Starting phenix.real_space_refine on Thu Dec 7 20:39:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/12_2023/8cxo_27062_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/12_2023/8cxo_27062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/12_2023/8cxo_27062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/12_2023/8cxo_27062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/12_2023/8cxo_27062_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/12_2023/8cxo_27062_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2863 2.51 5 N 724 2.21 5 O 775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4392 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4392 Unusual residues: {'CLR': 1} Classifications: {'peptide': 551, 'undetermined': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 535, None: 1} Not linked: pdbres="LEU A 556 " pdbres="CLR A1301 " Chain breaks: 1 Time building chain proxies: 3.14, per 1000 atoms: 0.71 Number of scatterers: 4392 At special positions: 0 Unit cell: (75.985, 65.13, 123.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 775 8.00 N 724 7.00 C 2863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 299 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 511 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 836.2 milliseconds 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1010 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 4 sheets defined 59.5% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 228 through 263 removed outlier: 3.998A pdb=" N ASP A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASN A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 270 through 289 removed outlier: 4.691A pdb=" N GLN A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N PHE A 289 " --> pdb=" O TRP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 317 through 348 removed outlier: 4.079A pdb=" N PHE A 347 " --> pdb=" O TRP A 343 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS A 348 " --> pdb=" O HIS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 382 removed outlier: 4.205A pdb=" N THR A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER A 362 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 364 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 366 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP A 369 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 370 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 371 " --> pdb=" O THR A 368 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 401 through 407 Processing helix chain 'A' and resid 409 through 437 Processing helix chain 'A' and resid 1016 through 1026 Processing helix chain 'A' and resid 1048 through 1060 removed outlier: 4.213A pdb=" N SER A1060 " --> pdb=" O GLU A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1066 removed outlier: 3.967A pdb=" N GLN A1065 " --> pdb=" O LYS A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1102 through 1111 Processing helix chain 'A' and resid 1126 through 1133 removed outlier: 4.011A pdb=" N GLU A1130 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A1131 " --> pdb=" O ALA A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1148 removed outlier: 4.029A pdb=" N ARG A1147 " --> pdb=" O GLY A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1177 Processing helix chain 'A' and resid 1182 through 1192 Processing helix chain 'A' and resid 1207 through 452 Processing helix chain 'A' and resid 455 through 496 removed outlier: 3.599A pdb=" N PHE A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 495 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 540 removed outlier: 3.690A pdb=" N GLY A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TRP A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL A 540 " --> pdb=" O MET A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing sheet with id= A, first strand: chain 'A' and resid 201 through 203 Processing sheet with id= B, first strand: chain 'A' and resid 385 through 388 removed outlier: 3.551A pdb=" N ASP A 388 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 393 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1033 through 1038 Processing sheet with id= D, first strand: chain 'A' and resid 1114 through 1117 removed outlier: 6.217A pdb=" N ILE A1137 " --> pdb=" O VAL A1115 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE A1117 " --> pdb=" O ILE A1137 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A1139 " --> pdb=" O ILE A1117 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A1156 " --> pdb=" O ALA A1140 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 230 hydrogen bonds defined for protein. 