Starting phenix.real_space_refine on Thu Mar 6 02:47:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tth_41608/03_2025/8tth_41608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tth_41608/03_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_41608/03_2025/8tth_41608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tth_41608/03_2025/8tth_41608.map" model { file = "/net/cci-nas-00/data/ceres_data/8tth_41608/03_2025/8tth_41608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tth_41608/03_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-5624/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: 3.53, per 1000 atoms: 0.76 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: 1.61 Conformation dependent library (CDL) restraints added in 634.9 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: 0.59 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: 1.47 Time building geometry restraints manager: 1.91 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: 6.270 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.010 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:3.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- 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 : 0.472 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: 0.1749 time to fit residues: 30.3909 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 : 0.695 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.160244 restraints weight = 6205.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.165100 restraints weight = 3452.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.168411 restraints weight = 2350.362| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 74 SER cc_start: 0.7660 (p) cc_final: 0.7403 (p) outliers start: 21 outliers final: 12 residues processed: 144 average time/residue: 0.1271 time to fit residues: 24.5250 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 : 0.495 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.181814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.155389 restraints weight = 6162.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.159908 restraints weight = 3575.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.162845 restraints weight = 2499.380| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4735 Z= 0.252 Angle : 0.632 8.241 6422 Z= 0.328 Chirality : 0.045 0.218 734 Planarity : 0.005 0.051 792 Dihedral : 5.149 57.850 643 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.20 % Allowed : 28.00 % Favored : 66.80 % 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: 0.93 (0.36), residues: 595 helix: 1.57 (0.30), residues: 328 sheet: 0.27 (0.51), residues: 110 loop : -1.11 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 62 HIS 0.004 0.001 HIS A 155 PHE 0.020 0.002 PHE C 134 TYR 0.017 0.002 TYR C 133 ARG 0.002 0.000 ARG A 380 *********************** 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 159 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8718 (mm) cc_final: 0.8505 (mm) REVERT: C 94 PHE cc_start: 0.7735 (m-10) cc_final: 0.7193 (m-10) REVERT: C 109 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6621 (mmt) REVERT: D 73 TYR cc_start: 0.7810 (p90) cc_final: 0.7393 (p90) REVERT: D 74 SER cc_start: 0.7781 (p) cc_final: 0.7580 (p) outliers start: 26 outliers final: 18 residues processed: 151 average time/residue: 0.1252 time to fit residues: 25.3624 Evaluate side-chains 147 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 0.0170 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.185092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.158892 restraints weight = 6145.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.163411 restraints weight = 3526.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.166504 restraints weight = 2444.205| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4735 Z= 0.180 Angle : 0.598 7.756 6422 Z= 0.307 Chirality : 0.043 0.218 734 Planarity : 0.004 0.047 792 Dihedral : 5.081 58.886 643 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.00 % Allowed : 29.80 % 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: 1.10 (0.37), residues: 595 helix: 1.69 (0.30), residues: 328 sheet: 0.39 (0.51), residues: 110 loop : -1.04 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 293 HIS 0.004 0.001 HIS A 155 PHE 0.019 0.002 PHE C 134 TYR 0.013 0.001 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: 25 poor density : 139 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7902 (pttt) cc_final: 0.7612 (pttt) REVERT: A 323 GLU cc_start: 0.7664 (pm20) cc_final: 0.6997 (tt0) REVERT: C 94 PHE cc_start: 0.7656 (m-10) cc_final: 0.7111 (m-10) REVERT: C 109 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6403 (mmt) REVERT: D 73 TYR cc_start: 0.7838 (p90) cc_final: 0.7422 (p90) outliers start: 25 outliers final: 17 residues processed: 156 average time/residue: 0.1168 time to fit residues: 24.6291 Evaluate side-chains 150 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 208 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 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 16 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.179553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.152072 restraints weight = 6300.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.156761 restraints weight = 3527.