Starting phenix.real_space_refine on Tue Feb 11 04:37:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sbb_40303/02_2025/8sbb_40303.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sbb_40303/02_2025/8sbb_40303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sbb_40303/02_2025/8sbb_40303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sbb_40303/02_2025/8sbb_40303.map" model { file = "/net/cci-nas-00/data/ceres_data/8sbb_40303/02_2025/8sbb_40303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sbb_40303/02_2025/8sbb_40303.cif" } resolution = 3.59 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= 0.012 sd= 0.152 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: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 10 5.16 5 C 2634 2.51 5 N 705 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 4049 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3110 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 26, 'TRANS': 353} Chain: "B" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' FE': 2, 'D12': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.15, per 1000 atoms: 0.78 Number of scatterers: 4049 At special positions: 0 Unit cell: (96.9, 88.35, 69.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 10 16.00 O 698 8.00 N 705 7.00 C 2634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 97 " distance=2.04 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: 1.10 Conformation dependent library (CDL) restraints added in 489.2 milliseconds 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 52.3% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 removed outlier: 3.650A pdb=" N TRP A 29 " --> pdb=" O ARG A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 26 through 29' Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 37 through 49 Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.748A pdb=" N PHE A 55 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 removed outlier: 3.553A pdb=" N TYR A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.835A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 92 through 100 removed outlier: 4.516A pdb=" N THR A 98 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 119 removed outlier: 4.060A pdb=" N ILE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 147 removed outlier: 3.882A pdb=" N ILE A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.938A pdb=" N ARG A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 199 through 225 Proline residue: A 209 - end of helix removed outlier: 3.895A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 256 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 259 through 282 removed outlier: 3.543A pdb=" N LEU A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.636A pdb=" N ASN A 312 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.543A pdb=" N HIS A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.671A pdb=" N MET A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.546A pdb=" N TRP A 361 " --> pdb=" O PHE A 357 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 9 removed outlier: 3.623A pdb=" N GLN B 7 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 23 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR B 70 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 54 removed outlier: 6.128A pdb=" N TRP B 38 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY B 52 " --> pdb=" O MET B 36 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET B 36 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 94 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 95 " --> pdb=" O GLY B 117 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 483 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: 1.01 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 681 1.32 - 1.44: 1229 1.44 - 1.56: 2249 1.56 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 4175 Sorted by residual: bond pdb=" CA TYR A 21 " pdb=" C TYR A 21 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.34e-02 5.57e+03 2.67e+01 bond pdb=" N ARG B 73 " pdb=" CA ARG B 73 " ideal model delta sigma weight residual 1.458 1.488 -0.030 6.30e-03 2.52e+04 2.22e+01 bond pdb=" N ARG B 32 " pdb=" CA ARG B 32 " ideal model delta sigma weight residual 1.459 1.490 -0.031 9.10e-03 1.21e+04 1.16e+01 bond pdb=" CA ALA A 142 " pdb=" CB ALA A 142 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.57e-02 4.06e+03 1.10e+01 bond pdb=" C LEU A 141 " pdb=" O LEU A 141 " ideal model delta sigma weight residual 1.236 1.195 0.042 1.26e-02 6.30e+03 1.09e+01 ... (remaining 4170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 5112 2.11 - 4.22: 497 4.22 - 6.33: 68 6.33 - 8.44: 13 8.44 - 10.55: 3 Bond angle restraints: 5693 Sorted by residual: angle pdb=" N LEU A 318 " pdb=" CA LEU A 318 " pdb=" C LEU A 318 " ideal model delta sigma weight residual 114.31 104.74 9.57 1.29e+00 6.01e-01 5.50e+01 angle pdb=" N GLY A 140 " pdb=" CA GLY A 140 " pdb=" C GLY A 140 " ideal model delta sigma weight residual 112.73 105.63 7.10 1.20e+00 6.94e-01 3.50e+01 angle pdb=" N ILE B 30 " pdb=" CA ILE B 30 " pdb=" C ILE B 30 " ideal model delta sigma weight residual 112.90 107.36 5.54 9.60e-01 1.09e+00 3.32e+01 angle pdb=" N THR A 145 " pdb=" CA THR A 145 " pdb=" C THR A 145 " ideal model delta sigma weight residual 113.50 106.73 6.77 1.23e+00 6.61e-01 3.03e+01 angle pdb=" CA GLY A 256 " pdb=" C GLY A 256 " pdb=" O GLY A 256 " ideal model delta sigma weight residual 122.29 118.00 4.29 8.10e-01 1.52e+00 2.81e+01 ... (remaining 5688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 2071 15.29 - 30.58: 242 30.58 - 45.86: 69 45.86 - 61.15: 