Starting phenix.real_space_refine on Mon Jan 13 21:51:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2c_38850/01_2025/8y2c_38850.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2c_38850/01_2025/8y2c_38850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y2c_38850/01_2025/8y2c_38850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2c_38850/01_2025/8y2c_38850.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2c_38850/01_2025/8y2c_38850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2c_38850/01_2025/8y2c_38850.cif" } resolution = 3.16 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= 0.001 sd= 0.044 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 23 5.16 5 C 2805 2.51 5 N 660 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4207 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4179 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 505} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.11, per 1000 atoms: 0.74 Number of scatterers: 4207 At special positions: 0 Unit cell: (78.2, 68, 89.25, 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 23 16.00 O 719 8.00 N 660 7.00 C 2805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 189 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 181 " " NAG A 702 " - " ASN A 188 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 495.5 milliseconds 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 974 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 76.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.508A pdb=" N PHE A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.875A pdb=" N TYR A 88 " --> pdb=" O TRP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.656A pdb=" N ILE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 140 through 170 removed outlier: 3.627A pdb=" N VAL A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.777A pdb=" N GLN A 226 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 227 " --> pdb=" O LEU A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 227' Processing helix chain 'A' and resid 237 through 256 removed outlier: 3.786A pdb=" N CYS A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 287 removed outlier: 3.543A pdb=" N THR A 271 " --> pdb=" O TRP A 267 " (cutoff:3.500A) Proline residue: A 273 - end of helix removed outlier: 3.732A pdb=" N ARG A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.707A pdb=" N ALA A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.709A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 306' Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.581A pdb=" N CYS A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 342 through 376 removed outlier: 3.506A pdb=" N VAL A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.579A pdb=" N TYR A 394 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.684A pdb=" N TRP A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 461 removed outlier: 3.808A pdb=" N PHE A 448 " --> pdb=" O HIS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 removed outlier: 3.699A pdb=" N THR A 465 " --> pdb=" O PHE A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 467 through 479 removed outlier: 3.957A pdb=" N VAL A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 517 through 526 Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.906A pdb=" N PHE A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 570 removed outlier: 3.653A pdb=" N ASN A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.568A pdb=" N TYR A 575 " --> pdb=" O MET A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 600 through 605 removed outlier: 4.023A pdb=" N ASP A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 547 through 548 removed outlier: 3.528A pdb=" N TYR A 548 " --> pdb=" O TYR A 551 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1253 1.34 - 1.46: 1127 1.46 - 1.58: 1923 1.58 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 4337 Sorted by residual: bond pdb=" CB VAL A 495 " pdb=" CG1 VAL A 495 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.63e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" C5 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" CG MET A 116 " pdb=" SD MET A 116 " ideal model delta sigma weight residual 1.803 1.776 0.027 2.50e-02 1.60e+03 1.17e+00 bond pdb=" CB MET A 116 " pdb=" CG MET A 116 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.12e+00 ... (remaining 4332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 5841 1.84 - 3.67: 69 3.67 - 5.51: 9 5.51 - 7.35: 1 7.35 - 9.18: 1 Bond angle restraints: 5921 Sorted by residual: angle pdb=" C VAL A 495 " pdb=" CA VAL A 495 " pdb=" CB VAL A 495 " ideal model delta sigma weight residual 112.16 108.04 4.12 1.55e+00 4.16e-01 7.07e+00 angle pdb=" C PHE A 543 " pdb=" N ARG A 544 " pdb=" CA ARG A 544 " ideal model delta sigma weight residual 121.80 127.76 -5.96 2.44e+00 1.68e-01 5.97e+00 angle pdb=" CG MET A 116 " pdb=" SD MET A 116 " pdb=" CE MET A 116 " ideal model delta sigma weight residual 100.90 95.78 5.12 2.20e+00 2.07e-01 5.42e+00 angle pdb=" C TYR A 115 " pdb=" N MET A 116 " pdb=" CA MET A 116 " ideal model delta sigma weight residual 120.54 123.25 -2.71 1.35e+00 