636 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: 1.20 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1374 1.34 - 1.46: 1147 1.46 - 1.58: 1935 1.58 - 1.70: 0 1.70 - 1.82: 45 Bond restraints: 4501 Sorted by residual: bond pdb=" C13 CLR A1301 " pdb=" C14 CLR A1301 " ideal model delta sigma weight residual 1.537 1.504 0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 CLR A1301 " pdb=" C10 CLR A1301 " ideal model delta sigma weight residual 1.544 1.515 0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C16 CLR A1301 " pdb=" C17 CLR A1301 " ideal model delta sigma weight residual 1.554 1.528 0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" C15 CLR A1301 " pdb=" C16 CLR A1301 " ideal model delta sigma weight residual 1.541 1.517 0.024 2.00e-02 2.50e+03 1.45e+00 bond pdb=" CA VAL A 214 " pdb=" CB VAL A 214 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.31e-02 5.83e+03 1.19e+00 ... (remaining 4496 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.01: 103 107.01 - 113.77: 2461 113.77 - 120.53: 1873 120.53 - 127.29: 1609 127.29 - 134.04: 50 Bond angle restraints: 6096 Sorted by residual: angle pdb=" N CYS A1004 " pdb=" CA CYS A1004 " pdb=" C CYS A1004 " ideal model delta sigma weight residual 107.20 112.41 -5.21 1.70e+00 3.46e-01 9.41e+00 angle pdb=" C TYR A 211 " pdb=" N GLU A 212 " pdb=" CA GLU A 212 " ideal model delta sigma weight residual 121.19 125.96 -4.77 1.59e+00 3.96e-01 8.98e+00 angle pdb=" N TYR A 266 " pdb=" CA TYR A 266 " pdb=" C TYR A 266 " ideal model delta sigma weight residual 109.81 115.33 -5.52 2.21e+00 2.05e-01 6.24e+00 angle pdb=" N GLY A1001 " pdb=" CA GLY A1001 " pdb=" C GLY A1001 " ideal model delta sigma weight residual 113.99 116.99 -3.00 1.28e+00 6.10e-01 5.50e+00 angle pdb=" C6 CLR A1301 " pdb=" C7 CLR A1301 " pdb=" C8 CLR A1301 " ideal model delta sigma weight residual 113.19 106.26 6.93 3.00e+00 1.11e-01 5.34e+00 ... (remaining 6091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 2541 17.14 - 34.28: 110 34.28 - 51.42: 20 51.42 - 68.56: 3 68.56 - 85.70: 1 Dihedral angle restraints: 2675 sinusoidal: 1098 harmonic: 1577 Sorted by residual: dihedral pdb=" CB CYS A 494 " pdb=" SG CYS A 494 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual 93.00 145.05 -52.05 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CA LEU A 441 " pdb=" C LEU A 441 " pdb=" N GLY A1001 " pdb=" CA GLY A1001 " ideal model delta harmonic sigma weight residual -180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA TYR A 211 " pdb=" C TYR A 211 " pdb=" N GLU A 212 " pdb=" CA GLU A 212 " ideal model delta harmonic sigma weight residual 180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 2672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 553 0.045 - 0.089: 90 0.089 - 0.134: 29 0.134 - 0.178: 4 0.178 - 0.223: 1 Chirality restraints: 677 Sorted by residual: chirality pdb=" C10 CLR A1301 " pdb=" C1 CLR A1301 " pdb=" C5 CLR A1301 " pdb=" C9 CLR A1301 " both_signs ideal model delta sigma weight residual False -2.85 -2.63 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE A1139 " pdb=" N ILE A1139 " pdb=" C ILE A1139 " pdb=" CB ILE A1139 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE A1137 " pdb=" N ILE A1137 " pdb=" C ILE A1137 " pdb=" CB ILE A1137 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 674 not shown) Planarity restraints: 759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1122 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A1123 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A1123 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A1123 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 437 " 0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO A 438 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 438 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 438 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A1201 " -0.005 2.00e-02 2.50e+03 1.05e-02 1.09e+00 pdb=" C MET A1201 " 0.018 2.00e-02 2.50e+03 pdb=" O MET A1201 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP A1202 " -0.006 2.00e-02 2.50e+03 ... (remaining 756 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1447 2.84 - 3.36: 4352 3.36 - 3.87: 7307 3.87 - 4.39: 8527 4.39 - 4.90: 13890 Nonbonded interactions: 35523 Sorted by model distance: nonbonded pdb=" O MET A1201 " pdb=" N ILE A1203 " model vdw 2.329 2.520 nonbonded pdb=" N GLU A1098 " pdb=" OE1 GLU A1098 " model vdw 2.346 2.520 nonbonded pdb=" NZ LYS A 434 " pdb=" C2 CLR A1301 " model vdw 2.353 3.520 nonbonded pdb=" O ARG A1204 " pdb=" ND2 ASN A 450 " model vdw 2.398 2.520 nonbonded pdb=" O GLU A1056 " pdb=" OG SER A1059 " model vdw 2.420 2.440 ... (remaining 35518 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 group one per residue 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: 0.840 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: 3.730 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.540 Find NCS groups from input model: 0.110 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 0.033 4501 Z= 0.234 Angle : 0.581 6.930 6096 Z= 0.314 Chirality : 0.040 0.223 677 Planarity : 0.003 0.031 759 Dihedral : 10.103 85.704 1653 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.74 