Starting phenix.real_space_refine on Fri Dec 27 08:40:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc4_40337/12_2024/8sc4_40337.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc4_40337/12_2024/8sc4_40337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sc4_40337/12_2024/8sc4_40337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc4_40337/12_2024/8sc4_40337.map" model { file = "/net/cci-nas-00/data/ceres_data/8sc4_40337/12_2024/8sc4_40337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc4_40337/12_2024/8sc4_40337.cif" } resolution = 3.46 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= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 2335 2.51 5 N 579 2.21 5 O 599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3544 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3535 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 24, 'TRANS': 431} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.81, per 1000 atoms: 0.79 Number of scatterers: 3544 At special positions: 0 Unit cell: (88.803, 81.972, 67.4561, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 599 8.00 N 579 7.00 C 2335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 449.1 milliseconds 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 2 sheets defined 82.0% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 4.356A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 65 through 73 removed outlier: 4.048A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.570A pdb=" N GLY A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 145 through 173 removed outlier: 3.946A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.942A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 4.152A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 258 removed outlier: 4.439A pdb=" N ARG A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 280 Proline residue: A 271 - end of helix removed outlier: 3.680A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 340 through 372 Processing helix chain 'A' and resid 374 through 401 removed outlier: 3.666A pdb=" N SER A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 402 through 423 removed outlier: 3.580A pdb=" N ILE A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 removed outlier: 3.580A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 485 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.824A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 253 hydrogen bonds defined for protein. 735 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: 1.02 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1089 1.35 - 1.46: 929 1.46 - 1.58: 1575 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 3639 Sorted by residual: bond pdb=" N GLN A 241 " pdb=" CA GLN A 241 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.32e+00 bond pdb=" C07 MF8 A 601 " pdb=" N09 MF8 A 601 " ideal model delta sigma weight residual 1.358 1.317 0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C07 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.393 1.354 0.039 2.00e-02 2.50e+03 3.87e+00 bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.314 -0.033 2.00e-02 2.50e+03 2.78e+00 bond pdb=" C04 MF8 A 601 " pdb=" N05 MF8 A 601 " ideal model delta sigma weight residual 1.284 1.316 -0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 3634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 4628 1.21 - 2.43: 270 2.43 - 3.64: 45 3.64 - 4.86: 16 4.86 - 6.07: 4 Bond angle restraints: 4963 Sorted by residual: angle pdb=" C LEU A 180 " pdb=" N GLY A 181 " pdb=" CA GLY A 181 " ideal model delta sigma weight residual 119.94 122.86 -2.92 1.11e+00 8.12e-01 6.93e+00 angle pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " ideal model delta sigma weight residual 114.40 120.31 -5.91 2.30e+00 1.89e-01 6.60e+00 angle pdb=" N GLN A 241 " pdb=" CA GLN A 241 " pdb=" C GLN A 241 " ideal model delta sigma weight residual 111.07 108.38 2.69 1.07e+00 8.73e-01 6.34e+00 angle pdb=" C ASN A 374 " pdb=" N LEU A 375 " pdb=" CA LEU A 375 " ideal model delta sigma weight residual 120.54 123.86 -3.32 1.35e+00 5.49e-01 6.06e+00 angle pdb=" CA GLN A 241 " pdb=" C GLN A 241 " pdb=" O GLN A 241 " ideal model delta sigma weight residual 120.82 118.35 2.47 1.05e+00 9.07e-01 5.52e+00 ... (remaining 4958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 1938 14.28 - 28.56: 130 28.56 - 42.84: 35 42.84 - 57.12: 5 57.12 - 71.40: 2 Dihedral angle restraints: 2110 sinusoidal: 804 harmonic: 1306 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -47.29 -38.71 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" CA SER A 424 " pdb=" C SER A 424 " pdb=" N PRO A 425 " pdb=" CA PRO A 425 " ideal model delta harmonic sigma weight residual 180.00 -165.86 -14.14 