5.49e-01 4.03e+00 angle pdb=" C VAL A 495 " pdb=" N ALA A 496 " pdb=" CA ALA A 496 " ideal model delta sigma weight residual 121.81 118.31 3.50 1.83e+00 2.99e-01 3.66e+00 ... (remaining 5916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.19: 2148 21.19 - 42.37: 264 42.37 - 63.56: 47 63.56 - 84.74: 10 84.74 - 105.92: 5 Dihedral angle restraints: 2474 sinusoidal: 950 harmonic: 1524 Sorted by residual: dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" C5 NAG A 701 " ideal model delta sinusoidal sigma weight residual 53.78 -52.14 105.92 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" O4 NAG A 701 " ideal model delta sinusoidal sigma weight residual 175.11 70.28 104.83 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" C5 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" O3 NAG A 701 " ideal model delta sinusoidal sigma weight residual -174.13 -69.84 -104.29 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 2471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 457 0.034 - 0.068: 171 0.068 - 0.102: 35 0.102 - 0.136: 12 0.136 - 0.170: 2 Chirality restraints: 677 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 181 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 188 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CB ILE A 564 " pdb=" CA ILE A 564 " pdb=" CG1 ILE A 564 " pdb=" CG2 ILE A 564 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 674 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 394 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO A 395 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 395 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 395 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 106 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C MET A 106 " 0.027 2.00e-02 2.50e+03 pdb=" O MET A 106 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 107 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 494 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C GLY A 494 " 0.022 2.00e-02 2.50e+03 pdb=" O GLY A 494 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL A 495 " -0.007 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 89 2.71 - 3.26: 4100 3.26 - 3.80: 6562 3.80 - 4.35: 7730 4.35 - 4.90: 13853 Nonbonded interactions: 32334 Sorted by model distance: nonbonded pdb=" OH TYR A 593 " pdb=" OD1 ASP A 605 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASN A 82 " pdb=" OG SER A 357 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" O ILE A 379 " model vdw 2.282 3.040 nonbonded pdb=" NH1 ARG A 125 " pdb=" O ASN A 336 " model vdw 2.293 3.120 nonbonded pdb=" O GLU A 126 " pdb=" OG SER A 334 " model vdw 2.300 3.040 ... (remaining 32329 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.070 Process input model: 14.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 0.042 4337 Z= 0.193 Angle : 0.509 9.182 5921 Z= 0.257 Chirality : 0.038 0.170 677 Planarity : 0.004 0.054 723 Dihedral : 19.028 105.925 1497 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 34.68 % Favored : 65.32 % 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: 0.76 (0.38), residues: 523 helix: 1.36 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.64 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 256 HIS 0.004 0.001 HIS A 442 PHE 0.011 0.001 PHE A 155 TYR 0.017 0.001 TYR A 370 ARG 0.001 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.460 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1431 time to fit residues: 6.9465 Evaluate side-chains 34 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 15 optimal weight: 0.0010 chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.158785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136909 restraints weight = 5275.501| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.92 r_work: 0.3472 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4337 Z= 0.140 Angle : 0.482 7.995 5921 Z= 0.236 Chirality : 0.038 0.175 677 Planarity : 0.004 0.051 723 Dihedral : 7.378 52.404 611 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.15 % Allowed : 32.43 % Favored : 64.41 % 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: 1.11 (0.38), residues: 523 helix: 1.65 (0.29), residues: 369 sheet: None (None), residues: 0 loop : -1.56 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 PHE 0.010 0.001 PHE A 155 TYR 0.007 0.001 TYR A 575 ARG 0.001 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.407 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 45 average time/residue: 0.1321 time to fit residues: 8.1090 Evaluate side-chains 43 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 613 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.157150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133471 restraints weight = 5200.621| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.17 r_work: 0.3316 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4337 Z= 0.154 Angle : 0.475 10.175 5921 Z= 0.232 Chirality : 0.037 0.167 677 Planarity : 0.004 0.052 723 Dihedral : 4.434 29.547 611 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.93 % Allowed : 33.33 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.39), residues: 523 