Starting phenix.real_space_refine on Sun Mar 10 16:52:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp5_32669/03_2024/7wp5_32669.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp5_32669/03_2024/7wp5_32669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp5_32669/03_2024/7wp5_32669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp5_32669/03_2024/7wp5_32669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp5_32669/03_2024/7wp5_32669.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp5_32669/03_2024/7wp5_32669.pdb" } resolution = 3.9 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= 0.008 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 15 5.16 5 C 2118 2.51 5 N 563 2.21 5 O 644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 340": "OE1" <-> "OE2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3340 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 811 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "F" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1484 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 10, 'TRANS': 172} 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: 2.37, per 1000 atoms: 0.71 Number of scatterers: 3340 At special positions: 0 Unit cell: (77.022, 80.912, 81.69, 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 15 16.00 O 644 8.00 N 563 7.00 C 2118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 564.4 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 7 sheets defined 2.4% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.688A pdb=" N ASP F 339 " --> pdb=" O CYS F 336 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU F 340 " --> pdb=" O PRO F 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 336 through 340' Processing helix chain 'F' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.750A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 50 removed outlier: 5.740A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.600A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.618A pdb=" N GLY H 10 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR H 125 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 103 through 104 removed outlier: 3.606A pdb=" N TYR H 103 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN H 111 " --> pdb=" O TYR H 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 358 through 359 removed outlier: 3.735A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 376 through 379 removed outlier: 3.527A pdb=" N THR F 376 " --> pdb=" O ALA F 435 " (cutoff:3.500A) 63 hydrogen bonds defined for protein. 153 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1052 1.34 - 1.46: 852 1.46 - 1.58: 1503 1.58 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3426 Sorted by residual: bond pdb=" CA SER F 446 " pdb=" C SER F 446 " ideal model delta sigma weight residual 1.522 1.544 -0.022 1.37e-02 5.33e+03 2.59e+00 bond pdb=" CA CYS F 336 " pdb=" C CYS F 336 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.31e+00 bond pdb=" C3 NAG A 1 " pdb=" O3 NAG A 1 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C3 NAG A 2 " pdb=" O3 NAG A 2 " ideal model delta sigma weight residual 1.403 1.431 -0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C4 NAG A 1 " pdb=" O4 NAG A 1 " ideal model delta sigma weight residual 1.409 1.435 -0.026 2.00e-02 2.50e+03 1.75e+00 ... (remaining 3421 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.31: 89 106.31 - 113.22: 1712 113.22 - 120.14: 1241 120.14 - 127.05: 1560 127.05 - 133.97: 52 Bond angle restraints: 4654 Sorted by residual: angle pdb=" C ASN F 477 " pdb=" N LYS F 478 " pdb=" CA LYS F 478 " ideal model delta sigma weight residual 121.80 132.91 -11.11 2.44e+00 1.68e-01 2.07e+01 angle pdb=" C GLY L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C TYR F 369 " pdb=" N ASN F 370 " pdb=" CA ASN F 370 " ideal model delta sigma weight residual 122.19 128.42 -6.23 1.41e+00 5.03e-01 1.95e+01 angle pdb=" C SER F 359 " pdb=" N ASN F 360 " pdb=" CA ASN F 360 " ideal model delta sigma weight residual 122.46 128.68 -6.22 1.41e+00 5.03e-01 1.95e+01 angle pdb=" CA LEU F 371 " pdb=" CB LEU F 371 " pdb=" CG LEU F 371 " ideal model delta sigma weight residual 116.30 129.31 -13.01 3.50e+00 8.16e-02 1.38e+01 ... (remaining 4649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.85: 1729 14.85 - 29.70: 224 29.70 - 44.55: 56 44.55 - 59.41: 6 59.41 - 74.26: 5 Dihedral angle restraints: 