Starting phenix.real_space_refine on Wed Mar 5 19:57:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc1_40334/03_2025/8sc1_40334.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc1_40334/03_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_40334/03_2025/8sc1_40334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc1_40334/03_2025/8sc1_40334.map" model { file = "/net/cci-nas-00/data/ceres_data/8sc1_40334/03_2025/8sc1_40334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc1_40334/03_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-5624/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: 2.62, per 1000 atoms: 0.76 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: 0.79 Conformation dependent library (CDL) restraints added in 384.8 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: 0.32 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: 0.87 Time building geometry restraints manager: 0.95 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: 1.050 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.140 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.700 ------------------------------------------------------------------------------- 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 3537 Z= 0.178 Angle : 0.679 6.060 4821 Z= 0.396 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 *********************** 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 : 0.282 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: 0.9942 time to fit residues: 54.7158 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 : 0.367 ------------------------------------------------------------------------------- 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 = 0.197651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.152721 restraints weight = 3548.064| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.89 r_work: 0.3459 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3537 Z= 0.215 Angle : 0.613 6.640 4821 Z= 0.316 Chirality : 0.038 0.118 561 Planarity : 0.005 0.035 597 Dihedral : 4.139 15.541 480 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 367 PHE 0.014 0.002 PHE A 32 TYR 0.010 0.001 TYR A 240 ARG 0.002 0.000 ARG A 402 *********************** 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 : 0.367 Fit side-chains REVERT: A 51 GLN cc_start: 0.8656 (tt0) cc_final: 0.8097 (tm-30) REVERT: A 92 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6569 (mp0) REVERT: A 218 MET cc_start: 0.7440 (mmm) cc_final: 0.7170 (mmm) REVERT: A 396 THR cc_start: 0.7737 (m) cc_final: 0.7331 (p) REVERT: A 408 MET cc_start: 0.8116 (mmm) cc_final: 0.7906 (mmm) REVERT: A 492 GLN cc_start: 0.7139 (mt0) cc_final: 0.6363 (tp-100) outliers start: 9 outliers final: 1 residues processed: 40 average time/residue: 0.9904 time to fit residues: 41.3377 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 : 0.332 ------------------------------------------------------------------------------- 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: 0.6980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.3980 chunk 3 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.199204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.153962 restraints weight = 3545.267| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.02 r_work: 0.3496 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3537 Z= 0.164 Angle : 0.531 5.644 4821 Z= 0.274 Chirality : 0.036 0.113 561 Planarity : 0.004 0.033 597 Dihedral : 3.791 15.132 480 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.87 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: 1.83 (0.41), residues: 442 helix: 1.41 (0.29), residues: 311 sheet: None (None), residues: 0 loop : 1.01 (0.59), residues: 131 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 0.013 0.001 PHE A 22 TYR 0.007 0.001 TYR A 240 ARG 0.003 0.000 ARG A 402 *********************** 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 40 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.317 Fit side-chains REVERT: A 51 GLN cc_start: 0.8574 (tt0) cc_final: 0.8040 (tm-30) REVERT: A 92 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6558 (mp0) REVERT: A 218 MET cc_start: 0.7305 (mmm) cc_final: 0.7089 (mmm) REVERT: A 239 MET cc_start: 0.6525 (ptp) cc_final: 0.5118 (tpt) REVERT: A 396 THR cc_start: 0.7677 (m) cc_final: 0.7168 (p) REVERT: A 408 MET cc_start: 0.8070 (mmm) cc_final: 0.7855 (mmm) REVERT: A 492 GLN cc_start: 0.7189 (mt0) cc_final: 0.6629 (tm-30) outliers start: 7 outliers final: 2 residues processed: 37 average time/residue: 0.8644 time to fit residues: 33.6414 Evaluate side-chains 36 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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: 0.2980 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.197357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.152042 restraints weight = 3591.445| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.98 r_work: 0.3405 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3537 Z= 0.198 Angle : 0.561 6.040 4821 Z= 0.288 Chirality : 0.037 0.117 561 Planarity : 0.005 0.036 597 Dihedral : 3.743 14.180 480 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.70 % Allowed : 6.49 % Favored : 90.81 % 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: 1.70 (0.40), residues: 442 helix: 1.34 (0.29), residues: 316 sheet: None (None), residues: 0 loop : 0.86 (0.58), 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 439 *********************** 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 51 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.277 Fit