Starting phenix.real_space_refine on Fri Dec 27 07:50:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsc_32753/12_2024/7wsc_32753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsc_32753/12_2024/7wsc_32753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsc_32753/12_2024/7wsc_32753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsc_32753/12_2024/7wsc_32753.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsc_32753/12_2024/7wsc_32753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsc_32753/12_2024/7wsc_32753.cif" } resolution = 3.78 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= 0.019 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 2156 2.51 5 N 563 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3369 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "H" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1024 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 813 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} 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: 4.07, per 1000 atoms: 1.21 Number of scatterers: 3369 At special positions: 0 Unit cell: (63.13, 87.74, 74.9, 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 635 8.00 N 563 7.00 C 2156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.02 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.01 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 422.0 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 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: 7 helices and 6 sheets defined 9.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'R' and resid 338 through 344 Processing helix chain 'R' and resid 364 through 369 removed outlier: 3.593A pdb=" N TYR R 369 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 388 removed outlier: 4.117A pdb=" N ASN R 388 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 407 No H-bonds generated for 'chain 'R' and resid 405 through 407' Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.870A pdb=" N ASP H 109 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR H 110 " --> pdb=" O VAL H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 110' Processing helix chain 'L' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.915A pdb=" N ASN R 354 " --> pdb=" O SER R 399 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER R 399 " --> pdb=" O ASN R 354 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS R 356 " --> pdb=" O ALA R 397 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA R 397 " --> pdb=" O LYS R 356 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL R 512 " --> pdb=" O ASP R 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.861A pdb=" N LEU H 37 " --> pdb=" O MET H 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 65 through 70 removed outlier: 6.433A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU H 69 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE H 53 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 112 " --> pdb=" O GLN H 58 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL H 144 " --> pdb=" O ALA H 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.736A pdb=" N THR L 24 " --> pdb=" O ARG L 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 69 through 70 removed outlier: 3.554A pdb=" N ILE L 109 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 183 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: 0.84 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 532 1.26 - 1.40: 979 1.40 - 1.54: 1912 1.54 - 1.68: 17 1.68 - 1.82: 18 Bond restraints: 3458 Sorted by residual: bond pdb=" CA TYR R 380 " pdb=" C TYR R 380 " ideal model delta sigma weight residual 1.524 1.395 0.129 1.35e-02 5.49e+03 9.08e+01 bond pdb=" C PHE R 377 " pdb=" O PHE R 377 " ideal model delta sigma weight residual 1.235 1.116 0.120 1.26e-02 6.30e+03 9.01e+01 bond pdb=" C VAL R 382 " pdb=" O VAL R 382 " ideal model delta sigma weight residual 1.236 1.153 0.083 1.03e-02 9.43e+03 6.47e+01 bond pdb=" CB TYR R 380 " pdb=" CG