Starting phenix.real_space_refine on Thu Mar 6 00:31:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2c_38850/03_2025/8y2c_38850.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2c_38850/03_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_38850/03_2025/8y2c_38850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2c_38850/03_2025/8y2c_38850.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2c_38850/03_2025/8y2c_38850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2c_38850/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.72, per 1000 atoms: 0.88 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: 1.08 Conformation dependent library (CDL) restraints added in 732.9 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: 0.45 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: 1.86 Time building geometry restraints manager: 1.37 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.160 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- 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 : 0.392 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1368 time to fit residues: 6.6817 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 : 0.433 ------------------------------------------------------------------------------- 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 = 0.158784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136908 restraints weight = 5275.506| |-----------------------------------------------------------------------------| 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: 0.3362 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0600 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 52.409 611 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 : 0.540 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 45 average time/residue: 0.1410 time to fit residues: 8.6745 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 : 0.773 ------------------------------------------------------------------------------- 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: 0.0570 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 0.0970 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5096 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.158310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134683 restraints weight = 5184.582| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.17 r_work: 0.3387 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4337 Z= 0.134 Angle : 0.461 9.451 5921 Z= 0.226 Chirality : 0.037 0.165 677 Planarity : 0.004 0.051 723 Dihedral : 4.389 28.892 611 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.70 % Allowed : 33.11 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.39), residues: 523 helix: 1.54 (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 0.007 0.001 TRP A 556 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 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: 12 poor density : 37 time to evaluate : 0.453 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 45 average time/residue: 0.1069 time to fit residues: 7.1810 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 : 0.414 ------------------------------------------------------------------------------- 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 282 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: 0.9980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.156502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132888 restraints weight = 5175.177| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.15 r_work: 0.3397 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4337 Z= 0.171 Angle : 0.467 8.955 5921 Z= 0.230 Chirality : 0.037 0.173 677 Planarity : 0.004 0.053 723 Dihedral : 4.091 25.684 611 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.83 % Allowed : 31.98 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.39), residues: 523 helix: 1.48 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.48 (0.49), 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 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: 17 poor density : 34 time to evaluate : 0.448 Fit side-chains REVERT: A 544 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6399 (ptt-90) outliers start: 17 outliers final: 14 residues processed: 45 average time/residue: 0.1573 time to fit residues: 9.7827 Evaluate side-chains 48 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.156011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132376 restraints weight = 5349.668| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.14 r_work: 0.3277 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4337 Z= 0.171 Angle : 0.459 8.967 5921 Z= 0.228 Chirality : 0.037 0.169 677 Planarity : 0.004 0.053 723 Dihedral : 4.002 24.283 611 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.28 % Allowed : 32.43 % 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: 1.06 (0.39), residues: 523 helix: 1.50 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.51 (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 0.012 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 : 0.456 Fit side-chains REVERT: A 116 MET cc_start: 0.8177 (ttp) cc_final: 0.7954 (ttt) REVERT: A 381 ASP cc_start: 0.8465 (t0) cc_final: 0.8020 (t0) REVERT: A 544 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6470 (ptt-90) outliers start: 19 outliers final: 14 residues processed: 50 average time/residue: 0.1432 time to fit residues: 9.6256 Evaluate side-chains 51 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 45 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.156391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132954 restraints weight = 5193.070| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.10 r_work: 0.3286 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4337 Z= 0.157 Angle : 0.451 8.600 5921 Z= 0.224 Chirality : 0.037 0.164 677 Planarity : 0.004 0.052 723 Dihedral : 3.906 23.505 611 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: 1.07 (0.39), residues: 523 helix: 1.50 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.51 (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 0.010 0.001 PHE A 412 TYR 0.010 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 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.437 Fit side-chains REVERT: A 116 MET cc_start: 0.8126 (ttp) cc_final: 0.7813 (ttt) REVERT: A 381 ASP cc_start: 0.8529 (t0) cc_final: 0.7988 (t0) REVERT: A 544 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6470 (ptt-90) outliers start: 20 outliers final: 15 residues processed: 51 average time/residue: 0.1388 time to fit residues: 9.6068 Evaluate side-chains 52 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.154509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.131004 restraints weight = 5192.880| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.10 