_final: 0.6158 (mt0) REVERT: C 94 PHE cc_start: 0.7811 (m-10) cc_final: 0.7257 (m-10) REVERT: C 109 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6388 (mmt) REVERT: D 73 TYR cc_start: 0.7955 (p90) cc_final: 0.7445 (p90) outliers start: 32 outliers final: 21 residues processed: 157 average time/residue: 0.1218 time to fit residues: 25.7024 Evaluate side-chains 152 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 A residue 353 VAL Chi-restraints excluded: chain C residue 27 GLU 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 139 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.182655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.155054 restraints weight = 6149.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.159871 restraints weight = 3515.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.163190 restraints weight = 2414.000| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4735 Z= 0.201 Angle : 0.617 7.841 6422 Z= 0.318 Chirality : 0.044 0.225 734 Planarity : 0.004 0.049 792 Dihedral : 5.251 57.540 643 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 6.20 % Allowed : 28.60 % 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 (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: 1.03 (0.37), residues: 595 helix: 1.64 (0.30), residues: 327 sheet: 0.24 (0.50), residues: 106 loop : -0.91 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 293 HIS 0.003 0.001 HIS C 61 PHE 0.027 0.002 PHE A 161 TYR 0.020 0.002 TYR D 79 ARG 0.001 0.000 ARG A 324 *********************** 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 168 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 378 GLN cc_start: 0.6528 (tt0) cc_final: 0.6138 (mt0) REVERT: C 94 PHE cc_start: 0.7792 (m-10) cc_final: 0.7240 (m-10) REVERT: C 106 TYR cc_start: 0.7144 (m-80) cc_final: 0.6332 (m-80) REVERT: C 109 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6358 (mmt) REVERT: D 73 TYR cc_start: 0.7998 (p90) cc_final: 0.7522 (p90) outliers start: 31 outliers final: 22 residues processed: 160 average time/residue: 0.1201 time to fit residues: 26.0845 Evaluate side-chains 150 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 196 LEU 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 D residue 26 ILE Chi-restraints excluded: chain D residue 41 ASP 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 44 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.182743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.155191 restraints weight = 6159.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.160143 restraints weight = 3493.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.163440 restraints weight = 2386.547| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4735 Z= 0.209 Angle : 0.647 8.030 6422 Z= 0.331 Chirality : 0.045 0.226 734 Planarity : 0.005 0.048 792 Dihedral : 5.276 57.983 643 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.80 % Allowed : 28.60 % 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 (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: 0.98 (0.36), residues: 595 helix: 1.69 (0.30), residues: 320 sheet: 0.34 (0.50), residues: 106 loop : -1.13 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.025 0.002 PHE A 161 TYR 0.021 0.002 TYR A 292 ARG 0.002 0.000 ARG A 324 *********************** 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 169 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7631 (pttm) cc_final: 0.7332 (pttt) REVERT: A 323 GLU cc_start: 0.7525 (pm20) cc_final: 0.7061 (tt0) REVERT: A 378 GLN cc_start: 0.6512 (tt0) cc_final: 0.6121 (mt0) REVERT: C 94 PHE cc_start: 0.7781 (m-10) cc_final: 0.7250 (m-10) REVERT: C 106 TYR cc_start: 0.7133 (m-80) cc_final: 0.6345 (m-80) REVERT: C 109 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6383 (mmt) REVERT: D 73 TYR cc_start: 0.7986 (p90) cc_final: 0.7454 (p90) outliers start: 34 outliers final: 26 residues processed: 158 average time/residue: 0.1279 time to fit residues: 27.0631 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 : 0.519 ------------------------------------------------------------------------------- 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 156 ARG Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 234 ASN 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 71 LEU 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 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.182547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.154914 restraints weight = 6156.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.159864 restraints weight = 3520.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163033 restraints weight = 2421.158| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4735 Z= 0.213 Angle : 0.652 8.348 6422 Z= 0.333 Chirality : 0.045 0.225 734 Planarity : 0.004 0.048 792 Dihedral : 5.273 57.258 643 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 6.20 % Allowed : 30.00 % 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 (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: 1.06 (0.37), residues: 595 helix: 1.67 (0.30), residues: 326 sheet: 0.23 (0.49), residues: 110 loop : -0.90 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 293 HIS 0.003 0.001 HIS C 61 PHE 0.026 0.002 PHE A 161 TYR 0.021 0.002 TYR A 292 ARG 0.001 0.000 ARG C 113 *********************** 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 164 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7626 (pttm) cc_final: 0.7320 (pttt) REVERT: A 323 GLU cc_start: 0.7696 (pm20) cc_final: 0.7128 (tt0) REVERT: A 378 GLN cc_start: 0.6493 (tt0) cc_final: 0.6093 (mt0) REVERT: C 94 PHE cc_start: 0.7814 (m-10) cc_final: 0.7301 (m-10) REVERT: C 106 TYR cc_start: 0.7088 (m-80) cc_final: 0.6271 (m-80) REVERT: C 109 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.6532 (mmt) REVERT: D 73 TYR cc_start: 0.8033 (p90) cc_final: 0.7507 (p90) outliers start: 31 outliers final: 24 residues processed: 157 average time/residue: 0.1308 time to fit residues: 27.4437 Evaluate side-chains 155 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 156 ARG Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 234 ASN 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 71 LEU 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 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.0670 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.183518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.156327 restraints weight = 6148.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.161333 restraints weight = 3486.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.164641 restraints weight = 2375.560| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4735 Z= 0.206 Angle : 0.661 9.829 6422 Z= 0.335 Chirality : 0.045 0.225 734 Planarity : 0.005 0.050 792 Dihedral : 5.289 58.070 643 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.80 % Allowed : 30.60 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.08 (0.37), residues: 595 helix: 1.69 (0.30), residues: 326 sheet: 0.29 (0.49), residues: 110 loop : -0.94 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.018 0.002 PHE C 134 TYR 0.024 0.002 TYR A 292 ARG 0.001 0.000 ARG C 45 *********************** 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 162 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7613 (pttm) cc_final: 0.7314 (pttt) REVERT: A 323 GLU cc_start: 0.7667 (pm20) cc_final: 0.7028 (tt0) REVERT: A 378 GLN cc_start: 0.6471 (tt0) cc_final: 0.6075 (mt0) REVERT: C 94 PHE cc_start: 0.7784 (m-10) cc_final: 0.7288 (m-10) REVERT: C 106 TYR cc_start: 0.7081 (m-80) cc_final: 0.6266 (m-80) REVERT: C 109 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.6453 (mmt) REVERT: D 73 TYR cc_start: 0.8061 (p90) cc_final: 0.7479 (p90) outliers start: 29 outliers final: 24 residues processed: 154 average time/residue: 0.1280 time to fit residues: 26.3586 Evaluate side-chains 156 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU 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 196 LEU 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 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 139 SER 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 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 34 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.184051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156811 restraints weight = 6086.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.161764 restraints weight = 3445.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165130 restraints weight = 2354.965| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4735 Z= 0.210 Angle : 0.665 9.317 6422 Z= 0.336 Chirality : 0.046 0.221 734 Planarity : 0.005 0.056 792 Dihedral : 5.285 57.880 643 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.40 % Allowed : 31.60 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.11 (0.36), residues: 595 helix: 1.65 (0.30), residues: 326 sheet: 0.34 (0.49), residues: 110 loop : -0.83 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 293 HIS 0.004 0.001 HIS A 155 PHE 0.023 0.002 PHE A 161 TYR 0.025 0.002 TYR A 235 ARG 0.001 0.000 ARG C 45 ********************** 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 157 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7644 (pttm) cc_final: 0.7362 (pttt) REVERT: C 94 PHE cc_start: 0.7808 (m-10) cc_final: 0.7311 (m-10) REVERT: C 109 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6408 (mmt) REVERT: D 73 TYR cc_start: 0.8088 (p90) cc_final: 0.7585 (p90) outliers start: 27 outliers final: 23 residues processed: 150 average time/residue: 0.1308 time to fit residues: 26.0326 Evaluate side-chains 153 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE 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 196 LEU 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 139 SER 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 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 33 optimal weight: 0.7980 chunk 50 optimal weight: 0.0470 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.184663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.157278 restraints weight = 6161.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.162353 restraints weight = 3466.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.165722 restraints weight = 2348.771| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4735 Z= 0.199 Angle : 0.662 8.718 6422 Z= 0.335 Chirality : 0.045 0.221 734 Planarity : 0.005 0.052 792 Dihedral : 5.234 58.511 643 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.40 % Allowed : 31.80 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.06 (0.36), residues: 595 helix: 1.63 (0.30), residues: 327 sheet: 0.32 (0.49), residues: 110 loop : -0.91 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 293 HIS 0.004 0.001 HIS A 155 PHE 0.016 0.001 PHE C 134 TYR 0.025 0.002 TYR A 292 ARG 0.001 0.000 ARG A 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1659.89 seconds wall clock time: 30 minutes 23.71 seconds (1823.71 seconds total)