side-chains REVERT: A 51 GLN cc_start: 0.8578 (tt0) cc_final: 0.7964 (tm-30) REVERT: A 92 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: A 218 MET cc_start: 0.7294 (mmm) cc_final: 0.7089 (mmm) REVERT: A 241 GLN cc_start: 0.6802 (mm-40) cc_final: 0.6302 (tm-30) REVERT: A 396 THR cc_start: 0.7509 (m) cc_final: 0.6973 (p) REVERT: A 408 MET cc_start: 0.8068 (mmm) cc_final: 0.7813 (mmm) REVERT: A 451 LEU cc_start: 0.6730 (mp) cc_final: 0.6187 (tt) REVERT: A 492 GLN cc_start: 0.7492 (mt0) cc_final: 0.6843 (tm-30) outliers start: 10 outliers final: 4 residues processed: 48 average time/residue: 0.9716 time to fit residues: 48.6771 Evaluate side-chains 42 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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: 0.5980 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.0040 chunk 43 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.199402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.154479 restraints weight = 3623.225| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.92 r_work: 0.3472 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3537 Z= 0.156 Angle : 0.509 5.550 4821 Z= 0.262 Chirality : 0.036 0.114 561 Planarity : 0.004 0.035 597 Dihedral : 3.570 13.115 480 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.70 % Allowed : 7.57 % 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: 2.09 (0.41), residues: 442 helix: 1.62 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.06 (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 0.013 0.001 PHE A 22 TYR 0.007 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 *********************** 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 49 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.331 Fit side-chains REVERT: A 51 GLN cc_start: 0.8484 (tt0) cc_final: 0.7999 (tm-30) REVERT: A 92 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: A 239 MET cc_start: 0.6409 (ptp) cc_final: 0.5208 (tpt) REVERT: A 241 GLN cc_start: 0.6776 (mm-40) cc_final: 0.6476 (tm-30) REVERT: A 396 THR cc_start: 0.7740 (m) cc_final: 0.7270 (p) REVERT: A 408 MET cc_start: 0.8084 (mmm) cc_final: 0.7856 (mmm) REVERT: A 451 LEU cc_start: 0.7027 (mp) cc_final: 0.6515 (tt) outliers start: 10 outliers final: 3 residues processed: 45 average time/residue: 1.0391 time to fit residues: 48.7187 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 : 0.364 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.198266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152775 restraints weight = 3647.173| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.97 r_work: 0.3459 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3537 Z= 0.175 Angle : 0.524 5.592 4821 Z= 0.271 Chirality : 0.036 0.113 561 Planarity : 0.004 0.036 597 Dihedral : 3.600 16.815 480 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: 2.02 (0.40), residues: 442 helix: 1.59 (0.29), residues: 316 sheet: None (None), residues: 0 loop : 0.95 (0.58), 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 0.002 0.000 ARG A 402 *********************** 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 50 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.377 Fit side-chains REVERT: A 51 GLN cc_start: 0.8486 (tt0) cc_final: 0.7968 (tm-30) REVERT: A 92 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: A 241 GLN cc_start: 0.6805 (mm-40) cc_final: 0.6468 (tm-30) REVERT: A 396 THR cc_start: 0.7748 (m) cc_final: 0.7258 (p) REVERT: A 408 MET cc_start: 0.8073 (mmm) cc_final: 0.7844 (mmm) REVERT: A 451 LEU cc_start: 0.7170 (mp) cc_final: 0.6656 (tt) outliers start: 10 outliers final: 5 residues processed: 46 average time/residue: 0.9426 time to fit residues: 45.1417 Evaluate side-chains 43 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.0020 chunk 21 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 overall best weight: 0.4748 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.199644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154355 restraints weight = 3593.238| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.34 r_work: 0.3485 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3537 Z= 0.152 Angle : 0.505 5.532 4821 Z= 0.261 Chirality : 0.035 0.115 561 Planarity : 0.004 0.034 597 Dihedral : 3.529 16.929 480 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.70 % Allowed : 8.38 % Favored : 88.92 % 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: 1.74 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.16 (0.59), 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 *********************** 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 48 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.346 Fit side-chains REVERT: A 51 GLN cc_start: 0.8611 (tt0) cc_final: 0.8063 (tm-30) REVERT: A 92 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: A 239 MET cc_start: 0.6674 (ptp) cc_final: 0.5069 (tpt) REVERT: A 241 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6648 (tm-30) REVERT: A 396 THR cc_start: 0.7717 (m) cc_final: 0.7204 (p) REVERT: A 408 MET cc_start: 0.8228 (mmm) cc_final: 0.7998 (mmm) REVERT: A 451 LEU cc_start: 0.7038 (mp) cc_final: 0.6471 (tt) outliers start: 10 outliers final: 4 residues processed: 44 average time/residue: 0.9611 time to fit residues: 44.1089 Evaluate side-chains 45 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 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 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: 1.