2020 sinusoidal: 800 harmonic: 1220 Sorted by residual: dihedral pdb=" CA ASN F 460 " pdb=" C ASN F 460 " pdb=" N LEU F 461 " pdb=" CA LEU F 461 " ideal model delta harmonic sigma weight residual -180.00 -147.27 -32.73 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA ASN F 477 " pdb=" C ASN F 477 " pdb=" N LYS F 478 " pdb=" CA LYS F 478 " ideal model delta harmonic sigma weight residual -180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ASN H 115 " pdb=" C ASN H 115 " pdb=" N TYR H 116 " pdb=" CA TYR H 116 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 2017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 392 0.066 - 0.132: 80 0.132 - 0.198: 21 0.198 - 0.264: 1 0.264 - 0.329: 1 Chirality restraints: 495 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN F 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.11e+00 chirality pdb=" CB THR H 91 " pdb=" CA THR H 91 " pdb=" OG1 THR H 91 " pdb=" CG2 THR H 91 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 492 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.278 2.00e-02 2.50e+03 2.38e-01 7.10e+02 pdb=" C7 NAG A 1 " 0.061 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.016 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.402 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.028 2.00e-02 2.50e+03 2.34e-02 6.84e+00 pdb=" C7 NAG A 2 " -0.007 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.021 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.037 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 411 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO F 412 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 412 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 412 " 0.029 5.00e-02 4.00e+02 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 935 2.80 - 3.33: 2725 3.33 - 3.85: 5189 3.85 - 4.38: 5630 4.38 - 4.90: 9998 Nonbonded interactions: 24477 Sorted by model distance: nonbonded pdb=" OD2 ASP F 442 " pdb=" OH TYR F 451 " model vdw 2.278 2.440 nonbonded pdb=" OD2 ASP F 398 " pdb=" OH TYR F 423 " model vdw 2.305 2.440 nonbonded pdb=" NE2 HIS L 36 " pdb=" O ASN H 115 " model vdw 2.326 2.520 nonbonded pdb=" NE2 GLN L 39 " pdb=" OD1 ASP L 84 " model vdw 2.364 2.520 nonbonded pdb=" OG SER H 130 " pdb=" N SER H 131 " model vdw 2.373 2.520 ... (remaining 24472 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=0.00 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: 8.380 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: 38.560 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.940 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 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 : 0.005 0.039 3426 Z= 0.332 Angle : 1.025 13.015 4654 Z= 0.561 Chirality : 0.060 0.329 495 Planarity : 0.012 0.238 603 Dihedral : 13.947 74.258 1245 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.07 % Favored : 90.69 % Rotamer: Outliers : 0.56 % Allowed : 10.64 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.27 (0.34), residues: 419 helix: -5.34 (0.29), residues: 11 sheet: -1.85 (0.43), residues: 135 loop : -3.47 (0.29), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.005 0.002 HIS L 36 PHE 0.017 0.003 PHE F 515 TYR 0.018 0.002 TYR F 508 ARG 0.004 0.001 ARG L 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 108 LEU cc_start: 0.8612 (tp) cc_final: 0.8356 (tt) REVERT: H 51 MET cc_start: 0.8020 (ttp) cc_final: 0.7744 (ttm) REVERT: F 339 ASP cc_start: 0.7344 (t70) cc_final: 0.6803 (t70) REVERT: F 368 LEU cc_start: 0.8505 (mt) cc_final: 0.8287 (mt) REVERT: F 406 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7872 (mm-30) outliers start: 2 outliers final: 1 residues processed: 113 average time/residue: 0.1881 time to fit residues: 25.1199 Evaluate side-chains 83 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 497 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 38 optimal weight: 0.0570 chunk 11 optimal weight: 0.4980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3426 Z= 0.169 Angle : 0.687 8.372 4654 Z= 0.346 Chirality : 0.046 0.200 495 Planarity : 0.004 0.030 603 Dihedral : 6.378 39.163 522 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.31 % Favored : 90.45 % Rotamer: Outliers : 3.08 % Allowed : 19.89 % Favored : 77.03 % 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: -3.64 (0.37), residues: 419 helix: -3.98 (1.08), residues: 13 sheet: -1.41 (0.43), residues: 143 loop : -3.10 (0.32), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 37 HIS 0.003 0.001 HIS L 36 PHE 0.014 0.002 PHE F 374 TYR 0.024 0.001 TYR F 369 ARG 0.006 0.001 ARG F 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: L 50 ILE cc_start: 0.8919 (mt) cc_final: 0.8678 (mm) REVERT: L 108 LEU cc_start: 0.8571 (tp) cc_final: 0.8327 (tt) REVERT: H 51 MET cc_start: 0.7552 (ttp) cc_final: 0.7303 (ttm) REVERT: H 116 TYR cc_start: 0.8398 (m-80) cc_final: 0.8097 (m-80) REVERT: F 365 TYR cc_start: 0.8170 (m-10) cc_final: 0.7902 (m-10) REVERT: F 368 LEU cc_start: 0.8378 (mt) cc_final: 0.8111 (mt) REVERT: F 406 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8321 (mm-30) outliers start: 11 outliers final: 7 residues processed: 90 average time/residue: 0.1420 time to fit residues: 15.7492 Evaluate side-chains 90 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 497 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.0010 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 ASN ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3426 Z= 0.220 Angle : 0.667 7.762 4654 Z= 0.337 Chirality : 0.046 0.184 495 Planarity : 0.004 0.029 603 Dihedral : 6.193 34.316 522 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.83 % Favored : 90.93 % Rotamer: Outliers : 5.60 % Allowed : 19.33 % Favored : 75.07 % 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: -3.49 (0.37), residues: 419 helix: -4.06 (1.00), residues: 13 sheet: -1.18 (0.44), residues: 136 loop : -3.03 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 37 HIS 0.003 0.001 HIS L 36 PHE 0.021 0.002 PHE H 27 TYR 0.014 0.001 TYR F 369 ARG 0.004 0.001 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: L 108 LEU cc_start: 0.8629 (tp) cc_final: 0.8364 (tt) REVERT: L 111 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7369 (mt) REVERT: H 38 ARG cc_start: 0.7941 (ptm-80) cc_final: 0.7197 (ptm160) REVERT: H 51 MET cc_start: 0.7709 (ttp) cc_final: 0.7458 (ttm) REVERT: H 116 TYR cc_start: 0.8453 (m-80) cc_final: 0.8095 (m-80) REVERT: F 365 TYR cc_start: 0.8219 (m-10) cc_final: 0.7883 (m-10) REVERT: F 406 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8107 (mm-30) REVERT: F 425 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8293 (mp) outliers start: 20 outliers final: 13 residues processed: 95 average time/residue: 0.1294 time to fit residues: 15.3742 Evaluate side-chains 96 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 0.0040 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3426 Z= 0.227 Angle : 0.682 7.927 4654 Z= 0.341 Chirality : 0.044 0.138 495 Planarity : 0.004 0.032 603 Dihedral : 6.776 46.338 520 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.26 % Favored : 89.50 % Rotamer: Outliers : 5.04 % Allowed : 21.57 % Favored : 73.39 % 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: -3.41 (0.37), residues: 419 helix: -4.07 (0.99), residues: 13 sheet: -1.08 (0.43), residues: 136 loop : -3.00 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 436 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.002 PHE H 27 TYR 0.014 0.001 TYR F 369 ARG 0.005 0.001 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: L 108 LEU cc_start: 0.8615 (tp) cc_final: 0.8372 (tt) REVERT: H 38 ARG cc_start: 0.8078 (ptm-80) cc_final: 0.7446 (ptm160) REVERT: H 51 MET cc_start: 0.7708 (ttp) cc_final: 0.7506 (ttm) REVERT: H 116 TYR cc_start: 0.8422 (m-80) cc_final: 0.8105 (m-80) REVERT: F 365 TYR cc_start: 0.8248 (m-10) cc_final: 0.7901 (m-10) REVERT: F 406 GLU cc_start: 0.8710 (mm-30) cc_final: 0.7728 (mm-30) REVERT: F 425 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8290 (mp) outliers start: 18 outliers final: 12 residues processed: 94 average time/residue: 0.1287 time to fit residues: 15.2734 Evaluate side-chains 92 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3426 Z= 0.251 Angle : 0.682 8.225 4654 Z= 0.342 Chirality : 0.044 0.137 495 Planarity : 0.004 0.032 603 Dihedral : 6.605 40.828 520 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.50 % Favored : 89.26 % Rotamer: Outliers : 5.88 % Allowed : 23.53 % Favored : 70.59 % 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: -3.33 (0.37), residues: 419 helix: -5.84 (0.27), residues: 5 sheet: -1.13 (0.43), residues: 138 loop : -2.91 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 436 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.002 PHE H 27 TYR 0.014 0.001 TYR F 369 ARG 0.003 