Starting phenix.real_space_refine on Fri May 9 18:49:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc1_40334/05_2025/8sc1_40334.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc1_40334/05_2025/8sc1_40334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sc1_40334/05_2025/8sc1_40334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc1_40334/05_2025/8sc1_40334.map" model { file = "/net/cci-nas-00/data/ceres_data/8sc1_40334/05_2025/8sc1_40334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc1_40334/05_2025/8sc1_40334.cif" } resolution = 2.92 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= 0.034 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 30 5.16 5 C 2270 2.51 5 N 559 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3447 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3447 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 1 Time building chain proxies: 2.59, per 1000 atoms: 0.75 Number of scatterers: 3447 At special positions: 0 Unit cell: (92.02, 84.28, 65.36, 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 30 16.00 O 588 8.00 N 559 7.00 C 2270 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=2.04 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: 0.75 Conformation dependent library (CDL) restraints added in 489.8 milliseconds 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 816 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 2 sheets defined 83.4% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.559A pdb=" N ILE A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (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 74 removed outlier: 3.873A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.997A pdb=" N SER A 108 " --> pdb=" O PRO A 105 " (cutoff:3.500A) 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 145 Processing helix chain 'A' and resid 146 through 173 removed outlier: 3.961A pdb=" N LEU A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.953A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.838A pdb=" N VAL A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.705A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Proline residue: A 271 - end of helix removed outlier: 3.881A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.522A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 372 removed outlier: 3.551A pdb=" N ILE A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.558A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 removed outlier: 3.682A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 420 removed outlier: 3.537A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 removed outlier: 4.048A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 removed outlier: 4.522A pdb=" N ASN A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 464 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 487 removed outlier: 3.626A pdb=" N ILE A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.742A pdb=" N GLY A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 4.163A 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 removed outlier: 3.540A pdb=" N HIS A 49 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 238 hydrogen bonds defined for protein. 684 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: 0.95 Time building geometry restraints manager: 0.90 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: 1064 1.35 - 1.47: 908 1.47 - 1.59: 1520 1.59 - 1.71: 0 1.71 - 1.84: 45 Bond restraints: 3537 Sorted by residual: bond pdb=" CA THR A 480 " pdb=" C THR A 480 " ideal model delta sigma weight residual 1.522 1.533 -0.011 1.29e-02 6.01e+03 7.91e-01 bond pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " ideal model delta sigma weight residual 1.808 1.836 -0.028 3.30e-02 9.18e+02 6.96e-01 bond pdb=" CA LEU A 494 " pdb=" C LEU A 494 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.91e-01 bond pdb=" C ILE A 387 " pdb=" O ILE A 387 " ideal model delta sigma weight residual 1.240 1.250 -0.010 1.26e-02 6.30e+03 6.41e-01 bond pdb=" C GLY A 253 " pdb=" O GLY A 253 " ideal model delta sigma weight residual 1.235 1.245 -0.010 1.35e-02 5.49e+03 5.59e-01 ... (remaining 