r_work: 0.3286 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4337 Z= 0.206 Angle : 0.483 9.581 5921 Z= 0.239 Chirality : 0.038 0.174 677 Planarity : 0.004 0.054 723 Dihedral : 4.052 24.897 611 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.18 % Allowed : 31.98 % 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: 1.08 (0.38), residues: 523 helix: 1.63 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.60 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 PHE 0.015 0.001 PHE A 412 TYR 0.012 0.001 TYR A 370 ARG 0.001 0.000 ARG A 544 *********************** 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 59 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 36 time to evaluate : 0.462 Fit side-chains REVERT: A 116 MET cc_start: 0.8191 (ttp) cc_final: 0.7894 (ttt) REVERT: A 164 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7562 (tp) REVERT: A 381 ASP cc_start: 0.8560 (t0) cc_final: 0.8023 (t0) REVERT: A 544 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6490 (ptt-90) outliers start: 23 outliers final: 17 residues processed: 52 average time/residue: 0.1421 time to fit residues: 10.0442 Evaluate side-chains 54 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 164 LEU 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 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: 3.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.0270 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.156561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.133102 restraints weight = 5164.712| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.10 r_work: 0.3235 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.0911 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= 0.151 Angle : 0.449 8.309 5921 Z= 0.223 Chirality : 0.037 0.160 677 Planarity : 0.004 0.052 723 Dihedral : 3.855 23.362 611 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.28 % Allowed : 32.21 % 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: 1.09 (0.38), residues: 523 helix: 1.52 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.50 (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 0.013 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: 19 poor density : 37 time to evaluate : 0.455 Fit side-chains REVERT: A 116 MET cc_start: 0.8106 (ttp) cc_final: 0.7801 (ttt) REVERT: A 164 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7441 (tp) REVERT: A 381 ASP cc_start: 0.8534 (t0) cc_final: 0.7832 (t0) REVERT: A 544 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6418 (ptt-90) outliers start: 19 outliers final: 15 residues processed: 50 average time/residue: 0.1386 time to fit residues: 9.4770 Evaluate side-chains 54 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 164 LEU 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 324 VAL 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 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: 0.5980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.0970 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.157343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133860 restraints weight = 5207.790| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.11 r_work: 0.3319 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.0980 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= 0.144 Angle : 0.441 8.246 5921 Z= 0.219 Chirality : 0.037 0.154 677 Planarity : 0.004 0.052 723 Dihedral : 3.723 21.703 611 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.05 % Allowed : 32.43 % 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: 1.20 (0.39), residues: 523 helix: 1.60 (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 0.013 0.001 TYR A 370 ARG 0.001 0.000 ARG A 85 *********************** 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 : 0.451 Fit side-chains REVERT: A 116 MET cc_start: 0.8193 (ttp) cc_final: 0.7891 (ttt) REVERT: A 381 ASP cc_start: 0.8505 (t0) cc_final: 0.7909 (t0) REVERT: A 544 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6492 (ptt-90) outliers start: 18 outliers final: 17 residues processed: 50 average time/residue: 0.1385 time to fit residues: 9.4477 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 : 0.457 ------------------------------------------------------------------------------- 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: 0.9990 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.0040 chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 19 optimal weight: 0.0770 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.0570 chunk 3 optimal weight: 0.0980 overall best weight: 0.1668 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.161725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.137944 restraints weight = 5126.942| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.16 r_work: 0.3452 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4337 Z= 0.103 Angle : 0.406 6.587 5921 Z= 0.202 Chirality : 0.035 0.132 677 Planarity : 0.004 0.051 723 Dihedral : 3.366 18.569 611 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.25 % Allowed : 34.23 % 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: 1.42 (0.39), residues: 523 helix: 1.75 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.35 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 556 HIS 0.002 0.000 HIS A 179 PHE 0.011 0.001 PHE A 155 TYR 0.011 0.001 TYR A 370 ARG 0.001 0.000 ARG A 344 ********************** 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: 10 poor density : 42 time to evaluate : 0.395 Fit side-chains REVERT: A 116 MET cc_start: 0.8081 (ttp) cc_final: 0.7785 (ttt) REVERT: A 381 ASP cc_start: 0.8376 (t0) cc_final: 0.7785 (t0) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 0.1146 time to fit residues: 7.7883 Evaluate side-chains 48 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 256 TRP 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 469 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 27 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.157525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.133626 restraints weight = 5199.359| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.17 r_work: 0.3296 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1132 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= 0.169 Angle : 0.451 8.666 5921 Z= 0.222 Chirality : 0.037 0.155 677 Planarity : 0.004 0.052 723 Dihedral : 3.562 20.255 611 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.25 % Allowed : 33.78 % Favored : 63.96 % 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: 1.38 (0.39), residues: 523 helix: 1.73 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.38 (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 0.009 0.001 TYR A 88 ARG 0.001 0.000 ARG A 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2380.10 seconds wall clock time: 42 minutes 0.35 seconds (2520.35 seconds total)