TYR R 380 " ideal model delta sigma weight residual 1.512 1.341 0.171 2.20e-02 2.07e+03 6.07e+01 bond pdb=" CA ALA R 475 " pdb=" C ALA R 475 " ideal model delta sigma weight residual 1.523 1.436 0.088 1.25e-02 6.40e+03 4.91e+01 ... (remaining 3453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.03: 4634 6.03 - 12.06: 48 12.06 - 18.09: 10 18.09 - 24.12: 1 24.12 - 30.15: 2 Bond angle restraints: 4695 Sorted by residual: angle pdb=" N GLY R 482 " pdb=" CA GLY R 482 " pdb=" C GLY R 482 " ideal model delta sigma weight residual 113.18 85.51 27.67 2.37e+00 1.78e-01 1.36e+02 angle pdb=" C PHE R 490 " pdb=" N PRO R 491 " pdb=" CA PRO R 491 " ideal model delta sigma weight residual 119.84 132.96 -13.12 1.25e+00 6.40e-01 1.10e+02 angle pdb=" N PHE R 486 " pdb=" CA PHE R 486 " pdb=" C PHE R 486 " ideal model delta sigma weight residual 111.04 95.20 15.84 1.55e+00 4.16e-01 1.04e+02 angle pdb=" N ALA R 475 " pdb=" CA ALA R 475 " pdb=" C ALA R 475 " ideal model delta sigma weight residual 107.98 89.55 18.43 1.88e+00 2.83e-01 9.61e+01 angle pdb=" CA PRO L 37 " pdb=" N PRO L 37 " pdb=" CD PRO L 37 " ideal model delta sigma weight residual 112.00 98.55 13.45 1.40e+00 5.10e-01 9.23e+01 ... (remaining 4690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 1778 15.87 - 31.73: 183 31.73 - 47.60: 60 47.60 - 63.46: 15 63.46 - 79.32: 8 Dihedral angle restraints: 2044 sinusoidal: 827 harmonic: 1217 Sorted by residual: dihedral pdb=" CB CYS R 391 " pdb=" SG CYS R 391 " pdb=" SG CYS R 525 " pdb=" CB CYS R 525 " ideal model delta sinusoidal sigma weight residual -86.00 -6.68 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" N CYS R 488 " pdb=" C CYS R 488 " pdb=" CA CYS R 488 " pdb=" CB CYS R 488 " ideal model delta harmonic sigma weight residual 122.80 106.51 16.29 0 2.50e+00 1.60e-01 4.25e+01 dihedral pdb=" CA ARG H 71 " pdb=" C ARG H 71 " pdb=" N TYR H 72 " pdb=" CA TYR H 72 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 2041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 476 0.158 - 0.317: 11 0.317 - 0.475: 6 0.475 - 0.633: 4 0.633 - 0.791: 2 Chirality restraints: 499 Sorted by residual: chirality pdb=" CA CYS R 379 " pdb=" N CYS R 379 " pdb=" C CYS R 379 " pdb=" CB CYS R 379 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA ASN R 477 " pdb=" N ASN R 477 " pdb=" C ASN R 477 " pdb=" CB ASN R 477 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CB VAL R 483 " pdb=" CA VAL R 483 " pdb=" CG1 VAL R 483 " pdb=" CG2 VAL R 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.06 -0.57 2.00e-01 2.50e+01 8.19e+00 ... (remaining 496 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 490 " -0.119 5.00e-02 4.00e+02 1.69e-01 4.60e+01 pdb=" N PRO R 491 " 0.291 5.00e-02 4.00e+02 pdb=" CA PRO R 491 " -0.111 5.00e-02 4.00e+02 pdb=" CD PRO R 491 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 368 " -0.032 2.00e-02 2.50e+03 6.42e-02 4.12e+01 pdb=" C LEU R 368 " 0.111 2.00e-02 2.50e+03 pdb=" O LEU R 368 " -0.042 2.00e-02 2.50e+03 pdb=" N TYR R 369 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 477 " 0.032 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C ASN R 477 " -0.110 2.00e-02 2.50e+03 pdb=" O ASN R 477 " 0.043 2.00e-02 2.50e+03 pdb=" N LYS R 478 " 0.035 2.00e-02 2.50e+03 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 9 2.26 - 2.92: 1670 2.92 - 3.58: 4936 3.58 - 4.24: 7946 4.24 - 4.90: 13267 Nonbonded interactions: 27828 Sorted by model distance: nonbonded pdb=" O TYR R 473 " pdb=" O CYS R 488 " model vdw 1.600 3.040 nonbonded pdb=" OG1 THR L 33 " pdb=" OE2 GLU L 36 " model vdw 2.071 3.040 nonbonded pdb=" O ASN R 477 " pdb=" ND2 ASN R 477 " model vdw 2.084 3.120 nonbonded pdb=" OG SER H 36 " pdb=" O MET H 102 " model vdw 2.088 3.040 nonbonded pdb=" OD1 ASP H 73 " pdb=" OG SER H 75 " model vdw 2.118 3.040 ... (remaining 27823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.140 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.013 0.171 3458 Z= 0.821 Angle : 1.667 30.153 4695 Z= 0.880 Chirality : 0.101 0.791 499 Planarity : 0.012 0.169 604 Dihedral : 15.341 79.299 1263 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 41.09 Ramachandran Plot: Outliers : 3.62 % Allowed : 14.73 % Favored : 81.64 % Rotamer: Outliers : 4.99 % Allowed : 1.94 % Favored : 93.07 % Cbeta Deviations : 1.31 % Peptide Plane: Cis-proline : 10.00 % 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: -4.09 (0.39), residues: 414 helix: -5.03 (0.30), residues: 12 sheet: -2.57 (0.41), residues: 129 loop : -2.82 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 59 HIS 0.015 0.005 HIS H 54 PHE 0.056 0.004 PHE R 490 TYR 0.023 0.002 TYR H 51 ARG 0.039 0.002 ARG R 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.401 Fit side-chains REVERT: R 377 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: R 423 TYR cc_start: 0.7992 (t80) cc_final: 0.7695 (t80) REVERT: R 455 LEU cc_start: 0.7505 (pt) cc_final: 0.7293 (pt) REVERT: R 486 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6242 (t80) REVERT: L 32 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7557 (p) REVERT: L 50 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7213 (tm-30) REVERT: L 111 TYR cc_start: 0.8367 (m-80) cc_final: 0.7826 (m-80) outliers start: 18 outliers final: 9 residues processed: 131 average time/residue: 0.1700 time to fit residues: 27.1370 Evaluate side-chains 103 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 474 GLN Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 486 PHE Chi-restraints excluded: chain R residue 487 ASN Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain L residue 32 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 474 GLN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 3458 Z= 0.423 Angle : 0.991 13.883 4695 Z= 0.492 Chirality : 0.056 0.373 499 Planarity : 0.010 0.149 604 Dihedral : 10.162 86.175 542 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.72 % Allowed : 12.80 % Favored : 86.47 % Rotamer: Outliers : 6.37 % Allowed : 14.40 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.66 (0.39), residues: 414 helix: -3.30 (1.06), residues: 12 sheet: -2.49 (0.40), residues: 128 loop : -2.46 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 59 HIS 0.009 0.003 HIS H 54 PHE 0.025 0.003 PHE R 486 TYR 0.023 0.002 TYR H 51 ARG 0.009 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 374 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6032 (p90) REVERT: R 377 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: R 423 TYR cc_start: 0.8143 (t80) cc_final: 0.7881 (t80) REVERT: R 472 ILE cc_start: 0.3950 (OUTLIER) cc_final: 0.3725 (mm) REVERT: L 26 SER cc_start: 0.6925 (OUTLIER) cc_final: 0.6653 (p) REVERT: L 28 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7268 (tt) REVERT: L 50 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7263 (tm-30) REVERT: L 111 TYR cc_start: 0.8465 (m-80) cc_final: 0.7750 (m-80) outliers start: 23 outliers final: 14 residues processed: 116 average time/residue: 0.1501 time to fit residues: 21.3615 Evaluate side-chains 116 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 358 ILE Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 480 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 488 CYS Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 493 ARG Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 3458 Z= 0.317 Angle : 0.862 13.871 4695 Z= 0.432 Chirality : 0.051 0.187 499 Planarity : 0.008 0.139 604 Dihedral : 8.398 58.606 534 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.87 % Favored : 88.41 % Rotamer: Outliers : 6.65 % Allowed : 17.45 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.40), residues: 414 helix: -3.35 (0.99), residues: 12 sheet: -2.48 (0.41), residues: 130 loop : -2.08 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 59 HIS 0.005 0.002 HIS H 54 PHE 0.016 0.002 PHE H 48 TYR 0.019 0.002 TYR H 51 ARG 0.007 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: R 423 TYR cc_start: 0.8089 (t80) cc_final: 0.7817 (t80) REVERT: R 452 LEU cc_start: 0.8183 (mt) cc_final: 0.7971 (mt) REVERT: H 72 TYR cc_start: 0.7072 (p90) cc_final: 0.6558 (p90) REVERT: L 28 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7237 (tt) REVERT: L 50 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7362 (tm-30) REVERT: L 52 ASN cc_start: 0.8520 (p0) cc_final: 0.8109 (p0) REVERT: L 62 GLN cc_start: 0.8816 (pt0) cc_final: 0.8556 (pt0) REVERT: L 74 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8449 (tt) REVERT: L 111 TYR cc_start: 0.8253 (m-80) cc_final: 0.7701 (m-80) outliers start: 24 outliers final: 14 residues processed: 124 average time/residue: 0.1415 time to fit residues: 21.4979 Evaluate side-chains 117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 GLN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 3458 Z= 0.288 Angle : 0.812 13.640 4695 Z= 0.404 Chirality : 0.048 0.164 499 Planarity : 0.007 0.133 604 Dihedral : 7.763 54.865 527 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.11 % Favored : 88.41 % Rotamer: Outliers : 6.93 % Allowed : 20.50 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.18 (0.41), residues: 414 helix: -3.30 (1.00), residues: 12 sheet: -2.50 (0.41), residues: 133 loop : -1.88 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 59 HIS 0.003 0.001 HIS H 54 PHE 0.012 0.002 PHE R 375 TYR 0.012 0.001 TYR H 51 ARG 0.006 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: R 423 TYR cc_start: 0.8096 (t80) cc_final: 0.7811 (t80) REVERT: L 28 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7564 (tt) REVERT: L 62 GLN cc_start: 0.8692 (pt0) cc_final: 0.8029 (pt0) REVERT: L 74 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8378 (tt) REVERT: L 111 TYR cc_start: 0.8277 (m-80) cc_final: 0.7705 (m-80) outliers start: 25 outliers final: 17 residues processed: 116 average time/residue: 0.1433 time to fit residues: 20.6990 Evaluate side-chains 120 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 3458 Z= 0.308 Angle : 0.822 13.331 4695 Z= 0.407 Chirality : 0.048 0.161 499 Planarity : 0.007 0.128 604 Dihedral : 7.286 50.723 525 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.63 % Favored : 88.89 % Rotamer: Outliers : 7.48 % Allowed : 21.05 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.03 (0.41), residues: 414 helix: -3.24 (0.99), residues: 12 sheet: -2.45 (0.42), residues: 135 loop : -1.73 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 59 HIS 0.002 0.001 HIS H 54 PHE 0.014 0.002 PHE H 133 TYR 0.021 0.002 TYR L 56 ARG 0.006 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8108 (t80) cc_final: 0.7817 (t80) REVERT: R 489 TYR cc_start: 0.5750 (OUTLIER) cc_final: 0.5492 (t80) REVERT: H 123 TYR cc_start: 0.8636 (p90) cc_final: 0.8337 (p90) REVERT: L 50 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7644 (tm-30) REVERT: L 62 GLN cc_start: 0.8650 (pt0) cc_final: 0.8032 (pt0) REVERT: L 74 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8453 (tt) REVERT: L 111 TYR cc_start: 0.8200 (m-80) cc_final: 0.7745 (m-80) outliers start: 27 outliers final: 23 residues processed: 113 average time/residue: 0.1661 time to fit residues: 22.9603 Evaluate side-chains 121 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 3458 Z= 0.282 Angle : 0.810 13.578 4695 Z= 0.397 Chirality : 0.047 0.153 499 Planarity : 0.007 0.124 604 Dihedral : 6.808 48.623 523 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.63 % Favored : 88.89 % Rotamer: Outliers : 6.65 % Allowed : 23.82 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.03 (0.41), residues: 414 helix: -3.65 (0.72), residues: 18 sheet: -2.39 (0.43), residues: 132 loop : -1.70 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 PHE 0.011 0.002 PHE H 87 TYR 0.018 0.001 TYR L 73 ARG 0.007 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 423 TYR cc_start: 0.8100 (t80) cc_final: 0.7793 (t80) REVERT: R 489 TYR cc_start: 0.5785 (OUTLIER) cc_final: 0.5456 (t80) REVERT: H 123 TYR cc_start: 0.8582 (p90) cc_final: 0.8319 (p90) REVERT: L 50 