25 61.15 - 76.44: 8 Dihedral angle restraints: 2415 sinusoidal: 971 harmonic: 1444 Sorted by residual: dihedral pdb=" CA PHE A 316 " pdb=" C PHE A 316 " pdb=" N HIS A 317 " pdb=" CA HIS A 317 " ideal model delta harmonic sigma weight residual -180.00 -152.27 -27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ARG A 320 " pdb=" C ARG A 320 " pdb=" N HIS A 321 " pdb=" CA HIS A 321 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLY A 374 " pdb=" C GLY A 374 " pdb=" N ARG A 375 " pdb=" CA ARG A 375 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 2412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 325 0.053 - 0.105: 212 0.105 - 0.157: 51 0.157 - 0.210: 15 0.210 - 0.262: 5 Chirality restraints: 608 Sorted by residual: chirality pdb=" CB VAL A 37 " pdb=" CA VAL A 37 " pdb=" CG1 VAL A 37 " pdb=" CG2 VAL A 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA TYR A 21 " pdb=" N TYR A 21 " pdb=" C TYR A 21 " pdb=" CB TYR A 21 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA TYR A 348 " pdb=" N TYR A 348 " pdb=" C TYR A 348 " pdb=" CB TYR A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 605 not shown) Planarity restraints: 717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 344 " 0.050 5.00e-02 4.00e+02 7.66e-02 9.39e+00 pdb=" N PRO A 345 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 80 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO A 81 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 180 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C GLY A 180 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY A 180 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS A 181 " 0.016 2.00e-02 2.50e+03 ... (remaining 714 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 351 2.70 - 3.25: 4125 3.25 - 3.80: 6375 3.80 - 4.35: 7734 4.35 - 4.90: 12694 Nonbonded interactions: 31279 Sorted by model distance: nonbonded pdb=" NE2 HIS A 325 " pdb="FE FE A 401 " model vdw 2.146 2.340 nonbonded pdb=" O GLY B 44 " pdb=" NZ LYS B 45 " model vdw 2.147 3.120 nonbonded pdb=" NE2 HIS A 282 " pdb="FE FE A 401 " model vdw 2.156 2.340 nonbonded pdb=" OG SER B 19 " pdb=" O MET B 84 " model vdw 2.210 3.040 nonbonded pdb=" NE2 HIS A 324 " pdb="FE FE A 402 " model vdw 2.227 2.340 ... (remaining 31274 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=1.00 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: 0.570 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.030 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.016 0.108 4175 Z= 1.048 Angle : 1.326 10.553 5693 Z= 0.830 Chirality : 0.071 0.262 608 Planarity : 0.009 0.077 717 Dihedral : 15.679 76.438 1494 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.95 % Favored : 85.05 % Rotamer: Outliers : 3.99 % Allowed : 12.68 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.32 (0.28), residues: 495 helix: -2.80 (0.28), residues: 230 sheet: -3.34 (0.71), residues: 34 loop : -4.42 (0.28), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 125 HIS 0.010 0.002 HIS A 151 PHE 0.022 0.004 PHE A 173 TYR 0.032 0.004 TYR A 93 ARG 0.007 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8790 (tp) cc_final: 0.8464 (mt) REVERT: B 35 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7734 (t) REVERT: B 54 SER cc_start: 0.8234 (t) cc_final: 0.7888 (m) outliers start: 17 outliers final: 3 residues processed: 106 average time/residue: 0.2063 time to fit residues: 26.0454 Evaluate side-chains 58 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 72 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.184194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.141893 restraints weight = 5547.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145648 restraints weight = 2756.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.147913 restraints weight = 1818.749| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4175 Z= 0.246 Angle : 0.771 6.671 5693 Z= 0.402 Chirality : 0.045 0.158 608 Planarity : 0.007 0.057 717 Dihedral : 5.858 36.362 574 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.06 % Favored : 93.74 % Rotamer: Outliers : 3.05 % Allowed : 17.37 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.33), residues: 495 helix: -0.98 (0.34), residues: 230 sheet: -2.59 (0.65), residues: 39 loop : -3.85 (0.29), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 125 HIS 0.006 0.001 HIS A 147 PHE 0.018 0.002 PHE A 262 TYR 0.019 0.002 TYR B 61 ARG 0.006 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.506 Fit side-chains REVERT: A 64 LEU cc_start: 0.8699 (tp) cc_final: 0.8443 (mp) REVERT: A 176 GLU cc_start: 0.8016 (tp30) cc_final: 0.7699 (tm-30) REVERT: A 288 GLN cc_start: 0.7380 (mm-40) cc_final: 0.7040 (mm-40) REVERT: B 23 SER cc_start: 0.7901 (p) cc_final: 0.7497 (m) REVERT: B 54 SER cc_start: 0.7859 (t) cc_final: 0.7445 (m) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.1603 time to fit residues: 15.2369 Evaluate side-chains 61 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 46 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 385 ASN ** B 75 ASN ** 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 = 0.4281 r_free = 0.4281 target = 0.184809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141596 restraints weight = 5572.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.145204 restraints weight = 2848.