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.191591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.145245 restraints weight = 3559.631| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.14 r_work: 0.3391 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3537 Z= 0.328 Angle : 0.670 6.872 4821 Z= 0.347 Chirality : 0.041 0.130 561 Planarity : 0.005 0.045 597 Dihedral : 3.973 16.881 480 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.97 % Allowed : 8.38 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.40), residues: 442 helix: 1.03 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.69 (0.58), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 261 HIS 0.004 0.002 HIS A 48 PHE 0.014 0.002 PHE A 151 TYR 0.011 0.002 TYR A 352 ARG 0.002 0.000 ARG A 346 *********************** 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 52 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.344 Fit side-chains REVERT: A 51 GLN cc_start: 0.8503 (tt0) cc_final: 0.7947 (tm-30) REVERT: A 92 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: A 147 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8705 (mttm) REVERT: A 241 GLN cc_start: 0.7101 (mm-40) cc_final: 0.6773 (tm-30) REVERT: A 271 PRO cc_start: 0.6798 (Cg_exo) cc_final: 0.6575 (Cg_endo) REVERT: A 396 THR cc_start: 0.7780 (m) cc_final: 0.7521 (t) REVERT: A 408 MET cc_start: 0.8142 (mmm) cc_final: 0.7921 (mmm) REVERT: A 451 LEU cc_start: 0.7270 (mp) cc_final: 0.6715 (tt) outliers start: 11 outliers final: 5 residues processed: 48 average time/residue: 0.9400 time to fit residues: 47.0648 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 : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 147 LYS 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: 1.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.0670 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.195900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.149632 restraints weight = 3506.547| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.07 r_work: 0.3463 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3537 Z= 0.182 Angle : 0.548 5.750 4821 Z= 0.285 Chirality : 0.036 0.113 561 Planarity : 0.005 0.035 597 Dihedral : 3.721 17.205 480 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.43 % Allowed : 9.73 % Favored : 87.84 % 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: 1.72 (0.40), residues: 442 helix: 1.38 (0.29), residues: 322 sheet: None (None), residues: 0 loop : 0.75 (0.59), residues: 120 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 0.009 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 *********************** 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 45 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.329 Fit side-chains REVERT: A 51 GLN cc_start: 0.8586 (tt0) cc_final: 0.8039 (tm-30) REVERT: A 92 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: A 239 MET cc_start: 0.6749 (ptp) cc_final: 0.5156 (tpt) REVERT: A 241 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6798 (tm-30) REVERT: A 396 THR cc_start: 0.7741 (m) cc_final: 0.7229 (p) REVERT: A 451 LEU cc_start: 0.7166 (mp) cc_final: 0.6611 (tt) outliers start: 9 outliers final: 5 residues processed: 41 average time/residue: 0.9488 time to fit residues: 40.6092 Evaluate side-chains 45 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 4 optimal weight: 0.0570 chunk 34 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.199874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.152890 restraints weight = 3571.211| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.22 r_work: 0.3476 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3537 Z= 0.157 Angle : 0.510 5.537 4821 Z= 0.264 Chirality : 0.035 0.115 561 Planarity : 0.004 0.034 597 Dihedral : 3.536 17.022 480 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.35 % Allowed : 11.62 % Favored : 87.03 % 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: 2.48 (0.41), residues: 442 helix: 1.91 (0.30), residues: 306 sheet: None (None), residues: 0 loop : 1.27 (0.56), residues: 136 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 0.013 0.001 PHE A 22 TYR 0.009 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 ********************** 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 44 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.336 Fit side-chains REVERT: A 51 GLN cc_start: 0.8411 (tt0) cc_final: 0.7936 (tm-30) REVERT: A 92 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: A 239 MET cc_start: 0.6459 (ptp) cc_final: 0.5033 (tpt) REVERT: A 241 GLN cc_start: 0.6950 (mm-40) cc_final: 0.6699 (tm-30) REVERT: A 368 MET cc_start: 0.8711 (ttm) cc_final: 0.8394 (ttp) REVERT: A 396 THR cc_start: 0.7793 (m) cc_final: 0.7325 (p) REVERT: A 451 LEU cc_start: 0.7303 (mp) cc_final: 0.6750 (tt) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.8867 time to fit residues: 38.0269 Evaluate side-chains 41 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.196811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.151424 restraints weight = 3539.986| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.93 r_work: 0.3474 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3537 Z= 0.178 Angle : 0.533 5.625 4821 Z= 0.275 Chirality : 0.036 0.115 561 Planarity : 0.004 0.036 597 Dihedral : 3.587 16.651 480 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.62 % Allowed : 10.81 % 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: 2.08 (0.40), residues: 442 helix: 1.64 (0.30), residues: 316 sheet: None (None), residues: 0 loop : 0.94 (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 0.010 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2681.27 seconds wall clock time: 46 minutes 38.57 seconds (2798.57 seconds total)