helix: 1.49 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.47 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 PHE 0.010 0.001 PHE A 155 TYR 0.008 0.001 TYR A 88 ARG 0.001 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.339 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 45 average time/residue: 0.1244 time to fit residues: 7.8160 Evaluate side-chains 42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 613 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.0770 chunk 37 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.157809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.134133 restraints weight = 5161.710| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.16 r_work: 0.3413 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4337 Z= 0.142 Angle : 0.448 8.245 5921 Z= 0.221 Chirality : 0.037 0.165 677 Planarity : 0.004 0.051 723 Dihedral : 3.946 23.812 611 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.15 % Allowed : 33.56 % Favored : 63.29 % 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: 1.10 (0.39), residues: 523 helix: 1.52 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.47 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 PHE 0.010 0.001 PHE A 155 TYR 0.008 0.001 TYR A 370 ARG 0.001 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.458 Fit side-chains REVERT: A 381 ASP cc_start: 0.8423 (t0) cc_final: 0.7956 (t0) REVERT: A 544 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6396 (ptt-90) outliers start: 14 outliers final: 11 residues processed: 46 average time/residue: 0.1480 time to fit residues: 9.1440 Evaluate side-chains 49 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 0.0170 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.157015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.133403 restraints weight = 5333.902| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.13 r_work: 0.3313 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4337 Z= 0.151 Angle : 0.444 8.478 5921 Z= 0.220 Chirality : 0.037 0.164 677 Planarity : 0.004 0.052 723 Dihedral : 3.881 23.223 611 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.28 % Allowed : 33.11 % Favored : 62.61 % 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: 1.14 (0.39), residues: 523 helix: 1.56 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.48 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 PHE 0.010 0.001 PHE A 412 TYR 0.010 0.001 TYR A 115 ARG 0.001 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.448 Fit side-chains REVERT: A 116 MET cc_start: 0.8150 (ttp) cc_final: 0.7841 (ttp) REVERT: A 381 ASP cc_start: 0.8474 (t0) cc_final: 0.7995 (t0) REVERT: A 544 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6483 (ptt-90) outliers start: 19 outliers final: 13 residues processed: 50 average time/residue: 0.1413 time to fit residues: 9.4742 Evaluate side-chains 51 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.0040 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.157519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133934 restraints weight = 5186.986| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.11 r_work: 0.3275 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4337 Z= 0.141 Angle : 0.437 8.147 5921 Z= 0.217 Chirality : 0.037 0.161 677 Planarity : 0.004 0.051 723 Dihedral : 3.796 22.843 611 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.05 % Allowed : 33.11 % Favored : 62.84 % 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: 1.18 (0.39), residues: 523 helix: 1.58 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.45 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 PHE 0.010 0.001 PHE A 155 TYR 0.009 0.001 TYR A 370 ARG 0.001 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.425 Fit side-chains REVERT: A 116 MET cc_start: 0.8114 (ttp) cc_final: 0.7833 (ttt) REVERT: A 381 ASP cc_start: 0.8504 (t0) cc_final: 0.7964 (t0) REVERT: A 544 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.6447 (ptt-90) outliers start: 18 outliers final: 13 residues processed: 51 average time/residue: 0.1385 time to fit residues: 9.5311 Evaluate side-chains 53 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 613 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 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 = 0.3760 r_free = 0.3760 target = 0.156955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133475 restraints weight = 5175.928| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.09 r_work: 0.3398 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4337 Z= 0.155 Angle : 0.446 8.497 5921 Z= 0.221 Chirality : 0.037 0.162 677 Planarity : 0.004 0.052 723 Dihedral : 3.811 22.801 611 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.50 % Allowed : 32.43 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.39), residues: 523 helix: 1.57 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.44 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 PHE 0.011 0.001 PHE A 412 TYR 0.010 0.001 TYR A 370 ARG 0.001 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.463 Fit side-chains REVERT: A 116 MET cc_start: 0.8109 (ttp) cc_final: 0.7787 (ttt) REVERT: A 