3532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 4509 1.21 - 2.42: 252 2.42 - 3.64: 40 3.64 - 4.85: 12 4.85 - 6.06: 8 Bond angle restraints: 4821 Sorted by residual: angle pdb=" N VAL A 212 " pdb=" CA VAL A 212 " pdb=" C VAL A 212 " ideal model delta sigma weight residual 109.34 115.13 -5.79 2.08e+00 2.31e-01 7.74e+00 angle pdb=" CA CYS A 121 " pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " ideal model delta sigma weight residual 114.40 120.46 -6.06 2.30e+00 1.89e-01 6.94e+00 angle pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " ideal model delta sigma weight residual 114.40 120.45 -6.05 2.30e+00 1.89e-01 6.93e+00 angle pdb=" N TYR A 404 " pdb=" CA TYR A 404 " pdb=" C TYR A 404 " ideal model delta sigma weight residual 109.81 115.25 -5.44 2.21e+00 2.05e-01 6.05e+00 angle pdb=" CA TRP A 261 " pdb=" CB TRP A 261 " pdb=" CG TRP A 261 " ideal model delta sigma weight residual 113.60 118.11 -4.51 1.90e+00 2.77e-01 5.64e+00 ... (remaining 4816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.66: 1924 14.66 - 29.32: 99 29.32 - 43.97: 24 43.97 - 58.63: 9 58.63 - 73.29: 2 Dihedral angle restraints: 2058 sinusoidal: 782 harmonic: 1276 Sorted by residual: dihedral pdb=" CA TYR A 72 " pdb=" C TYR A 72 " pdb=" N THR A 73 " pdb=" CA THR A 73 " ideal model delta harmonic sigma weight residual -180.00 -157.79 -22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA CYS A 50 " pdb=" C CYS A 50 " pdb=" N GLN A 51 " pdb=" CA GLN A 51 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ARG A 399 " pdb=" C ARG A 399 " pdb=" N VAL A 400 " pdb=" CA VAL A 400 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 2055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 321 0.027 - 0.055: 158 0.055 - 0.082: 54 0.082 - 0.110: 14 0.110 - 0.137: 14 Chirality restraints: 561 Sorted by residual: chirality pdb=" CA PRO A 341 " pdb=" N PRO A 341 " pdb=" C PRO A 341 " pdb=" CB PRO A 341 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA TYR A 72 " pdb=" N TYR A 72 " pdb=" C TYR A 72 " pdb=" CB TYR A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.82e-01 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 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 558 not shown) Planarity restraints: 597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 182 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C THR A 182 " -0.049 2.00e-02 2.50e+03 pdb=" O THR A 182 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 183 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 72 " 0.011 2.00e-02 2.50e+03 1.70e-02 5.78e+00 pdb=" CG TYR A 72 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 72 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 72 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 72 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 72 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 72 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR A 72 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 206 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C ARG A 206 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG A 206 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 207 " 0.013 2.00e-02 2.50e+03 ... (remaining 594 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 781 2.79 - 3.32: 3376 3.32 - 3.85: 5235 3.85 - 4.37: 6164 4.37 - 4.90: 10862 Nonbonded interactions: 26418 Sorted by model distance: nonbonded pdb=" O LYS A 147 " pdb=" OH TYR A 199 " model vdw 2.266 3.040 nonbonded pdb=" NH2 ARG A 402 " pdb=" OE2 GLU A 455 " model vdw 2.384 3.120 nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.476 3.040 nonbonded pdb=" N ASP A 426 " pdb=" OD1 ASP A 426 " model vdw 2.508 3.120 nonbonded pdb=" N ASP A 149 " pdb=" OD1 ASP A 149 " model vdw 2.564 3.120 ... (remaining 26413 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: 0.840 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 12.810 Find NCS groups from input model: 0.030 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:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3540 Z= 0.152 Angle : 0.685 6.060 4827 Z= 0.399 Chirality : 0.040 0.137 561 Planarity : 0.008 0.058 597 Dihedral : 10.470 73.290 1233 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -0.78 (0.39), residues: 442 helix: -1.04 (0.27), residues: 298 sheet: None (None), residues: 0 loop : 1.20 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 261 HIS 0.002 0.001 HIS A 48 PHE 0.014 0.002 PHE A 22 TYR 0.023 0.003 TYR A 72 ARG 0.015 0.002 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.14640 ( 238) hydrogen bonds : angle 6.22326 ( 684) SS BOND : bond 0.00605 ( 3) SS BOND : angle 2.57538 ( 6) covalent geometry : bond 0.00276 ( 3537) covalent geometry : angle 0.67940 ( 4821) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.333 Fit side-chains REVERT: A 51 GLN cc_start: 0.8286 (tt0) cc_final: 0.7836 (mm-40) REVERT: A 218 MET cc_start: 0.7361 (mmm) cc_final: 0.6832 (mtm) REVERT: A 351 MET cc_start: 0.8254 (mtt) cc_final: 0.7981 (mtm) REVERT: A 396 THR cc_start: 0.7819 (m) cc_final: 0.7451 (p) REVERT: A 408 MET cc_start: 0.8154 (mmm) cc_final: 0.7936 (mmm) REVERT: A 480 THR cc_start: 0.7728 (m) cc_final: 0.7442 (m) REVERT: A 492 GLN cc_start: 0.6991 (mt0) cc_final: 0.6666 (tp-100) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.9492 time to fit residues: 52.2951 Evaluate side-chains 36 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.197659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.152827 restraints weight = 3547.293| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.88 r_work: 0.3460 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3540 Z= 0.152 Angle : 0.621 6.605 4827 Z= 0.320 Chirality : 0.038 0.118 561 Planarity : 0.005 0.035 597 Dihedral : 4.139 15.543 480 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.43 % Allowed : 4.05 % Favored : 93.51 % 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: 1.04 (0.40), residues: 442 helix: 0.75 (0.29), residues: 316 sheet: None (None), residues: 0 loop : 0.91 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 261 HIS 0.002 0.001 HIS A 48 PHE 0.014 0.002 PHE A 32 TYR 0.010 0.001 TYR A 240 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.05709 ( 238) hydrogen bonds : angle 4.36222 ( 684) SS BOND : bond 0.00352 ( 3) SS BOND : angle 3.02363 ( 6) covalent geometry : bond 0.00326 ( 3537) covalent geometry : angle 0.61236 ( 4821) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.332 Fit side-chains REVERT: A 51 GLN cc_start: 0.8666 (tt0) cc_final: 0.8090 (tm-30) REVERT: A 92 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: A 218 MET cc_start: 0.7454 (mmm) cc_final: 0.7188 (mmm) REVERT: A 396 THR cc_start: 0.7761 (m) cc_final: 0.7363 (p) REVERT: A 408 MET cc_start: 0.8141 (mmm) cc_final: 0.7934 (mmm) REVERT: A 492 GLN cc_start: 0.7143 (mt0) cc_final: 0.6383 (tp-100) outliers start: 9 outliers final: 1 residues processed: 40 average time/residue: 0.9626 time to fit residues: 40.1869 Evaluate side-chains 32 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 402 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 17 optimal weight: 0.0000 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.201124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156400 restraints weight = 3544.561| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.01 r_work: 0.3508 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3540 Z= 0.111 Angle : 0.514 5.534 4827 Z= 0.265 Chirality : 0.036 0.114 561 Planarity : 0.004 0.033 597 Dihedral : 3.726 15.283 480 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.89 % Allowed : 6.49 % Favored : 91.62 % 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: 2.27 (0.41), residues: 442 helix: 1.65 (0.30), residues: 305 sheet: None (None), residues: 0 loop : 1.45 (0.60), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.001 0.001 HIS A 49 PHE 0.013 0.001 PHE A 22 TYR 0.007 0.001 TYR A 240 ARG 0.003 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 238) hydrogen bonds : angle 3.98804 ( 684) SS BOND : bond 0.00216 ( 3) SS BOND : angle 2.26317 ( 6) covalent geometry : bond 0.00218 ( 3537) covalent geometry : angle 0.50763 ( 4821) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.344 Fit side-chains REVERT: A 51 GLN cc_start: 0.8622 (tt0) cc_final: 0.8149 (tm-30) REVERT: A 92 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6613 (mp0) REVERT: A 218 MET