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7632 (tm-30) REVERT: L 62 GLN cc_start: 0.8627 (pt0) cc_final: 0.8077 (pt0) REVERT: L 74 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8450 (tt) REVERT: L 111 TYR cc_start: 0.8263 (m-80) cc_final: 0.7829 (m-80) outliers start: 24 outliers final: 18 residues processed: 114 average time/residue: 0.1579 time to fit residues: 22.2284 Evaluate side-chains 114 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain R residue 524 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 450 ASN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 3458 Z= 0.249 Angle : 0.798 13.646 4695 Z= 0.390 Chirality : 0.047 0.149 499 Planarity : 0.007 0.120 604 Dihedral : 6.563 47.247 523 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.66 % Favored : 89.86 % Rotamer: Outliers : 6.37 % Allowed : 25.21 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.88 (0.41), residues: 414 helix: -3.50 (0.78), residues: 18 sheet: -2.28 (0.43), residues: 133 loop : -1.59 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 59 HIS 0.001 0.001 HIS H 54 PHE 0.012 0.002 PHE H 87 TYR 0.020 0.001 TYR L 73 ARG 0.006 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: R 423 TYR cc_start: 0.8080 (t80) cc_final: 0.7802 (t80) REVERT: R 434 ILE cc_start: 0.8974 (mt) cc_final: 0.8561 (tt) REVERT: R 452 LEU cc_start: 0.8156 (mp) cc_final: 0.7875 (mt) REVERT: R 489 TYR cc_start: 0.6096 (OUTLIER) cc_final: 0.5763 (t80) REVERT: L 50 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7681 (tm-30) REVERT: L 62 GLN cc_start: 0.8560 (pt0) cc_final: 0.8154 (pt0) REVERT: L 74 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8427 (tt) REVERT: L 111 TYR cc_start: 0.8315 (m-80) cc_final: 0.7851 (m-80) outliers start: 23 outliers final: 16 residues processed: 111 average time/residue: 0.1579 time to fit residues: 21.3500 Evaluate side-chains 110 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 36 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 11 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 3458 Z= 0.250 Angle : 0.793 13.708 4695 Z= 0.390 Chirality : 0.046 0.146 499 Planarity : 0.007 0.118 604 Dihedral : 6.458 47.051 523 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.63 % Favored : 88.89 % Rotamer: Outliers : 6.09 % Allowed : 25.76 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.76 (0.42), residues: 414 helix: -3.50 (0.76), residues: 18 sheet: -2.11 (0.44), residues: 133 loop : -1.56 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 59 HIS 0.000 0.000 HIS H 54 PHE 0.013 0.002 PHE L 122 TYR 0.020 0.001 TYR L 73 ARG 0.007 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: R 423 TYR cc_start: 0.8111 (t80) cc_final: 0.7834 (t80) REVERT: R 434 ILE cc_start: 0.8951 (mt) cc_final: 0.8598 (tt) REVERT: R 452 LEU cc_start: 0.8147 (mp) cc_final: 0.7880 (mt) REVERT: R 489 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.5896 (t80) REVERT: H 72 TYR cc_start: 0.7107 (p90) cc_final: 0.6632 (p90) REVERT: L 50 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7724 (tm-30) REVERT: L 62 GLN cc_start: 0.8567 (pt0) cc_final: 0.8218 (pt0) REVERT: L 74 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8484 (tt) REVERT: L 111 TYR cc_start: 0.8292 (m-80) cc_final: 0.7888 (m-80) outliers start: 22 outliers final: 18 residues processed: 111 average time/residue: 0.1415 time to fit residues: 19.3503 Evaluate side-chains 117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 487 ASN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3458 Z= 0.276 Angle : 0.801 13.698 4695 Z= 0.396 Chirality : 0.046 0.147 499 Planarity : 0.006 0.116 604 Dihedral : 6.518 47.147 523 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.87 % Favored : 88.65 % Rotamer: Outliers : 6.65 % Allowed : 25.21 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.72 (0.42), residues: 414 helix: -3.54 (0.75), residues: 18 sheet: -1.99 (0.45), residues: 131 loop : -1.59 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 PHE 0.014 0.002 