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 108 LEU cc_start: 0.8595 (tp) cc_final: 0.8330 (tt) REVERT: H 51 MET cc_start: 0.7669 (ttp) cc_final: 0.7405 (ttm) REVERT: H 116 TYR cc_start: 0.8463 (m-80) cc_final: 0.8166 (m-80) REVERT: F 425 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8342 (mp) outliers start: 21 outliers final: 17 residues processed: 91 average time/residue: 0.1179 time to fit residues: 13.7149 Evaluate side-chains 94 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 3426 Z= 0.439 Angle : 0.853 9.512 4654 Z= 0.424 Chirality : 0.049 0.144 495 Planarity : 0.005 0.038 603 Dihedral : 7.226 38.481 520 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.60 % Favored : 86.16 % Rotamer: Outliers : 7.84 % Allowed : 22.41 % Favored : 69.75 % 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: -3.57 (0.37), residues: 419 helix: -5.84 (0.27), residues: 5 sheet: -1.40 (0.41), residues: 147 loop : -3.06 (0.33), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 100 HIS 0.005 0.002 HIS H 35 PHE 0.018 0.003 PHE F 515 TYR 0.014 0.002 TYR F 369 ARG 0.007 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 80 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: L 108 LEU cc_start: 0.8731 (tp) cc_final: 0.8360 (tt) REVERT: H 51 MET cc_start: 0.7740 (ttp) cc_final: 0.7524 (ttm) REVERT: F 365 TYR cc_start: 0.8388 (m-10) cc_final: 0.8057 (m-10) REVERT: F 406 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8640 (mm-30) REVERT: F 425 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8430 (mp) REVERT: F 495 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6833 (t80) outliers start: 28 outliers final: 20 residues processed: 98 average time/residue: 0.1213 time to fit residues: 15.0421 Evaluate side-chains 99 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 480 CYS Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3426 Z= 0.186 Angle : 0.699 8.494 4654 Z= 0.348 Chirality : 0.045 0.138 495 Planarity : 0.004 0.032 603 Dihedral : 6.409 35.287 520 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.11 % Favored : 91.65 % Rotamer: Outliers : 5.60 % Allowed : 24.93 % Favored : 69.47 % 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: -3.26 (0.37), residues: 419 helix: -5.82 (0.26), residues: 5 sheet: -1.14 (0.46), residues: 126 loop : -2.78 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 436 HIS 0.003 0.001 HIS L 36 PHE 0.012 0.001 PHE H 27 TYR 0.013 0.001 TYR F 369 ARG 0.006 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: L 108 LEU cc_start: 0.8433 (tp) cc_final: 0.8167 (tt) REVERT: H 28 THR cc_start: 0.8315 (m) cc_final: 0.8010 (p) REVERT: H 38 ARG cc_start: 0.8183 (ptm-80) cc_final: 0.7489 (ptm160) REVERT: H 51 MET cc_start: 0.7518 (ttp) cc_final: 0.7286 (ttm) REVERT: F 365 TYR cc_start: 0.8260 (m-10) cc_final: 0.7897 (m-10) REVERT: F 425 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8305 (mp) REVERT: F 495 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6625 (t80) outliers start: 20 outliers final: 14 residues processed: 88 average time/residue: 0.1098 time to fit residues: 12.8066 Evaluate side-chains 88 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 480 CYS Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.0020 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3426 Z= 0.212 Angle : 0.704 8.841 4654 Z= 0.347 Chirality : 0.045 0.210 495 Planarity : 0.004 0.031 603 Dihedral : 6.288 31.181 520 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.46 % Favored : 88.31 % Rotamer: Outliers : 5.88 % Allowed : 25.21 % Favored : 68.91 % 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: -3.20 (0.38), residues: 419 helix: -5.82 (0.26), residues: 5 sheet: -1.12 (0.46), residues: 126 loop : -2.72 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 436 HIS 0.002 0.001 HIS L 36 PHE 0.011 0.001 PHE H 27 TYR 0.013 0.001 TYR F 369 ARG 0.006 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: L 108 LEU cc_start: 0.8499 (tp) cc_final: 0.8188 (tt) REVERT: H 12 VAL cc_start: 0.6263 (t) cc_final: 0.6055 (t) REVERT: H 28 THR cc_start: 0.8358 (m) cc_final: 0.8051 (p) REVERT: H 38 ARG cc_start: 0.8202 (ptm-80) cc_final: 0.7539 (ptm160) REVERT: H 51 MET cc_start: 0.7527 (ttp) cc_final: 0.7301 (ttm) REVERT: F 365 TYR cc_start: 0.8258 (m-10) cc_final: 0.7899 (m-10) REVERT: F 406 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8624 (mm-30) REVERT: F 425 