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.90 (0.36), residues: 547 helix: 1.91 (0.28), residues: 317 sheet: 1.64 (0.82), residues: 29 loop : 0.24 (0.48), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1007 HIS 0.003 0.001 HIS A 231 PHE 0.015 0.001 PHE A1124 TYR 0.008 0.001 TYR A 398 ARG 0.003 0.000 ARG A1106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1650 time to fit residues: 47.1429 Evaluate side-chains 147 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 344 HIS A1065 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4501 Z= 0.204 Angle : 0.611 9.457 6096 Z= 0.317 Chirality : 0.043 0.147 677 Planarity : 0.004 0.026 759 Dihedral : 5.183 29.129 663 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.29 % Favored : 96.53 % Rotamer: Outliers : 3.88 % Allowed : 17.67 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.88 (0.35), residues: 547 helix: 2.33 (0.27), residues: 305 sheet: 1.49 (0.77), residues: 30 loop : -0.42 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 343 HIS 0.006 0.001 HIS A 344 PHE 0.018 0.002 PHE A 322 TYR 0.029 0.002 TYR A 211 ARG 0.005 0.001 ARG A1102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 16 residues processed: 164 average time/residue: 0.1389 time to fit residues: 29.4662 Evaluate side-chains 156 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0458 time to fit residues: 1.9688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN A 437 HIS A 481 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4501 Z= 0.306 Angle : 0.634 7.586 6096 Z= 0.329 Chirality : 0.044 0.147 677 Planarity : 0.004 0.031 759 Dihedral : 5.219 25.791 663 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.88 % Allowed : 18.97 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.46 (0.35), residues: 547 helix: 2.06 (0.28), residues: 307 sheet: 1.25 (0.75), residues: 30 loop : -0.76 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 484 HIS 0.002 0.001 HIS A 231 PHE 0.013 0.002 PHE A1124 TYR 0.024 0.002 TYR A 211 ARG 0.003 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 0.494 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 148 average time/residue: 0.1249 time to fit residues: 24.5935 Evaluate side-chains 124 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.493 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0473 time to fit residues: 1.6836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN A 481 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4501 Z= 0.179 Angle : 0.583 7.927 6096 Z= 0.294 Chirality : 0.043 0.142 677 Planarity : 0.003 0.036 759 Dihedral : 5.022 36.613 663 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.02 % Allowed : 21.77 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.31 (0.35), residues: 547 helix: 2.01 (0.28), residues: 310 sheet: 0.63 (0.86), residues: 30 loop : -0.89 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 484 HIS 0.001 0.000 HIS A1090 PHE 0.022 0.001 PHE A 373 TYR 0.021 0.001 TYR A 211 ARG 0.003 0.000 ARG A1102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 0.509 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 145 average time/residue: 0.1307 time to fit residues: 25.1123 Evaluate side-chains 135 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0523 time to fit residues: 1.4071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN ** A1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4501 Z= 0.351 Angle : 0.666 8.725 6096 Z= 0.342 Chirality : 0.045 0.142 677 Planarity : 0.004 0.032 759 Dihedral : 5.251 33.105 663 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.02 % Allowed : 22.41 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.34), residues: 547 helix: 1.89 (0.28), residues: 306 sheet: 0.36 (0.88), residues: 30 loop : -0.90 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 484 HIS 0.009 0.001 HIS A1090 PHE 0.022 0.002 PHE A 373 TYR 0.019 0.002 TYR A 211 ARG 0.002 0.000 ARG A1016 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.479 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 135 average time/residue: 0.1308 time to fit residues: 23.4533 Evaluate side-chains 116 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0452 time to fit residues: 1.5425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4501 Z= 0.175 Angle : 0.611 12.093 6096 Z= 0.303 Chirality : 0.043 0.157 677 Planarity : 0.003 0.028 759 Dihedral : 5.051 39.871 663 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.37 % Allowed : 24.57 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.22 (0.35), residues: 547 helix: 1.98 (0.28), residues: 309 sheet: 0.41 (0.90), residues: 30 loop : -0.97 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 484 HIS 0.002 0.001 HIS A 231 PHE 0.024 0.001 PHE A 373 TYR 0.014 0.001 TYR A 211 ARG 0.002 0.000 ARG A1102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 135 average time/residue: 0.1289 time to fit residues: 23.1747 Evaluate side-chains 125 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 