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.159916 restraints weight = 2418.249| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4735 Z= 0.273 Angle : 0.645 7.468 6422 Z= 0.336 Chirality : 0.045 0.219 734 Planarity : 0.005 0.052 792 Dihedral : 5.259 57.645 643 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.60 % Allowed : 28.20 % 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 (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: 0.83 (0.36), residues: 595 helix: 1.50 (0.30), residues: 328 sheet: 0.32 (0.50), residues: 109 loop : -1.27 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 62 HIS 0.003 0.001 HIS A 155 PHE 0.018 0.002 PHE C 134 TYR 0.019 0.002 TYR C 133 ARG 0.001 0.000 ARG D 90 *********************** 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 166 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7842 (pttt) cc_final: 0.7456 (pttt) REVERT: C 94 PHE cc_start: 0.7914 (m-10) cc_final: 0.7398 (m-10) REVERT: C 109 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6424 (mmt) REVERT: D 73 TYR cc_start: 0.8030 (p90) cc_final: 0.7597 (p90) outliers start: 33 outliers final: 25 residues processed: 155 average time/residue: 0.1185 time to fit residues: 24.7924 Evaluate side-chains 156 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.182575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.155520 restraints weight = 6150.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.160280 restraints weight = 3458.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.163547 restraints weight = 2358.492| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2101 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= 0.199 Angle : 0.630 8.125 6422 Z= 0.321 Chirality : 0.044 0.219 734 Planarity : 0.004 0.048 792 Dihedral : 5.213 57.509 643 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 7.00 % Allowed : 27.80 % 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: 1.07 (0.37), residues: 595 helix: 1.63 (0.30), residues: 327 sheet: 0.49 (0.51), residues: 106 loop : -1.00 (0.53), residues: 162 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 0.018 0.002 PHE C 134 TYR 0.018 0.002 TYR A 292 ARG 0.001 0.000 ARG A 98 *********************** 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 : 0.469 Fit side-chains REVERT: A 68 LYS cc_start: 0.7911 (pttt) cc_final: 0.7545 (pttt) REVERT: A 323 GLU cc_start: 0.7636 (pm20) cc_final: 0.6722 (tt0) REVERT: C 94 PHE cc_start: 0.7805 (m-10) cc_final: 0.7310 (m-10) REVERT: C 106 TYR cc_start: 0.7169 (m-80) cc_final: 0.6311 (m-80) REVERT: C 109 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6392 (mmt) REVERT: D 61 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: D 73 TYR cc_start: 0.7967 (p90) cc_final: 0.7469 (p90) outliers start: 35 outliers final: 27 residues processed: 161 average time/residue: 0.1195 time to fit residues: 26.1087 Evaluate side-chains 159 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 179 ASP 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 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 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 44 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.181589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.154482 restraints weight = 6190.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.159085 restraints weight = 3625.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.162248 restraints weight = 2532.530| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4735 Z= 0.229 Angle : 0.651 8.115 6422 Z= 0.333 Chirality : 0.045 0.221 734 Planarity : 0.005 0.048 792 Dihedral : 5.285 57.300 643 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 7.00 % Allowed : 28.20 % Favored : 64.80 % 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: 1.60 (0.30), residues: 326 sheet: 0.49 (0.50), residues: 106 loop : -0.95 (0.53), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 293 HIS 0.002 0.001 HIS C 61 PHE 0.017 0.002 PHE C 134 TYR 0.022 0.002 TYR A 292 ARG 0.001 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 170 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7891 (pttt) cc_final: 0.7600 (pttt) REVERT: A 323 GLU cc_start: 0.7682 (pm20) cc_final: 0.6789 (tt0) REVERT: C 94 PHE cc_start: 0.7822 (m-10) cc_final: 0.7333 (m-10) REVERT: C 106 TYR cc_start: 0.7161 (m-80) cc_final: 0.6341 (m-80) REVERT: C 109 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.6435 (mmt) REVERT: D 61 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: D 73 TYR cc_start: 0.7989 (p90) cc_final: 0.7492 (p90) outliers start: 35 outliers final: 27 residues processed: 160 average time/residue: 0.1211 time to fit residues: 25.9659 Evaluate side-chains 160 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 179 ASP 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 133 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.180224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.152720 restraints weight = 6158.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.157424 restraints weight = 3507.