Starting phenix.real_space_refine on Tue Feb 11 00:53:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc1_40334/02_2025/8sc1_40334.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc1_40334/02_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_40334/02_2025/8sc1_40334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc1_40334/02_2025/8sc1_40334.map" model { file = "/net/cci-nas-00/data/ceres_data/8sc1_40334/02_2025/8sc1_40334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc1_40334/02_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-5592/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: 2.69, per 1000 atoms: 0.78 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: 0.82 Conformation dependent library (CDL) restraints added in 431.1 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: 0.94 Time building geometry restraints manager: 0.98 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: 1.040 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.570 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: 0.010 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- 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 : 0.333 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: 0.9977 time to fit residues: 54.8821 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 : 0.372 ------------------------------------------------------------------------------- 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 3537 Z= 0.215 Angle : 0.612 6.605 4821 Z= 0.316 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 *********************** 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 : 0.369 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: 1.0009 time to fit residues: 41.7635 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 : 0.380 ------------------------------------------------------------------------------- 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 3537 Z= 0.145 Angle : 0.508 5.534 4821 Z= 0.262 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 *********************** 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 : 0.523 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: 0.9392 time to fit residues: 35.4753 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 : 0.350 ------------------------------------------------------------------------------- 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 3537 Z= 0.202 Angle : 0.567 6.358 4821 Z= 0.291 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 *********************** 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 : 0.387 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: 0.9922 time to fit residues: 46.5913 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 : 0.372 ------------------------------------------------------------------------------- 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: 7.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 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: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.196025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.151024 restraints weight = 3613.384| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.93 r_work: 0.3454 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2355 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= 0.184 Angle : 0.536 5.633 4821 Z= 0.276 Chirality : 0.037 0.115 561 Planarity : 0.004 0.036 597 Dihedral : 3.634 13.319 480 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.01 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: 1.95 (0.40), residues: 442 helix: 1.50 (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 0.008 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 51 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.382 Fit side-chains REVERT: A 51 GLN cc_start: 0.8550 (tt0) cc_final: 0.7923 (tm-30) REVERT: A 92 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: A 239 MET cc_start: 0.6538 (ptp) cc_final: 0.5147 (tpt) REVERT: A 241 GLN cc_start: 0.6817 (mm-40) cc_final: 0.6333 (tm-30) REVERT: A 396 THR cc_start: 0.7546 (m) cc_final: 0.6995 (p) REVERT: A 451 LEU cc_start: 0.6746 (mp) cc_final: 0.6217 (tt) REVERT: A 492 GLN cc_start: 0.7547 (mt0) cc_final: 0.7316 (mp10) outliers start: 12 outliers final: 5 residues processed: 46 average time/residue: 0.9228 time to fit residues: 44.4018 Evaluate side-chains 44 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 32 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 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 = 0.4154 r_free = 0.4154 target = 0.197176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.150608 restraints weight = 3644.503| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.12 r_work: 0.3439 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2442 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= 0.162 Angle : 0.510 5.558 4821 Z= 0.264 Chirality : 0.036 0.117 561 Planarity : 0.004 0.036 597 Dihedral : 3.580 16.879 480 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: 2.19 (0.41), residues: 442 helix: 1.67 (0.30), residues: 314 sheet: None (None), residues: 0 loop : 1.16 (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 *********************** 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 48 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.367 Fit side-chains REVERT: A 51 GLN cc_start: 0.8519 (tt0) cc_final: 0.8026 (tm-30) REVERT: A 92 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: A 241 GLN cc_start: 0.6916 (mm-40) cc_final: 0.6670 (tm-30) REVERT: A 396 THR cc_start: 0.7791 (m) cc_final: 0.7335 (p) REVERT: A 451 LEU cc_start: 0.7210 (mp) cc_final: 0.6714 (tt) outliers start: 10 outliers final: 5 residues processed: 43 average time/residue: 1.0218 time to fit residues: 45.7353 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 : 0.362 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.192370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.146455 restraints weight = 3589.615| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.05 r_work: 0.3400 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3537 Z= 0.290 Angle : 0.639 6.593 4821 Z= 0.331 Chirality : 0.040 0.127 561 Planarity : 0.005 0.046 597 Dihedral : 3.900 16.578 480 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: 1.36 (0.40), residues: 442 helix: 1.08 (0.29), residues: 321 sheet: None (None), residues: 0 loop : 0.72 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.004 0.001 HIS A 48 PHE 0.013 0.002 PHE A 151 TYR 0.010 