0 5.00e+00 4.00e-02 8.00e+00 dihedral pdb=" CA ASN A 374 " pdb=" C ASN A 374 " pdb=" N LEU A 375 " pdb=" CA LEU A 375 " ideal model delta harmonic sigma weight residual -180.00 -165.96 -14.04 0 5.00e+00 4.00e-02 7.88e+00 ... (remaining 2107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 361 0.033 - 0.066: 159 0.066 - 0.099: 41 0.099 - 0.132: 12 0.132 - 0.165: 1 Chirality restraints: 574 Sorted by residual: chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA PRO A 286 " pdb=" N PRO A 286 " pdb=" C PRO A 286 " pdb=" CB PRO A 286 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA VAL A 126 " pdb=" N VAL A 126 " pdb=" C VAL A 126 " pdb=" CB VAL A 126 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 571 not shown) Planarity restraints: 613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " -1.308 2.00e-02 2.50e+03 6.51e-01 9.54e+03 pdb=" C03 MF8 A 601 " 1.075 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " -0.093 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " 0.035 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " -0.105 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " 0.321 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " -0.546 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " 0.721 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 406 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C MET A 406 " 0.041 2.00e-02 2.50e+03 pdb=" O MET A 406 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 407 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 182 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C THR A 182 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 182 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 183 " 0.013 2.00e-02 2.50e+03 ... (remaining 610 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 964 2.82 - 3.34: 3680 3.34 - 3.86: 5933 3.86 - 4.38: 6701 4.38 - 4.90: 11468 Nonbonded interactions: 28746 Sorted by model distance: nonbonded pdb=" OG SER A 196 " pdb=" OG SER A 201 " model vdw 2.296 3.040 nonbonded pdb=" NH1 ARG A 175 " pdb=" O LEU A 290 " model vdw 2.334 3.120 nonbonded pdb=" O VAL A 74 " pdb=" NH2 ARG A 113 " model vdw 2.385 3.120 nonbonded pdb=" OG1 THR A 245 " pdb=" OE1 GLU A 386 " model vdw 2.437 3.040 nonbonded pdb=" O ALA A 506 " pdb=" OG1 THR A 510 " model vdw 2.472 3.040 ... (remaining 28741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic 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: 0.700 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: 13.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.004 0.041 3639 Z= 0.241 Angle : 0.683 6.073 4963 Z= 0.390 Chirality : 0.039 0.165 574 Planarity : 0.027 0.651 613 Dihedral : 10.980 71.396 1265 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -0.96 (0.38), residues: 452 helix: -0.84 (0.26), residues: 329 sheet: None (None), residues: 0 loop : 0.59 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 288 HIS 0.003 0.001 HIS A 48 PHE 0.032 0.002 PHE A 173 TYR 0.012 0.002 TYR A 168 ARG 0.006 0.001 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 132 SER cc_start: 0.8553 (p) cc_final: 0.8200 (m) REVERT: A 218 MET cc_start: 0.7252 (mmm) cc_final: 0.6998 (mmt) REVERT: A 346 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7634 (mtt90) REVERT: A 378 ASP cc_start: 0.7707 (m-30) cc_final: 0.7330 (m-30) REVERT: A 418 LEU cc_start: 0.8570 (tp) cc_final: 0.8242 (tp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1623 time to fit residues: 23.8558 Evaluate side-chains 86 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.0070 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.0170 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 115 HIS A 428 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3639 Z= 0.186 Angle : 0.688 15.080 4963 Z= 0.330 Chirality : 0.040 0.214 574 Planarity : 0.005 0.074 613 Dihedral : 4.279 17.434 491 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 2.63 % Allowed : 10.53 % Favored : 86.84 % 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 (0.42), residues: 452 helix: 1.22 (0.29), residues: 329 sheet: None (None), residues: 0 loop : 1.51 (0.66), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 288 HIS 0.002 0.001 HIS A 49 PHE 0.021 0.002 PHE A 22 TYR 0.010 0.001 TYR A 352 ARG 0.007 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.390 Fit side-chains REVERT: A 22 PHE cc_start: 0.6264 (t80) cc_final: 0.5784 (t80) REVERT: A 121 CYS cc_start: 0.5460 (OUTLIER) cc_final: 0.5050 (m) REVERT: A 227 PHE cc_start: 0.7825 (t80) cc_final: 0.7468 (t80) REVERT: A 346 ARG cc_start: 0.7903 (mtt180) cc_final: 0.7544 (mtt90) REVERT: A 418 LEU cc_start: 0.8517 (tp) cc_final: 0.8213 (tp) outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.1352 