cc_start: 0.7375 (mmm) cc_final: 0.7168 (mmm) REVERT: A 239 MET cc_start: 0.6692 (ptp) cc_final: 0.5252 (tpt) REVERT: A 396 THR cc_start: 0.7792 (m) cc_final: 0.7326 (p) REVERT: A 492 GLN cc_start: 0.7126 (mt0) cc_final: 0.6295 (tp-100) outliers start: 7 outliers final: 2 residues processed: 36 average time/residue: 0.9003 time to fit residues: 34.1625 Evaluate side-chains 35 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 467 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.197386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.152048 restraints weight = 3586.981| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.97 r_work: 0.3442 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3540 Z= 0.142 Angle : 0.575 6.358 4827 Z= 0.294 Chirality : 0.037 0.119 561 Planarity : 0.005 0.035 597 Dihedral : 3.736 14.202 480 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.43 % Allowed : 7.03 % Favored : 90.54 % 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: 1.73 (0.40), residues: 442 helix: 1.35 (0.29), residues: 316 sheet: None (None), residues: 0 loop : 0.91 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE A 22 TYR 0.007 0.001 TYR A 457 ARG 0.001 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.05483 ( 238) hydrogen bonds : angle 4.06980 ( 684) SS BOND : bond 0.00317 ( 3) SS BOND : angle 2.66915 ( 6) covalent geometry : bond 0.00306 ( 3537) covalent geometry : angle 0.56719 ( 4821) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.337 Fit side-chains REVERT: A 51 GLN cc_start: 0.8513 (tt0) cc_final: 0.7992 (tm-30) REVERT: A 92 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: A 241 GLN cc_start: 0.6791 (mm-40) cc_final: 0.6489 (tm-30) REVERT: A 396 THR cc_start: 0.7669 (m) cc_final: 0.7191 (p) REVERT: A 451 LEU cc_start: 0.6988 (mp) cc_final: 0.6444 (tt) REVERT: A 492 GLN cc_start: 0.7411 (mt0) cc_final: 0.6974 (tm-30) outliers start: 9 outliers final: 4 residues processed: 45 average time/residue: 0.9855 time to fit residues: 46.2939 Evaluate side-chains 44 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.195916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.150951 restraints weight = 3613.778| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.93 r_work: 0.3468 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3540 Z= 0.131 Angle : 0.544 5.662 4827 Z= 0.279 Chirality : 0.037 0.115 561 Planarity : 0.004 0.036 597 Dihedral : 3.635 13.240 480 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.24 % Allowed : 7.03 % Favored : 89.73 % 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: 1.94 (0.40), residues: 442 helix: 1.49 (0.29), residues: 314 sheet: None (None), residues: 0 loop : 1.05 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE A 22 TYR 0.007 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.05051 ( 238) hydrogen bonds : angle 3.98110 ( 684) SS BOND : bond 0.00280 ( 3) SS BOND : angle 2.48925 ( 6) covalent geometry : bond 0.00282 ( 3537) covalent geometry : angle 0.53681 ( 4821) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.337 Fit side-chains REVERT: A 51 GLN cc_start: 0.8662 (tt0) cc_final: 0.8116 (tm-30) REVERT: A 92 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: A 239 MET cc_start: 0.6734 (ptp) cc_final: 0.5391 (tpt) REVERT: A 241 GLN cc_start: 0.7094 (mm-40) cc_final: 0.6676 (tm-30) REVERT: A 396 THR cc_start: 0.7706 (m) cc_final: 0.7203 (p) REVERT: A 451 LEU cc_start: 0.6982 (mp) cc_final: 0.6430 (tt) outliers start: 12 outliers final: 5 residues processed: 47 average time/residue: 0.8716 time to fit residues: 42.8459 Evaluate side-chains 42 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 32 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.197695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.152449 restraints weight = 3650.737| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.09 r_work: 0.3489 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3540 Z= 0.115 Angle : 0.510 5.547 4827 Z= 0.263 Chirality : 0.036 0.115 561 Planarity : 0.004 0.035 597 Dihedral : 3.559 17.129 480 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.43 % Allowed : 8.11 % Favored : 89.46 % 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: 