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8329 (mp) REVERT: F 495 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6658 (t80) outliers start: 21 outliers final: 17 residues processed: 87 average time/residue: 0.1032 time to fit residues: 12.0136 Evaluate side-chains 89 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 480 CYS Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3426 Z= 0.284 Angle : 0.740 9.077 4654 Z= 0.368 Chirality : 0.046 0.206 495 Planarity : 0.004 0.033 603 Dihedral : 6.429 29.704 520 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.93 % Favored : 87.83 % Rotamer: Outliers : 5.88 % Allowed : 25.21 % Favored : 68.91 % 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: -3.21 (0.38), residues: 419 helix: -5.82 (0.27), residues: 5 sheet: -1.12 (0.46), residues: 128 loop : -2.74 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 436 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.002 PHE F 515 TYR 0.013 0.002 TYR F 369 ARG 0.005 0.001 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: L 108 LEU cc_start: 0.8533 (tp) cc_final: 0.8209 (tt) REVERT: H 38 ARG cc_start: 0.8280 (ptm-80) cc_final: 0.7449 (ptm160) REVERT: H 51 MET cc_start: 0.7614 (ttp) cc_final: 0.7406 (ttm) REVERT: F 365 TYR cc_start: 0.8278 (m-10) cc_final: 0.7908 (m-10) REVERT: F 406 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8635 (mm-30) REVERT: F 425 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8366 (mp) REVERT: F 495 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6676 (t80) outliers start: 21 outliers final: 19 residues processed: 88 average time/residue: 0.1022 time to fit residues: 12.0591 Evaluate side-chains 92 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 480 CYS Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3426 Z= 0.250 Angle : 0.735 10.964 4654 Z= 0.365 Chirality : 0.046 0.192 495 Planarity : 0.004 0.032 603 Dihedral : 6.318 27.795 520 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.69 % Favored : 88.07 % Rotamer: Outliers : 6.16 % Allowed : 25.49 % Favored : 68.35 % 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: -3.13 (0.38), residues: 419 helix: -5.82 (0.26), residues: 5 sheet: -0.97 (0.46), residues: 123 loop : -2.71 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 436 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.002 PHE F 515 TYR 0.016 0.002 TYR L 93 ARG 0.004 0.000 ARG F 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 71 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: L 108 LEU cc_start: 0.8480 (tp) cc_final: 0.8137 (tt) REVERT: H 28 THR cc_start: 0.8367 (m) cc_final: 0.8027 (p) REVERT: H 38 ARG cc_start: 0.8250 (ptm-80) cc_final: 0.7468 (ptm160) REVERT: H 51 MET cc_start: 0.7549 (ttp) cc_final: 0.7286 (ttm) REVERT: F 365 TYR cc_start: 0.8269 (m-10) cc_final: 0.7924 (m-10) REVERT: F 406 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8649 (mm-30) REVERT: F 425 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8374 (mp) REVERT: F 495 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6290 (t80) outliers start: 22 outliers final: 20 residues processed: 86 average time/residue: 0.0982 time to fit residues: 11.4198 Evaluate side-chains 92 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 480 CYS Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 chunk 41 optimal weight: 0.6980 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.165717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.149510 restraints weight = 6567.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.154786 restraints weight = 4113.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155940 restraints weight = 2261.154| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3426 Z= 0.211 Angle : 0.703 8.191 4654 Z= 0.350 Chirality : 0.046 0.227 495 Planarity : 0.004 0.032 603 Dihedral : 6.074 25.487 520 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.98 % Favored : 88.78 % Rotamer: Outliers : 5.32 % Allowed : 26.89 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.38), residues: 419 helix: -5.82 (0.26), residues: 5 sheet: -0.99 (0.44), residues: 134 loop : -2.58 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 436 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.002 PHE H 27 TYR 0.020 0.001 TYR L 93 ARG 0.004 0.000 ARG F 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1553.61 seconds wall clock time: 28 minutes 42.90 seconds (1722.90 seconds total)