Starting phenix.real_space_refine on Fri Dec 27 10:19:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sbb_40303/12_2024/8sbb_40303.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sbb_40303/12_2024/8sbb_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_40303/12_2024/8sbb_40303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sbb_40303/12_2024/8sbb_40303.map" model { file = "/net/cci-nas-00/data/ceres_data/8sbb_40303/12_2024/8sbb_40303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sbb_40303/12_2024/8sbb_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.54, per 1000 atoms: 0.87 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 501.0 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: 0.49 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: 1.06 Time building geometry restraints manager: 1.25 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.450 ------------------------------------------------------------------------------- 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 : 0.466 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: 0.2072 time to fit residues: 26.1262 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 : 0.462 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.462 Fit side-chains REVERT: A 64 LEU cc_start: 0.8696 (tp) cc_final: 0.8437 (mp) REVERT: A 176 GLU cc_start: 0.7917 (tp30) cc_final: 0.7617 (tm-30) REVERT: A 288 GLN cc_start: 0.7113 (mm-40) cc_final: 0.6781 (mm-40) REVERT: B 23 SER cc_start: 0.7925 (p) cc_final: 0.7718 (m) REVERT: B 54 SER cc_start: 0.8112 (t) cc_final: 0.7705 (m) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.1416 time to fit residues: 13.3437 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 : 0.450 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 30 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4175 Z= 0.186 Angle : 0.662 6.414 5693 Z= 0.345 Chirality : 0.042 0.148 608 Planarity : 0.006 0.046 717 Dihedral : 5.202 28.847 568 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.82 % Allowed : 18.08 % Favored : 79.11 % 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: -2.47 (0.36), residues: 495 helix: -0.10 (0.37), residues: 230 sheet: -2.15 (0.66), residues: 39 loop : -3.30 (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 A 21 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 : 0.450 Fit side-chains REVERT: A 64 LEU cc_start: 0.8749 (tp) cc_final: 0.8448 (mp) REVERT: A 176 GLU cc_start: 0.7864 (tp30) cc_final: 0.7659 (tm-30) REVERT: A 288 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6828 (mm-40) REVERT: A 365 MET cc_start: 0.7978 (mmm) cc_final: 0.7671 (mmm) outliers start: 12 outliers final: 7 residues processed: 58 average time/residue: 0.1482 time to fit residues: 11.2119 Evaluate side-chains 50 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.0010 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 26 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3961 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= 0.196 Angle : 0.658 6.658 5693 Z= 0.339 Chirality : 0.043 0.137 608 Planarity : 0.005 0.045 717 Dihedral : 5.057 26.861 568 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.23 % Allowed : 16.90 % 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: -1.93 (0.37), residues: 495 helix: 0.18 (0.37), residues: 230 sheet: -1.27 (0.72), residues: 39 loop : -2.94 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 125 HIS 0.003 0.001 HIS A 147 PHE 0.011 0.001 PHE A 262 TYR 0.015 0.001 TYR B 61 ARG 0.002 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: 18 poor density : 47 time to evaluate : 0.453 Fit side-chains REVERT: A 288 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6887 (mm-40) REVERT: A 365 MET cc_start: 0.7968 (mmm) cc_final: 0.7645 (mmm) outliers start: 18 outliers final: 15 residues processed: 59 average time/residue: 0.1314 time to fit residues: 10.3812 Evaluate side-chains 61 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 97 LEU 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 288 GLN 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 35 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4175 Z= 0.232 Angle : 0.670 7.410 5693 Z= 0.345 Chirality : 0.043 0.129 608 Planarity : 0.005 0.043 717 Dihedral : 5.030 25.909 568 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.99 % Allowed : 17.37 % Favored : 78.64 % 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: -1.90 (0.37), residues: 495 helix: 0.28 (0.37), residues: 230 sheet: -2.28 (0.85), residues: 28 loop : -2.82 (0.34), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 216 HIS 0.003 0.001 HIS A 147 PHE 0.011 0.001 PHE A 262 TYR 0.013 0.002 TYR B 61 ARG 0.002 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 66 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.8042 (mmm) cc_final: 0.7645 (mmm) REVERT: B 114 TRP cc_start: 0.8736 (p90) cc_final: 0.8463 (p90) outliers start: 17 outliers final: 16 residues processed: 59 average time/residue: 0.1508 time to fit residues: 11.5491 Evaluate side-chains 63 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 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 288 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4483 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 : 0.634 6.884 5693 Z= 0.327 Chirality : 0.042 0.127 608 Planarity : 0.005 0.040 717 Dihedral : 4.890 26.657 568 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.23 % Allowed : 18.31 % Favored : 77.46 % 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: -1.64 (0.37), residues: 495 helix: 0.46 (0.38), residues: 227 sheet: -1.36 (0.71), residues: 37 loop : -2.74 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 216 HIS 0.002 0.001 HIS A 282 PHE 0.012 0.001 PHE A 262 TYR 0.011 0.001 TYR B 96 ARG 0.003 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 68 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.469 Fit side-chains REVERT: A 176 GLU cc_start: 0.8049 (tp30) cc_final: 0.7701 (tm-30) REVERT: A 288 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7305 (mm-40) REVERT: A 379 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7144 (tptp) REVERT: B 54 SER cc_start: 0.7761 (t) cc_final: 0.7484 (m) outliers start: 18 outliers final: 12 residues processed: 61 average time/residue: 0.1582 time to fit residues: 12.5673 Evaluate side-chains 61 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 175 ILE 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 288 GLN 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 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 26 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4175 