0.002 TYR A 352 ARG 0.002 0.000 ARG A 346 *********************** 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 52 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.347 Fit side-chains REVERT: A 51 GLN cc_start: 0.8529 (tt0) cc_final: 0.8025 (tm-30) REVERT: A 92 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: A 241 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6787 (tm-30) REVERT: A 271 PRO cc_start: 0.6792 (Cg_exo) cc_final: 0.6553 (Cg_endo) REVERT: A 396 THR cc_start: 0.7767 (m) cc_final: 0.7274 (p) REVERT: A 451 LEU cc_start: 0.7266 (mp) cc_final: 0.6693 (tt) outliers start: 11 outliers final: 7 residues processed: 46 average time/residue: 0.9480 time to fit residues: 45.4493 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 : 0.381 ------------------------------------------------------------------------------- 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 406 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.194599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.149043 restraints weight = 3557.099| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.06 r_work: 0.3447 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2664 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= 0.214 Angle : 0.578 6.043 4821 Z= 0.300 Chirality : 0.038 0.117 561 Planarity : 0.005 0.039 597 Dihedral : 3.791 16.928 480 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.24 % Allowed : 8.92 % 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: 1.57 (0.40), residues: 442 helix: 1.25 (0.29), residues: 322 sheet: None (None), residues: 0 loop : 0.76 (0.58), 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 0.001 0.000 ARG A 402 *********************** 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 48 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.346 Fit side-chains REVERT: A 51 GLN cc_start: 0.8493 (tt0) cc_final: 0.7881 (tm-30) REVERT: A 92 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: A 239 MET cc_start: 0.6516 (ptp) cc_final: 0.4925 (tpt) REVERT: A 241 GLN cc_start: 0.7100 (mm-40) cc_final: 0.6540 (tm-30) REVERT: A 396 THR cc_start: 0.7591 (m) cc_final: 0.7038 (p) REVERT: A 451 LEU cc_start: 0.6974 (mp) cc_final: 0.6406 (tt) outliers start: 12 outliers final: 7 residues processed: 43 average time/residue: 0.9255 time to fit residues: 41.5980 Evaluate side-chains 46 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 406 MET Chi-restraints excluded: chain A residue 467 MET 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: 2.9990 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.0020 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.197531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.151337 restraints weight = 3517.580| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.99 r_work: 0.3454 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2694 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= 0.159 Angle : 0.517 5.570 4821 Z= 0.268 Chirality : 0.036 0.112 561 Planarity : 0.004 0.037 597 Dihedral : 3.601 17.109 480 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.16 % Allowed : 10.54 % Favored : 87.30 % 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: 2.36 (0.41), residues: 442 helix: 1.80 (0.30), residues: 309 sheet: None (None), residues: 0 loop : 1.23 (0.57), residues: 133 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 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 46 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.345 Fit side-chains REVERT: A 51 GLN cc_start: 0.8462 (tt0) cc_final: 0.7983 (tm-30) REVERT: A 92 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: A 239 MET cc_start: 0.6555 (ptp) cc_final: 0.5077 (tpt) REVERT: A 241 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6773 (tm-30) REVERT: A 368 MET cc_start: 0.8753 (ttm) cc_final: 0.8433 (ttp) REVERT: A 396 THR cc_start: 0.7806 (m) cc_final: 0.7332 (p) REVERT: A 451 LEU cc_start: 0.7173 (mp) cc_final: 0.6686 (tt) outliers start: 8 outliers final: 4 residues processed: 44 average time/residue: 0.8659 time to fit residues: 39.9023 Evaluate side-chains 40 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.196916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150851 restraints weight = 3583.670| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.06 r_work: 0.3453 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2713 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= 0.173 Angle : 0.529 5.604 4821 Z= 0.273 Chirality : 0.036 0.114 561 Planarity : 0.004 0.039 597 Dihedral : 3.590 16.995 480 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 : 1.35 % Allowed : 11.35 % Favored : 87.30 % 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: 2.04 (0.41), residues: 442 helix: 1.58 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 1.00 (0.59), residues: 122 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 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 40 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.352 Fit side-chains REVERT: A 51 GLN cc_start: 0.8549 (tt0) cc_final: 0.8007 (tm-30) REVERT: A 92 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: A 239 MET cc_start: 0.6758 (ptp) cc_final: 0.5133 (tpt) REVERT: A 241 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6712 (tm-30) REVERT: A 396 THR cc_start: 0.7724 (m) cc_final: 0.7218 (p) REVERT: A 451 LEU cc_start: 0.7067 (mp) cc_final: 0.6497 (tt) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 1.0008 time to fit residues: 39.6431 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 : 0.362 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.0270 overall best weight: 0.5436 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.197568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.152172 restraints weight = 3546.590| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.87 r_work: 0.3468 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2764 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= 0.163 Angle : 0.515 5.570 4821 Z= 0.266 Chirality : 0.036 0.115 561 Planarity : 0.004 0.037 597 Dihedral : 3.537 16.656 480 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.89 % Allowed : 10.81 % Favored : 87.30 % 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: 2.11 (0.41), residues: 442 helix: 1.65 (0.29), residues: 320 sheet: None (None), residues: 0 loop : 0.98 (0.58), residues: 122 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2690.73 seconds wall clock time: 48 minutes 8.55 seconds (2888.55 seconds total)