PHE L 122 TYR 0.020 0.001 TYR L 73 ARG 0.007 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 434 ILE cc_start: 0.8966 (mt) cc_final: 0.8627 (tt) REVERT: R 489 TYR cc_start: 0.6265 (OUTLIER) cc_final: 0.5996 (t80) REVERT: H 72 TYR cc_start: 0.7070 (p90) cc_final: 0.6595 (p90) REVERT: L 50 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7687 (tm-30) REVERT: L 62 GLN cc_start: 0.8582 (pt0) cc_final: 0.8184 (pt0) REVERT: L 74 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8550 (tt) REVERT: L 111 TYR cc_start: 0.8278 (m-80) cc_final: 0.7857 (m-80) outliers start: 24 outliers final: 22 residues processed: 102 average time/residue: 0.1625 time to fit residues: 20.2000 Evaluate side-chains 111 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 487 ASN Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 29 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.0050 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 487 ASN L 25 GLN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 3458 Z= 0.234 Angle : 0.800 13.631 4695 Z= 0.394 Chirality : 0.046 0.171 499 Planarity : 0.006 0.114 604 Dihedral : 6.379 46.606 523 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.63 % Favored : 88.89 % Rotamer: Outliers : 6.37 % Allowed : 25.76 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.66 (0.42), residues: 414 helix: -3.42 (0.80), residues: 18 sheet: -1.88 (0.44), residues: 138 loop : -1.58 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 PHE 0.012 0.002 PHE L 122 TYR 0.020 0.001 TYR L 73 ARG 0.007 0.001 ARG H 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 377 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: R 423 TYR cc_start: 0.7821 (t80) cc_final: 0.7352 (t80) REVERT: R 434 ILE cc_start: 0.8921 (mt) cc_final: 0.8563 (tt) REVERT: R 489 TYR cc_start: 0.6120 (OUTLIER) cc_final: 0.5846 (t80) REVERT: H 72 TYR cc_start: 0.7044 (p90) cc_final: 0.6555 (p90) REVERT: L 50 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7658 (tm-30) REVERT: L 62 GLN cc_start: 0.8605 (pt0) cc_final: 0.8220 (pt0) REVERT: L 74 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8463 (tt) REVERT: L 111 TYR cc_start: 0.8222 (m-80) cc_final: 0.7832 (m-80) outliers start: 23 outliers final: 18 residues processed: 105 average time/residue: 0.1613 time to fit residues: 20.5573 Evaluate side-chains 111 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain R residue 395 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 478 LYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 487 ASN Chi-restraints excluded: chain R residue 489 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 126 TYR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0570 chunk 36 optimal weight: 0.0070 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.0030 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.2526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 487 ASN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.148844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125619 restraints weight = 5704.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129813 restraints weight = 3335.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132661 restraints weight = 2273.383| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 3458 Z= 0.218 Angle : 0.785 13.494 4695 Z= 0.387 Chirality : 0.045 0.146 499 Planarity : 0.006 0.112 604 Dihedral : 6.290 46.186 523 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.18 % Favored : 90.34 % Rotamer: Outliers : 6.37 % Allowed : 25.48 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.53 (0.42), residues: 414 helix: -3.35 (0.83), residues: 18 sheet: -1.72 (0.46), residues: 133 loop : -1.54 (0.41), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP L 59 HIS 0.001 0.000 HIS H 54 PHE 0.030 0.002 PHE H 133 TYR 0.020 0.002 TYR L 73 ARG 0.007 0.001 ARG H 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1443.37 seconds wall clock time: 27 minutes 20.93 seconds (1640.93 seconds total)