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.160679 restraints weight = 2421.546| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4735 Z= 0.259 Angle : 0.668 8.239 6422 Z= 0.343 Chirality : 0.045 0.222 734 Planarity : 0.005 0.049 792 Dihedral : 5.411 57.425 643 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 6.60 % Allowed : 28.40 % 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: 1.53 (0.30), residues: 326 sheet: 0.32 (0.50), residues: 106 loop : -1.01 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.025 0.002 PHE A 161 TYR 0.022 0.002 TYR A 292 ARG 0.001 0.000 ARG A 324 *********************** 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 163 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7885 (pttt) cc_final: 0.7095 (pttt) REVERT: C 94 PHE cc_start: 0.7880 (m-10) cc_final: 0.7384 (m-10) REVERT: C 106 TYR cc_start: 0.7208 (m-80) cc_final: 0.6366 (m-80) REVERT: C 109 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6348 (mmt) REVERT: D 61 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: D 73 TYR cc_start: 0.8055 (p90) cc_final: 0.7513 (p90) outliers start: 33 outliers final: 26 residues processed: 154 average time/residue: 0.1232 time to fit residues: 25.3943 Evaluate side-chains 154 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.0470 chunk 50 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.183531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.156241 restraints weight = 6157.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.161057 restraints weight = 3494.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.164274 restraints weight = 2401.065| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2401 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= 0.206 Angle : 0.669 9.271 6422 Z= 0.339 Chirality : 0.045 0.221 734 Planarity : 0.005 0.046 792 Dihedral : 5.416 57.733 643 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 6.60 % Allowed : 29.40 % 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 (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 (0.36), residues: 595 helix: 1.57 (0.30), residues: 326 sheet: 0.39 (0.49), residues: 106 loop : -0.85 (0.53), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 293 HIS 0.002 0.001 HIS A 155 PHE 0.017 0.002 PHE C 134 TYR 0.030 0.002 TYR A 235 ARG 0.001 0.000 ARG A 324 *********************** 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 161 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7890 (pttt) cc_final: 0.7113 (pttt) REVERT: A 323 GLU cc_start: 0.7275 (pm20) cc_final: 0.6660 (tt0) REVERT: C 94 PHE cc_start: 0.7828 (m-10) cc_final: 0.7315 (m-10) REVERT: C 106 TYR cc_start: 0.7116 (m-80) cc_final: 0.6270 (m-80) REVERT: C 109 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.6370 (mmt) REVERT: D 73 TYR cc_start: 0.8057 (p90) cc_final: 0.7571 (p90) outliers start: 33 outliers final: 27 residues processed: 151 average time/residue: 0.1241 time to fit residues: 25.0365 Evaluate side-chains 154 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU 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 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 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 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: 3.9990 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.183590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.155972 restraints weight = 6175.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.160842 restraints weight = 3568.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164139 restraints weight = 2464.738| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4735 Z= 0.211 Angle : 0.662 9.216 6422 Z= 0.336 Chirality : 0.045 0.220 734 Planarity : 0.005 0.048 792 Dihedral : 5.346 58.248 643 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.60 % Allowed : 30.20 % Favored : 64.20 % 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: 1.08 (0.36), residues: 595 helix: 1.60 (0.30), residues: 326 sheet: 0.43 (0.50), residues: 106 loop : -0.83 (0.53), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 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 113 ********************** 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 154 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7907 (pttt) cc_final: 0.7167 (pttt) REVERT: A 323 GLU cc_start: 0.7302 (pm20) cc_final: 0.6662 (tt0) REVERT: C 94 PHE cc_start: 0.7832 (m-10) cc_final: 0.7310 (m-10) REVERT: C 106 TYR cc_start: 0.7113 (m-80) cc_final: 0.6233 (m-80) REVERT: C 109 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6313 (mmt) REVERT: D 73 TYR cc_start: 0.8040 (p90) cc_final: 0.7500 (p90) outliers start: 28 outliers final: 26 residues processed: 147 average time/residue: 0.1285 time to fit residues: 25.1074 Evaluate side-chains 152 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 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 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 133 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 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: 0.9980 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.181208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154929 restraints weight = 6264.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.159476 restraints weight = 3630.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.162616 restraints weight = 2531.622| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4735 Z= 0.234 Angle : 0.686 9.229 6422 Z= 0.346 Chirality : 0.046 0.220 734 Planarity : 0.005 0.047 792 Dihedral : 5.363 57.429 643 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: 0.94 (0.36), residues: 595 helix: 1.52 (0.30), residues: 321 sheet: 0.40 (0.49), residues: 106 loop : -0.93 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 293 HIS 0.003 0.001 HIS A 155 PHE 0.016 0.002 PHE C 134 TYR 0.024 0.002 TYR A 292 ARG 0.002 0.000 ARG A 324 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1744.29 seconds wall clock time: 31 minutes 27.75 seconds (1887.75 seconds total)