Z= 0.210 Angle : 0.673 10.853 5693 Z= 0.339 Chirality : 0.043 0.228 608 Planarity : 0.005 0.039 717 Dihedral : 4.815 25.658 567 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.52 % Allowed : 19.72 % Favored : 76.76 % 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: -1.47 (0.38), residues: 495 helix: 0.61 (0.38), residues: 225 sheet: -1.41 (0.80), residues: 41 loop : -2.63 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 216 HIS 0.003 0.001 HIS A 308 PHE 0.011 0.001 PHE A 262 TYR 0.010 0.001 TYR B 96 ARG 0.003 0.000 ARG B 73 *********************** 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 61 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.498 Fit side-chains REVERT: A 176 GLU cc_start: 0.8011 (tp30) cc_final: 0.7750 (tm-30) REVERT: A 288 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7286 (mm-40) REVERT: A 379 LYS cc_start: 0.7926 (mmmt) cc_final: 0.7626 (mtpt) outliers start: 15 outliers final: 12 residues processed: 56 average time/residue: 0.1630 time to fit residues: 11.6970 Evaluate side-chains 58 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 288 GLN 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 80 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4799 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= 0.209 Angle : 0.663 10.309 5693 Z= 0.334 Chirality : 0.042 0.150 608 Planarity : 0.005 0.038 717 Dihedral : 4.765 25.992 567 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.23 % Allowed : 19.25 % Favored : 76.53 % 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: -1.28 (0.38), residues: 495 helix: 0.61 (0.38), residues: 226 sheet: -0.55 (0.73), residues: 50 loop : -2.59 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 216 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 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 64 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.477 Fit side-chains REVERT: A 176 GLU cc_start: 0.8004 (tp30) cc_final: 0.7770 (tm-30) REVERT: A 288 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7340 (mm-40) REVERT: A 379 LYS cc_start: 0.7881 (mmmt) cc_final: 0.7572 (mtpt) REVERT: A 388 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7326 (mm-30) REVERT: B 96 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.5272 (m-80) outliers start: 18 outliers final: 14 residues processed: 56 average time/residue: 0.1684 time to fit residues: 12.1068 Evaluate side-chains 63 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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 288 GLN 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 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 39 optimal weight: 0.0020 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 22 optimal weight: 0.0370 chunk 32 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.0270 chunk 4 optimal weight: 0.9990 overall best weight: 0.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4175 Z= 0.159 Angle : 0.634 10.108 5693 Z= 0.316 Chirality : 0.040 0.127 608 Planarity : 0.005 0.039 717 Dihedral : 4.597 23.253 567 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.88 % Allowed : 22.07 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.38), residues: 495 helix: 0.80 (0.38), residues: 225 sheet: -0.26 (0.73), residues: 50 loop : -2.48 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 125 HIS 0.003 0.001 HIS A 282 PHE 0.011 0.001 PHE A 262 TYR 0.012 0.001 TYR B 61 ARG 0.003 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: 8 poor density : 51 time to evaluate : 0.460 Fit side-chains REVERT: A 97 LEU cc_start: 0.9111 (tp) cc_final: 0.8689 (tt) REVERT: A 288 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7325 (mm-40) REVERT: A 379 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7554 (mtpt) REVERT: A 388 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7306 (mm-30) REVERT: B 96 TYR cc_start: 0.6108 (OUTLIER) cc_final: 0.5208 (m-80) outliers start: 8 outliers final: 6 residues processed: 56 average time/residue: 0.1697 time to fit residues: 12.0928 Evaluate side-chains 55 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 380 ILE 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 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.0570 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.0170 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5123 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= 0.170 Angle : 0.638 10.007 5693 Z= 0.320 Chirality : 0.041 0.135 608 Planarity : 0.005 0.038 717 Dihedral : 4.505 22.632 567 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.88 % Allowed : 22.54 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.38), residues: 495 helix: 0.90 (0.38), residues: 225 sheet: -0.04 (0.75), residues: 50 loop : -2.41 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 125 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 0.002 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 57 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.469 Fit side-chains REVERT: A 97 LEU cc_start: 0.9128 (tp) cc_final: 0.8528 (tt) REVERT: A 379 LYS cc_start: 0.7884 (mmmt) cc_final: 0.7570 (mtpt) REVERT: A 388 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7292 (mm-30) REVERT: B 96 TYR cc_start: 0.6094 (OUTLIER) cc_final: 0.5131 (m-80) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.2043 time to fit residues: 13.6700 Evaluate side-chains 52 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 380 ILE 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 7 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.168497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129454 restraints weight = 5246.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132338 restraints weight = 2931.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134150 restraints weight = 2069.205| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5171 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= 0.189 Angle : 0.657 9.804 5693 Z= 0.331 Chirality : 0.041 0.135 608 Planarity : 0.005 0.038 717 Dihedral : 4.538 23.559 567 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.35 % Allowed : 22.07 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.38), residues: 495 helix: 0.88 (0.38), residues: 225 sheet: 0.01 (0.76), residues: 50 loop : -2.39 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 216 HIS 0.002 0.001 HIS A 282 PHE 0.010 0.001 PHE A 262 TYR 0.012 0.001 TYR B 61 ARG 0.006 0.000 ARG A 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1122.62 seconds wall clock time: 20 minutes 55.91 seconds (1255.91 seconds total)