381 ASP cc_start: 0.8490 (t0) cc_final: 0.7900 (t0) REVERT: A 544 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6395 (ptt-90) outliers start: 20 outliers final: 18 residues processed: 52 average time/residue: 0.1407 time to fit residues: 10.0057 Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 10 optimal weight: 0.0670 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.0570 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.158147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.134402 restraints weight = 5147.946| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.15 r_work: 0.3306 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4337 Z= 0.127 Angle : 0.426 7.792 5921 Z= 0.211 Chirality : 0.036 0.153 677 Planarity : 0.004 0.051 723 Dihedral : 3.646 21.609 611 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.05 % Allowed : 32.66 % Favored : 63.29 % 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: 1.29 (0.39), residues: 523 helix: 1.66 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.43 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 556 HIS 0.003 0.001 HIS A 179 PHE 0.010 0.001 PHE A 155 TYR 0.008 0.001 TYR A 370 ARG 0.001 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.501 Fit side-chains REVERT: A 116 MET cc_start: 0.8083 (ttp) cc_final: 0.7761 (ttt) REVERT: A 381 ASP cc_start: 0.8476 (t0) cc_final: 0.7784 (t0) REVERT: A 544 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6417 (ptt-90) outliers start: 18 outliers final: 15 residues processed: 50 average time/residue: 0.1517 time to fit residues: 10.0451 Evaluate side-chains 54 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.156401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.132784 restraints weight = 5228.604| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.12 r_work: 0.3308 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4337 Z= 0.167 Angle : 0.452 8.875 5921 Z= 0.224 Chirality : 0.037 0.162 677 Planarity : 0.004 0.052 723 Dihedral : 3.778 22.687 611 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.05 % Allowed : 32.66 % Favored : 63.29 % 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: 1.21 (0.39), residues: 523 helix: 1.61 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.45 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 PHE 0.012 0.001 PHE A 412 TYR 0.010 0.001 TYR A 88 ARG 0.001 0.000 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.418 Fit side-chains REVERT: A 116 MET cc_start: 0.8174 (ttp) cc_final: 0.7872 (ttt) REVERT: A 381 ASP cc_start: 0.8527 (t0) cc_final: 0.7864 (t0) REVERT: A 544 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6490 (ptt-90) outliers start: 18 outliers final: 17 residues processed: 50 average time/residue: 0.1440 time to fit residues: 9.7690 Evaluate side-chains 55 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.0070 chunk 45 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.0070 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.159472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135684 restraints weight = 5157.182| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.16 r_work: 0.3345 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4337 Z= 0.115 Angle : 0.417 7.216 5921 Z= 0.207 Chirality : 0.036 0.143 677 Planarity : 0.004 0.050 723 Dihedral : 3.524 20.757 611 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.93 % Allowed : 33.78 % Favored : 63.29 % 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: 1.37 (0.38), residues: 523 helix: 1.72 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.37 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 556 HIS 0.003 0.001 HIS A 179 PHE 0.009 0.001 PHE A 155 TYR 0.007 0.001 TYR A 370 ARG 0.001 0.000 ARG A 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.466 Fit side-chains REVERT: A 116 MET cc_start: 0.8078 (ttp) cc_final: 0.7775 (ttt) REVERT: A 381 ASP cc_start: 0.8440 (t0) cc_final: 0.7855 (t0) REVERT: A 544 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6388 (ptt-90) outliers start: 13 outliers final: 12 residues processed: 47 average time/residue: 0.1469 time to fit residues: 9.2419 Evaluate side-chains 52 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 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 = 0.3769 r_free = 0.3769 target = 0.157811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134260 restraints weight = 5187.411| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.11 r_work: 0.3325 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4337 Z= 0.148 Angle : 0.440 8.491 5921 Z= 0.217 Chirality : 0.037 0.154 677 Planarity : 0.004 0.051 723 Dihedral : 3.600 21.418 611 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.15 % Allowed : 33.33 % Favored : 63.51 % 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: 1.36 (0.39), residues: 523 helix: 1.71 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.37 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 PHE 0.010 0.001 PHE A 412 TYR 0.008 0.001 TYR A 88 ARG 0.001 0.000 ARG A 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2248.33 seconds wall clock time: 41 minutes 24.65 seconds (2484.65 seconds total)