time to fit residues: 16.1479 Evaluate side-chains 84 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.0670 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 428 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3639 Z= 0.166 Angle : 0.660 14.640 4963 Z= 0.306 Chirality : 0.038 0.167 574 Planarity : 0.005 0.057 613 Dihedral : 4.058 17.378 491 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.16 % Allowed : 11.32 % Favored : 85.53 % 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: 2.45 (0.43), residues: 452 helix: 1.69 (0.30), residues: 323 sheet: None (None), residues: 0 loop : 1.78 (0.67), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.028 0.001 PHE A 22 TYR 0.012 0.001 TYR A 240 ARG 0.006 0.001 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5543 (OUTLIER) cc_final: 0.5157 (m) REVERT: A 227 PHE cc_start: 0.7876 (t80) cc_final: 0.7586 (t80) REVERT: A 346 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7491 (mtt90) REVERT: A 418 LEU cc_start: 0.8461 (tp) cc_final: 0.8085 (tp) outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 0.1310 time to fit residues: 15.3630 Evaluate side-chains 86 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 410 ASN A 453 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3639 Z= 0.239 Angle : 0.659 14.499 4963 Z= 0.310 Chirality : 0.040 0.137 574 Planarity : 0.004 0.054 613 Dihedral : 4.060 16.839 491 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.47 % Allowed : 12.63 % Favored : 82.89 % 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: 2.45 (0.43), residues: 452 helix: 1.70 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.74 (0.70), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS A 48 PHE 0.024 0.002 PHE A 22 TYR 0.009 0.001 TYR A 352 ARG 0.005 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.374 Fit side-chains REVERT: A 121 CYS cc_start: 0.5654 (OUTLIER) cc_final: 0.5271 (m) REVERT: A 227 PHE cc_start: 0.7939 (t80) cc_final: 0.7644 (t80) REVERT: A 242 MET cc_start: 0.6898 (mtm) cc_final: 0.6611 (mtt) REVERT: A 346 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7523 (mtt90) outliers start: 17 outliers final: 14 residues processed: 87 average time/residue: 0.1347 time to fit residues: 14.9350 Evaluate side-chains 92 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3639 Z= 0.193 Angle : 0.640 14.539 4963 Z= 0.300 Chirality : 0.039 0.195 574 Planarity : 0.004 0.046 613 Dihedral : 4.012 16.756 491 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.95 % Allowed : 15.00 % Favored : 81.05 % 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: 2.57 (0.43), residues: 452 helix: 1.86 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.57 (0.68), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.018 0.001 PHE A 22 TYR 0.007 0.001 TYR A 352 ARG 0.004 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5651 (OUTLIER) cc_final: 0.5270 (m) REVERT: A 218 MET cc_start: 0.7367 (mmt) cc_final: 0.6987 (mmt) REVERT: A 227 PHE cc_start: 0.7961 (t80) cc_final: 0.7668 (t80) REVERT: A 242 MET cc_start: 0.6877 (mtm) cc_final: 0.6639 (mtt) REVERT: A 346 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7451 (mtt90) outliers start: 15 outliers final: 11 residues processed: 89 average time/residue: 0.1233 time to fit residues: 14.2016 Evaluate side-chains 94 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3639 Z= 0.220 Angle : 0.669 14.513 4963 Z= 0.309 Chirality : 0.040 0.181 574 Planarity : 0.004 0.045 613 Dihedral : 3.987 16.253 491 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.21 % Allowed : 15.79 % Favored : 80.00 % 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: 2.57 (0.42), residues: 452 helix: 1.88 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.47 (0.68), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.016 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.006 0.001 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5617 (OUTLIER) cc_final: 0.5281 (m) REVERT: A 227 PHE cc_start: 0.7932 (t80) cc_final: 0.7631 (t80) REVERT: A 242 MET cc_start: 0.6772 (mtm) cc_final: 0.6510 (mtt) outliers start: 16 outliers final: 15 residues processed: 92 average time/residue: 0.1208 time to fit residues: 14.3383 Evaluate side-chains 94 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.0870 chunk 20 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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: 0.7563 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3639 Z= 0.180 Angle : 0.666 14.566 4963 Z= 0.305 Chirality : 0.039 0.189 574 Planarity : 0.004 0.042 613 Dihedral : 3.927 17.762 491 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.68 % Allowed : 16.58 % Favored : 79.74 % 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: 