2.24 (0.41), residues: 442 helix: 1.71 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.17 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 238) hydrogen bonds : angle 3.89711 ( 684) SS BOND : bond 0.00215 ( 3) SS BOND : angle 2.27343 ( 6) covalent geometry : bond 0.00235 ( 3537) covalent geometry : angle 0.50401 ( 4821) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.323 Fit side-chains REVERT: A 51 GLN cc_start: 0.8550 (tt0) cc_final: 0.7934 (tm-30) REVERT: A 92 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: A 241 GLN cc_start: 0.6843 (mm-40) cc_final: 0.6358 (tm-30) REVERT: A 396 THR cc_start: 0.7563 (m) cc_final: 0.7018 (p) REVERT: A 451 LEU cc_start: 0.6894 (mp) cc_final: 0.6329 (tt) outliers start: 9 outliers final: 3 residues processed: 42 average time/residue: 0.9417 time to fit residues: 41.1773 Evaluate side-chains 43 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 467 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 0.0570 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.197425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150899 restraints weight = 3602.440| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.01 r_work: 0.3460 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3540 Z= 0.119 Angle : 0.522 5.562 4827 Z= 0.269 Chirality : 0.036 0.114 561 Planarity : 0.004 0.038 597 Dihedral : 3.550 16.830 480 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.70 % Allowed : 8.11 % Favored : 89.19 % 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: 2.16 (0.41), residues: 442 helix: 1.68 (0.30), residues: 316 sheet: None (None), residues: 0 loop : 1.05 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 238) hydrogen bonds : angle 3.91132 ( 684) SS BOND : bond 0.00223 ( 3) SS BOND : angle 2.32556 ( 6) covalent geometry : bond 0.00246 ( 3537) covalent geometry : angle 0.51630 ( 4821) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.330 Fit side-chains REVERT: A 51 GLN cc_start: 0.8509 (tt0) cc_final: 0.8033 (tm-30) REVERT: A 92 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: A 239 MET cc_start: 0.6463 (ptp) cc_final: 0.5006 (tpt) REVERT: A 241 GLN cc_start: 0.7011 (mm-40) cc_final: 0.6776 (tm-30) REVERT: A 396 THR cc_start: 0.7808 (m) cc_final: 0.7358 (p) REVERT: A 451 LEU cc_start: 0.7248 (mp) cc_final: 0.6718 (tt) outliers start: 10 outliers final: 6 residues processed: 45 average time/residue: 0.8989 time to fit residues: 42.2520 Evaluate side-chains 44 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.197302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.151880 restraints weight = 3557.326| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.99 r_work: 0.3451 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3540 Z= 0.137 Angle : 0.554 5.697 4827 Z= 0.286 Chirality : 0.037 0.117 561 Planarity : 0.005 0.039 597 Dihedral : 3.637 16.803 480 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.97 % Allowed : 8.92 % Favored : 88.11 % 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: 1.98 (0.40), residues: 442 helix: 1.55 (0.29), residues: 316 sheet: None (None), residues: 0 loop : 0.97 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE A 22 TYR 0.009 0.001 TYR A 352 ARG 0.001 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.05282 ( 238) hydrogen bonds : angle 4.00146 ( 684) SS BOND : bond 0.00266 ( 3) SS BOND : angle 2.55879 ( 6) covalent geometry : bond 0.00297 ( 3537) covalent geometry : angle 0.54726 ( 4821) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.367 Fit side-chains REVERT: A 51 GLN cc_start: 0.8422 (tt0) cc_final: 0.7915 (tm-30) REVERT: A 92 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: A 239 MET cc_start: 0.6491 (ptp) cc_final: 0.5314 (tpt) REVERT: A 241 GLN cc_start: 0.6941 (mm-40) cc_final: 0.6659 (tm-30) REVERT: A 396 THR cc_start: 0.7762 (m) cc_final: 0.7280 (p) REVERT: A 451 LEU cc_start: 0.7290 (mp) cc_final: 0.6753 (tt) outliers start: 11 outliers final: 7 residues processed: 43 average time/residue: 0.9988 time to fit residues: 44.7880 Evaluate side-chains 45 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 38 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.0020 