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.147529 restraints weight = 1925.806| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4175 Z= 0.191 Angle : 0.669 6.425 5693 Z= 0.348 Chirality : 0.042 0.145 608 Planarity : 0.006 0.046 717 Dihedral : 5.222 28.870 568 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.82 % Allowed : 18.31 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.36), residues: 495 helix: -0.14 (0.37), residues: 230 sheet: -2.17 (0.66), residues: 39 loop : -3.32 (0.32), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 125 HIS 0.004 0.001 HIS A 282 PHE 0.014 0.001 PHE A 262 TYR 0.016 0.002 TYR B 61 ARG 0.003 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.452 Fit side-chains REVERT: A 64 LEU cc_start: 0.8770 (tp) cc_final: 0.8468 (mp) REVERT: A 288 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7117 (mm-40) REVERT: A 365 MET cc_start: 0.7901 (mmm) cc_final: 0.7614 (mmm) outliers start: 12 outliers final: 7 residues processed: 58 average time/residue: 0.1533 time to fit residues: 11.6651 Evaluate side-chains 49 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 71 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN ** B 75 ASN ** 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 = 0.4278 r_free = 0.4278 target = 0.184777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.142675 restraints weight = 5594.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.146277 restraints weight = 2816.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.148509 restraints weight = 1885.176| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4175 Z= 0.167 Angle : 0.645 6.514 5693 Z= 0.332 Chirality : 0.042 0.142 608 Planarity : 0.005 0.045 717 Dihedral : 5.009 27.258 568 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.99 % Allowed : 17.61 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.37), residues: 495 helix: 0.22 (0.37), residues: 230 sheet: -1.22 (0.72), residues: 39 loop : -2.91 (0.34), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 125 HIS 0.003 0.001 HIS A 182 PHE 0.012 0.001 PHE A 262 TYR 0.015 0.001 TYR B 61 ARG 0.003 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.491 Fit side-chains REVERT: A 176 GLU cc_start: 0.8121 (tp30) cc_final: 0.7740 (tm-30) REVERT: A 379 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7619 (mtpt) REVERT: B 23 SER cc_start: 0.8329 (t) cc_final: 0.8093 (m) outliers start: 17 outliers final: 13 residues processed: 60 average time/residue: 0.1483 time to fit residues: 11.9094 Evaluate side-chains 59 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 288 GLN A 302 HIS ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.163187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124793 restraints weight = 5553.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127391 restraints weight = 3266.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128853 restraints weight = 2371.527| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4175 Z= 0.351 Angle : 0.748 7.426 5693 Z= 0.386 Chirality : 0.046 0.146 608 Planarity : 0.006 0.042 717 Dihedral : 5.215 28.016 568 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.93 % Allowed : 16.90 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.37), residues: 495 helix: 0.09 (0.37), residues: 230 sheet: -1.34 (0.74), residues: 39 loop : -2.92 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 114 HIS 0.005 0.001 HIS A 147 PHE 0.013 0.002 PHE A 196 TYR 0.017 0.002 TYR A 93 ARG 0.003 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.456 Fit side-chains REVERT: B 84 MET cc_start: 0.8231 (ptp) cc_final: 0.7950 (pmm) outliers start: 21 outliers final: 18 residues processed: 63 average time/residue: 0.1528 time to fit residues: 12.4082 Evaluate side-chains 65 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 1 optimal weight: 0.0060 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 ASN ** 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 = 0.4003 r_free = 0.4003 target = 0.166817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.128430 restraints weight = 5392.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.131156 restraints weight = 3142.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.132971 restraints weight = 2255.868| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4175 Z= 0.201 Angle : 0.666 10.055 5693 Z= 0.341 Chirality : 0.042 0.128 608 Planarity : 0.005 0.040 717 Dihedral : 5.097 28.999 568 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.76 % Allowed : 19.01 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.37), residues: 495 helix: 0.32 (0.37), residues: 227 sheet: -1.39 (0.73), residues: 37 loop : -2.86 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 114 HIS 0.002 0.001 HIS A 182 PHE 0.013 0.001 PHE A 262 TYR 0.011 0.001 TYR B 61 ARG 0.004 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.395 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 56 average time/residue: 0.1529 time to fit residues: 11.2247 Evaluate side-chains 60 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.169288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.131601 restraints weight = 5348.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134281 restraints weight = 3075.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.136073 restraints weight = 2187.222| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4175 Z= 0.190 Angle : 0.640 9.563 5693 Z= 0.326 Chirality : 0.041 0.125 608 Planarity : 0.005 0.039 717 Dihedral : 4.916 25.845 568 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.29 % Allowed : 20.42 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.37), residues: 495 helix: 0.61 (0.38), residues: 225 sheet: -1.18 (0.73), residues: 37 loop : -2.75 (0.34), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 114 HIS 0.002 0.001 HIS A 182 PHE 0.012 0.001 PHE A 262 TYR 0.010 0.001 TYR B 96 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.421 Fit side-chains REVERT: A 176 GLU cc_start: 0.7867 (tp30) cc_final: 0.7537 (tm-30) REVERT: B 114 TRP cc_start: 0.8551 (p90) cc_final: 0.8207 (p90) outliers start: 14 outliers final: 13 residues processed: 53 average time/residue: 0.1626 time to fit residues: 11.2245 Evaluate side-chains 55 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 80 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 38 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.162032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.122696 restraints weight = 5359.