Starting phenix.real_space_refine on Mon Sep 23 17:36:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2c_38850/09_2024/8y2c_38850.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2c_38850/09_2024/8y2c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2c_38850/09_2024/8y2c_38850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2c_38850/09_2024/8y2c_38850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2c_38850/09_2024/8y2c_38850.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2c_38850/09_2024/8y2c_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-5461/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: 3.21, per 1000 atoms: 0.76 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: 1.15 Conformation dependent library (CDL) restraints added in 524.3 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: 0.46 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: 1.09 Time building geometry restraints manager: 1.28 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: 0.860 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.710 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.760 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1356 time to fit residues: 6.5806 Evaluate side-chains 34 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 fitting. rotamer outliers: 14 poor density : 36 time to evaluate : 0.445 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 45 average time/residue: 0.1366 time to fit residues: 8.3759 Evaluate side-chains 43 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 39 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.0731 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= 0.150 Angle : 0.472 9.682 5921 Z= 0.231 Chirality : 0.037 0.168 677 Planarity : 0.004 0.052 723 Dihedral : 4.460 29.446 611 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: 1.08 (0.39), residues: 523 helix: 1.50 (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 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 fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.458 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 45 average time/residue: 0.1231 time to fit residues: 7.7927 Evaluate side-chains 43 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 5 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4337 Z= 0.189 Angle : 0.482 9.327 5921 Z= 0.238 Chirality : 0.038 0.176 677 Planarity : 0.004 0.054 723 Dihedral : 4.162 25.637 611 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.60 % Allowed : 32.88 % 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: 0.99 (0.38), residues: 523 helix: 1.51 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -1.61 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 PHE 0.014 0.001 PHE A 412 TYR 0.010 0.001 TYR A 115 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 fitting. rotamer outliers: 16 poor density : 35 time to evaluate : 0.402 Fit side-chains REVERT: A 381 ASP cc_start: 0.8274 (t0) cc_final: 0.7791 (t0) REVERT: A 544 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6460 (ptt-90) outliers start: 16 outliers final: 12 residues processed: 45 average time/residue: 0.1462 time to fit residues: 8.7326 Evaluate side-chains 47 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 34 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4337 Z= 0.270 Angle : 0.539 10.539 5921 Z= 0.267 Chirality : 0.039 0.187 677 Planarity : 0.004 0.056 723 Dihedral : 4.446 29.927 611 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.86 % Allowed : 31.53 % 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: 0.78 (0.38), residues: 523 helix: 1.40 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.68 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 PHE 0.018 0.001 PHE A 412 TYR 0.016 0.001 TYR A 115 ARG 0.001 0.000 ARG A 615 *********************** 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 62 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 36 time to evaluate : 0.462 Fit side-chains REVERT: A 116 MET cc_start: 0.8105 (ttp) cc_final: 0.7747 (ttp) REVERT: A 164 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7559 (tp) REVERT: A 307 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: A 381 ASP cc_start: 0.8330 (t0) cc_final: 0.7839 (t0) REVERT: A 544 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6388 (ptt-90) REVERT: A 598 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6793 (mt-10) outliers start: 26 outliers final: 16 residues processed: 55 average time/residue: 0.1421 time to fit residues: 10.4818 Evaluate side-chains 54 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 35 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 307 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4337 Z= 0.163 Angle : 0.458 8.285 5921 Z= 0.229 Chirality : 0.037 0.162 677 Planarity : 0.004 0.052 723 Dihedral : 4.057 27.315 611 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.60 % Allowed : 33.56 % 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: 0.94 (0.38), residues: 523 helix: 1.49 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -1.66 (0.48), residues: 148 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 155 TYR 0.012 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 53 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 37 time to evaluate : 0.332 Fit side-chains REVERT: A 116 MET cc_start: 0.8029 (ttp) cc_final: 0.7745 (ttt) REVERT: A 381 ASP cc_start: 0.8322 (t0) cc_final: 0.7748 (t0) REVERT: A 544 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.6429 (ptt-90) outliers start: 16 outliers final: 13 residues processed: 47 average time/residue: 0.1444 time to fit residues: 9.0462 Evaluate side-chains 51 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 405 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4337 Z= 0.275 Angle : 0.537 10.732 5921 Z= 0.267 Chirality : 0.040 0.185 677 Planarity : 0.004 0.055 723 Dihedral : 4.403 30.981 611 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.18 % Allowed : 32.21 % 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: 0.74 (0.38), residues: 523 helix: 1.37 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.69 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 256 HIS 0.003 0.001 HIS A 179 PHE 0.019 0.001 PHE A 412 TYR 0.016 0.002 TYR A 370 ARG 0.001 0.000 ARG A 601 *********************** 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 fitting. rotamer outliers: 23 poor density : 36 time to evaluate : 0.442 Fit side-chains REVERT: A 116 MET cc_start: 0.8125 (ttp) cc_final: 0.7828 (ttt) REVERT: A 381 ASP cc_start: 0.8377 (t0) cc_final: 0.7764 (t0) REVERT: A 544 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6402 (ptt-90) REVERT: A 598 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6546 (mt-10) outliers start: 23 outliers final: 16 residues processed: 52 average time/residue: 0.1411 time to fit residues: 9.9511 Evaluate side-chains 52 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 35 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 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 422 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 567 SER 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 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 39 optimal weight: 0.0570 chunk 45 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.0921 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 : 0.450 8.115 5921 Z= 0.225 Chirality : 0.037 0.156 677 Planarity : 0.004 0.053 723 Dihedral : 3.962 26.857 611 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.28 % Allowed : 32.88 % 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: 0.98 (0.39), residues: 523 helix: 1.44 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.55 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 556 HIS 0.003 0.001 HIS A 179 PHE 0.011 0.001 PHE A 155 TYR 0.012 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 fitting. rotamer outliers: 19 poor density : 37 time to evaluate : 0.465 Fit side-chains REVERT: A 116 MET cc_start: 0.8013 (ttp) cc_final: 0.7759 (ttt) REVERT: A 164 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7552 (tp) REVERT: A 381 ASP cc_start: 0.8304 (t0) cc_final: 0.7587 (t0) REVERT: A 544 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6463 (ptt-90) outliers start: 19 outliers final: 15 residues processed: 51 average time/residue: 0.1448 time to fit residues: 9.9011 Evaluate side-chains 53 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 36 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 320 PHE Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 441 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 42 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0953 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= 0.149 Angle : 0.452 8.518 5921 Z= 0.224 Chirality : 0.037 0.156 677 Planarity : 0.004 0.053 723 Dihedral : 3.855 24.520 611 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.95 % Allowed : 32.21 % 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: 1.06 (0.39), residues: 523 helix: 1.49 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.49 (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 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 58 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 36 time to evaluate : 0.437 Fit side-chains REVERT: A 116 MET cc_start: 0.8021 (ttp) cc_final: 0.7766 (ttt) REVERT: A 272 MET cc_start: 0.6107 (OUTLIER) cc_final: 0.5836 (ttm) REVERT: A 381 ASP cc_start: 0.8275 (t0) cc_final: 0.7658 (t0) REVERT: A 544 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.6478 (ptt-90) outliers start: 22 outliers final: 17 residues processed: 52 average time/residue: 0.1357 time to fit residues: 9.5651 Evaluate side-chains 55 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 36 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 272 MET 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 422 SER Chi-restraints excluded: chain A residue 441 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 567 SER 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 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.0974 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= 0.158 Angle : 0.454 8.731 5921 Z= 0.224 Chirality : 0.037 0.158 677 Planarity : 0.004 0.053 723 Dihedral : 3.826 23.438 611 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.50 % Allowed : 32.88 % 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: 1.08 (0.39), residues: 523 helix: 1.50 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.48 (0.51), 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 0.012 0.001 TYR A 370 ARG 0.001 0.000 ARG A 544 ********************** 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 57 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 37 time to evaluate : 0.399 Fit side-chains REVERT: A 116 MET cc_start: 0.8024 (ttp) cc_final: 0.7765 (ttt) REVERT: A 272 MET cc_start: 0.6095 (OUTLIER) cc_final: 0.5831 (ttm) REVERT: A 381 ASP cc_start: 0.8214 (t0) cc_final: 0.7612 (t0) REVERT: A 544 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.6463 (ptt-90) outliers start: 20 outliers final: 18 residues processed: 51 average time/residue: 0.1363 time to fit residues: 9.4023 Evaluate side-chains 57 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 37 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 272 MET 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 422 SER Chi-restraints excluded: chain A residue 441 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 567 SER 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 5 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.0470 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.156372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.132413 restraints weight = 5157.556| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.13 r_work: 0.3268 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1036 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= 0.140 Angle : 0.441 8.190 5921 Z= 0.218 Chirality : 0.037 0.149 677 Planarity : 0.004 0.052 723 Dihedral : 3.707 21.473 611 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.73 % Allowed : 32.43 % 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: 1.17 (0.39), residues: 523 helix: 1.57 (0.28), residues: 382 sheet: None (None), residues: 0 loop : -1.45 (0.51), 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 0.010 0.001 PHE A 155 TYR 0.011 0.001 TYR A 370 ARG 0.001 0.000 ARG A 544 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1137.19 seconds wall clock time: 24 minutes 9.94 seconds (1449.94 seconds total)