2.77 (0.43), residues: 452 helix: 2.02 (0.30), residues: 330 sheet: None (None), residues: 0 loop : 1.59 (0.68), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.020 0.001 PHE A 348 TYR 0.009 0.001 TYR A 352 ARG 0.003 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5581 (OUTLIER) cc_final: 0.5253 (m) REVERT: A 227 PHE cc_start: 0.7880 (t80) cc_final: 0.7562 (t80) REVERT: A 486 ARG cc_start: 0.7558 (mmp80) cc_final: 0.7157 (mmm160) outliers start: 14 outliers final: 13 residues processed: 88 average time/residue: 0.1156 time to fit residues: 13.2693 Evaluate side-chains 94 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 12 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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: 0.7561 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3639 Z= 0.183 Angle : 0.669 14.568 4963 Z= 0.307 Chirality : 0.040 0.210 574 Planarity : 0.004 0.042 613 Dihedral : 3.896 17.467 491 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.21 % Allowed : 16.32 % Favored : 79.47 % 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: 2.79 (0.42), residues: 452 helix: 2.05 (0.30), residues: 330 sheet: None (None), residues: 0 loop : 1.53 (0.67), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.020 0.001 PHE A 348 TYR 0.009 0.001 TYR A 352 ARG 0.004 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5589 (OUTLIER) cc_final: 0.5274 (m) REVERT: A 227 PHE cc_start: 0.7821 (t80) cc_final: 0.7508 (t80) REVERT: A 486 ARG cc_start: 0.7558 (mmp80) cc_final: 0.7226 (mmm160) outliers start: 16 outliers final: 13 residues processed: 89 average time/residue: 0.1141 time to fit residues: 13.4199 Evaluate side-chains 88 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 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: 0.7610 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3639 Z= 0.228 Angle : 0.705 14.512 4963 Z= 0.329 Chirality : 0.041 0.222 574 Planarity : 0.004 0.039 613 Dihedral : 3.972 16.923 491 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.21 % Allowed : 16.84 % Favored : 78.95 % 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: 2.70 (0.42), residues: 452 helix: 2.01 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.41 (0.67), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.018 0.001 PHE A 348 TYR 0.013 0.001 TYR A 352 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5639 (OUTLIER) cc_final: 0.5317 (m) REVERT: A 227 PHE cc_start: 0.7869 (t80) cc_final: 0.7541 (t80) outliers start: 16 outliers final: 14 residues processed: 88 average time/residue: 0.1119 time to fit residues: 12.9865 Evaluate side-chains 89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.0670 chunk 32 optimal weight: 0.4980 chunk 5 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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: 0.7552 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3639 Z= 0.180 Angle : 0.690 14.577 4963 Z= 0.316 Chirality : 0.040 0.240 574 Planarity : 0.004 0.037 613 Dihedral : 3.904 17.025 491 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.68 % Allowed : 18.16 % Favored : 78.16 % 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: 2.89 (0.42), residues: 452 helix: 2.16 (0.30), residues: 323 sheet: None (None), residues: 0 loop : 1.52 (0.65), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.021 0.001 PHE A 348 TYR 0.009 0.001 TYR A 352 ARG 0.003 0.000 ARG A 488 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5513 (OUTLIER) cc_final: 0.5193 (m) REVERT: A 227 PHE cc_start: 0.7818 (t80) cc_final: 0.7471 (t80) REVERT: A 486 ARG cc_start: 0.7538 (mmp80) cc_final: 0.7162 (mmm160) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.1168 time to fit residues: 13.6455 Evaluate side-chains 90 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.0060 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.199575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.153940 restraints weight = 4679.400| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.75 r_work: 0.3695 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3639 Z= 0.193 Angle : 0.713 14.563 4963 Z= 0.328 Chirality : 0.041 0.223 574 Planarity : 0.004 0.038 613 Dihedral : 3.910 16.686 491 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.42 % Allowed : 18.42 % Favored : 78.16 % 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: 2.67 (0.42), residues: 452 helix: 1.98 (0.29), residues: 323 sheet: None (None), residues: 0 loop : 1.47 (0.65), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 PHE 0.021 0.001 PHE A 348 TYR 0.017 0.001 TYR A 256 ARG 0.002 0.000 ARG A 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1183.73 seconds wall clock time: 22 minutes 9.56 seconds (1329.56 seconds total)