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125262 restraints weight = 3106.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126708 restraints weight = 2257.275| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4175 Z= 0.352 Angle : 0.765 9.522 5693 Z= 0.391 Chirality : 0.046 0.209 608 Planarity : 0.006 0.038 717 Dihedral : 5.217 30.511 568 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.99 % Allowed : 20.19 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.38), residues: 495 helix: 0.27 (0.37), residues: 230 sheet: -0.54 (0.72), residues: 50 loop : -2.77 (0.37), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 216 HIS 0.005 0.001 HIS A 147 PHE 0.013 0.002 PHE A 196 TYR 0.016 0.002 TYR A 93 ARG 0.005 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.442 Fit side-chains REVERT: B 96 TYR cc_start: 0.6227 (OUTLIER) cc_final: 0.5377 (m-80) outliers start: 17 outliers final: 16 residues processed: 59 average time/residue: 0.1564 time to fit residues: 12.0587 Evaluate side-chains 64 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.0030 chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.0470 overall best weight: 0.5488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.168549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132450 restraints weight = 5417.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.133923 restraints weight = 3030.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135421 restraints weight = 2322.107| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4175 Z= 0.183 Angle : 0.663 9.352 5693 Z= 0.334 Chirality : 0.041 0.135 608 Planarity : 0.005 0.039 717 Dihedral : 5.020 29.680 568 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.29 % Allowed : 21.60 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.38), residues: 495 helix: 0.55 (0.38), residues: 226 sheet: -0.45 (0.72), residues: 50 loop : -2.65 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 114 HIS 0.002 0.001 HIS A 282 PHE 0.013 0.001 PHE A 262 TYR 0.012 0.001 TYR B 61 ARG 0.005 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.469 Fit side-chains REVERT: B 96 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.5414 (m-80) REVERT: B 114 TRP cc_start: 0.8478 (p90) cc_final: 0.8193 (p90) outliers start: 14 outliers final: 13 residues processed: 53 average time/residue: 0.1737 time to fit residues: 11.8072 Evaluate side-chains 58 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 96 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 43 optimal weight: 0.0040 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 0.0070 chunk 40 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 overall best weight: 0.4810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.168791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131489 restraints weight = 5342.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133273 restraints weight = 3017.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134988 restraints weight = 2120.051| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4175 Z= 0.177 Angle : 0.647 8.726 5693 Z= 0.328 Chirality : 0.041 0.133 608 Planarity : 0.005 0.038 717 Dihedral : 4.765 24.903 568 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.29 % Allowed : 21.60 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.38), residues: 495 helix: 0.75 (0.38), residues: 225 sheet: -0.22 (0.73), residues: 50 loop : -2.46 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 114 HIS 0.003 0.001 HIS A 282 PHE 0.010 0.001 PHE A 262 TYR 0.011 0.001 TYR B 61 ARG 0.003 0.000 ARG B 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.430 Fit side-chains REVERT: A 97 LEU cc_start: 0.9131 (tp) cc_final: 0.8707 (tt) REVERT: A 388 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 96 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.5331 (m-80) outliers start: 14 outliers final: 12 residues processed: 57 average time/residue: 0.1572 time to fit residues: 11.5793 Evaluate side-chains 56 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.167714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.130487 restraints weight = 5296.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132418 restraints weight = 2950.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.134295 restraints weight = 1983.408| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4175 Z= 0.198 Angle : 0.663 8.624 5693 Z= 0.335 Chirality : 0.042 0.119 608 Planarity : 0.005 0.038 717 Dihedral : 4.750 25.925 568 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.05 % Allowed : 22.30 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.38), residues: 495 helix: 0.71 (0.38), residues: 226 sheet: -0.24 (0.74), residues: 50 loop : -2.46 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 114 HIS 0.003 0.001 HIS A 321 PHE 0.010 0.001 PHE A 262 TYR 0.011 0.001 TYR B 61 ARG 0.004 0.000 ARG B 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1604.17 seconds wall clock time: 29 minutes 32.70 seconds (1772.70 seconds total)