0.505 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0485 time to fit residues: 1.1784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4501 Z= 0.181 Angle : 0.630 13.310 6096 Z= 0.311 Chirality : 0.042 0.159 677 Planarity : 0.003 0.034 759 Dihedral : 4.957 39.024 663 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.29 % Allowed : 27.59 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.24 (0.35), residues: 547 helix: 2.03 (0.28), residues: 309 sheet: 0.30 (0.88), residues: 30 loop : -0.99 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP A 484 HIS 0.001 0.000 HIS A 231 PHE 0.024 0.001 PHE A 373 TYR 0.015 0.001 TYR A1011 ARG 0.002 0.000 ARG A1102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 0.490 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 130 average time/residue: 0.1311 time to fit residues: 22.6732 Evaluate side-chains 124 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0540 time to fit residues: 1.1919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4501 Z= 0.361 Angle : 0.756 11.604 6096 Z= 0.382 Chirality : 0.047 0.192 677 Planarity : 0.004 0.042 759 Dihedral : 5.305 35.215 663 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.16 % Allowed : 25.65 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.86 (0.34), residues: 547 helix: 1.71 (0.28), residues: 310 sheet: -0.02 (0.92), residues: 30 loop : -1.14 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.112 0.004 TRP A 484 HIS 0.003 0.001 HIS A 474 PHE 0.023 0.002 PHE A 373 TYR 0.014 0.002 TYR A1011 ARG 0.003 0.001 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.511 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 106 average time/residue: 0.1533 time to fit residues: 20.9376 Evaluate side-chains 100 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.505 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0486 time to fit residues: 1.1043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 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: 0.7889 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4501 Z= 0.194 Angle : 0.698 14.893 6096 Z= 0.347 Chirality : 0.044 0.233 677 Planarity : 0.003 0.044 759 Dihedral : 5.067 40.855 663 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.22 % Allowed : 27.37 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.92 (0.35), residues: 547 helix: 1.75 (0.28), residues: 310 sheet: 0.11 (0.91), residues: 30 loop : -1.11 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.118 0.003 TRP A 484 HIS 0.002 0.001 HIS A 474 PHE 0.024 0.001 PHE A 373 TYR 0.018 0.001 TYR A 491 ARG 0.002 0.000 ARG A1040 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.467 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 122 average time/residue: 0.1225 time to fit residues: 20.1317 Evaluate side-chains 116 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.524 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0676 time to fit residues: 0.8157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.7955 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4501 Z= 0.356 Angle : 0.751 12.373 6096 Z= 0.384 Chirality : 0.047 0.208 677 Planarity : 0.004 0.037 759 Dihedral : 5.326 36.040 663 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.86 % Allowed : 28.66 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.01 (0.35), residues: 547 helix: 1.83 (0.28), residues: 299 sheet: -0.14 (0.90), residues: 30 loop : -0.86 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.003 TRP A 484 HIS 0.002 0.001 HIS A 474 PHE 0.022 0.002 PHE A 373 TYR 0.016 0.002 TYR A 237 ARG 0.005 0.001 ARG A1191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.450 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 105 average time/residue: 0.1297 time to fit residues: 18.1532 Evaluate side-chains 105 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0589 time to fit residues: 1.0282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.113544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093134 restraints weight = 10150.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096335 restraints weight = 5073.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098632 restraints weight = 3172.746| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4501 Z= 0.203 Angle : 0.716 14.828 6096 Z= 0.353 Chirality : 0.045 0.202 677 Planarity : 0.003 0.036 759 Dihedral : 5.131 40.751 663 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.22 % Allowed : 28.66 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.35), residues: 547 helix: 1.94 (0.28), residues: 298 sheet: -0.05 (0.89), residues: 30 loop : -0.87 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.003 TRP A 484 HIS 0.002 0.001 HIS A 231 PHE 0.025 0.001 PHE A 373 TYR 0.018 0.001 TYR A 491 ARG 0.001 0.000 ARG A1040 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1249.33 seconds wall clock time: 23 minutes 19.88 seconds (1399.88 seconds total)