chunk 13 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.197685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152016 restraints weight = 3523.073| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.06 r_work: 0.3427 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3540 Z= 0.118 Angle : 0.513 5.570 4827 Z= 0.264 Chirality : 0.036 0.116 561 Planarity : 0.004 0.036 597 Dihedral : 3.537 16.943 480 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.70 % Allowed : 9.73 % Favored : 87.57 % 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: 2.23 (0.41), residues: 442 helix: 1.74 (0.30), residues: 316 sheet: None (None), residues: 0 loop : 1.04 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE A 22 TYR 0.009 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.04575 ( 238) hydrogen bonds : angle 3.89914 ( 684) SS BOND : bond 0.00205 ( 3) SS BOND : angle 2.32255 ( 6) covalent geometry : bond 0.00243 ( 3537) covalent geometry : angle 0.50723 ( 4821) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.358 Fit side-chains REVERT: A 51 GLN cc_start: 0.8491 (tt0) cc_final: 0.8001 (tm-30) REVERT: A 92 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: A 239 MET cc_start: 0.6618 (ptp) cc_final: 0.5409 (tpt) REVERT: A 241 GLN cc_start: 0.7043 (mm-40) cc_final: 0.6783 (tm-30) REVERT: A 396 THR cc_start: 0.7792 (m) cc_final: 0.7327 (p) REVERT: A 451 LEU cc_start: 0.7245 (mp) cc_final: 0.6727 (tt) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 0.8738 time to fit residues: 40.2391 Evaluate side-chains 42 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.195497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149693 restraints weight = 3590.481| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.89 r_work: 0.3442 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3540 Z= 0.142 Angle : 0.559 5.722 4827 Z= 0.288 Chirality : 0.037 0.118 561 Planarity : 0.005 0.039 597 Dihedral : 3.642 16.667 480 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.89 % Allowed : 10.54 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.40), residues: 442 helix: 1.56 (0.29), residues: 316 sheet: None (None), residues: 0 loop : 0.96 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE A 22 TYR 0.010 0.001 TYR A 352 ARG 0.001 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.05380 ( 238) hydrogen bonds : angle 4.00003 ( 684) SS BOND : bond 0.00277 ( 3) SS BOND : angle 2.60315 ( 6) covalent geometry : bond 0.00311 ( 3537) covalent geometry : angle 0.55170 ( 4821) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.334 Fit side-chains REVERT: A 51 GLN cc_start: 0.8523 (tt0) cc_final: 0.8016 (tm-30) REVERT: A 92 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: A 241 GLN cc_start: 0.7020 (mm-40) cc_final: 0.6775 (tm-30) REVERT: A 396 THR cc_start: 0.7807 (m) cc_final: 0.7342 (p) REVERT: A 451 LEU cc_start: 0.7350 (mp) cc_final: 0.6824 (tt) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 0.9977 time to fit residues: 40.5724 Evaluate side-chains 44 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 26 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.197693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152089 restraints weight = 3534.617| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.00 r_work: 0.3451 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3540 Z= 0.135 Angle : 0.559 6.256 4827 Z= 0.288 Chirality : 0.037 0.132 561 Planarity : 0.004 0.037 597 Dihedral : 3.627 16.691 480 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.16 % Allowed : 10.27 % Favored : 87.57 % 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: 2.02 (0.40), residues: 442 helix: 1.59 (0.29), residues: 316 sheet: None (None), residues: 0 loop : 0.93 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE A 22 TYR 0.009 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.05162 ( 238) hydrogen bonds : angle 4.01672 ( 684) SS BOND : bond 0.00262 ( 3) SS BOND : angle 2.52342 ( 6) covalent geometry : bond 0.00292 ( 3537) covalent geometry : angle 0.55230 ( 4821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2562.17 seconds wall clock time: 44 minutes 56.57 seconds (2696.57 seconds total)