Starting phenix.real_space_refine on Fri Dec 27 06:19:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gsb_34228/12_2024/8gsb_34228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gsb_34228/12_2024/8gsb_34228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gsb_34228/12_2024/8gsb_34228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gsb_34228/12_2024/8gsb_34228.map" model { file = "/net/cci-nas-00/data/ceres_data/8gsb_34228/12_2024/8gsb_34228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gsb_34228/12_2024/8gsb_34228.cif" } resolution = 3.99 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= -0.002 sd= 0.038 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 16 5.16 5 C 2001 2.51 5 N 544 2.21 5 O 596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 3157 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1404 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain breaks: 1 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "K" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 3.61, per 1000 atoms: 1.14 Number of scatterers: 3157 At special positions: 0 Unit cell: (78.306, 60.624, 95.988, 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 16 16.00 O 596 8.00 N 544 7.00 C 2001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " 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 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 348.2 milliseconds 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 4.2% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.238A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 379 removed outlier: 3.751A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 379 removed outlier: 3.751A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.632A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.743A pdb=" N THR H 120 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.743A pdb=" N THR H 120 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.527A pdb=" N THR K 66 " --> pdb=" O THR K 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AA9, first strand: chain 'K' and resid 54 through 55 removed outlier: 6.456A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 204 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: 0.87 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: 1010 1.34 - 1.46: 819 1.46 - 1.58: 1389 1.58 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3237 Sorted by residual: bond pdb=" C PRO K 81 " pdb=" N GLU K 82 " ideal model delta sigma weight residual 1.334 1.280 0.054 1.38e-02 5.25e+03 1.54e+01 bond pdb=" C LEU K 74 " pdb=" N THR K 75 " ideal model delta sigma weight residual 1.331 1.388 -0.057 1.55e-02 4.16e+03 1.33e+01 bond pdb=" C GLN K 90 " pdb=" N GLN K 91 " ideal model delta sigma weight residual 1.330 1.378 -0.048 1.39e-02 5.18e+03 1.19e+01 bond pdb=" C ALA A 419 " pdb=" N ASP A 420 " ideal model delta sigma weight residual 1.333 1.290 0.043 1.51e-02 4.39e+03 8.15e+00 bond pdb=" C GLU H 46 " pdb=" N TRP H 47 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.31e-02 5.83e+03 7.24e+00 ... (remaining 3232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 4246 1.78 - 3.57: 125 3.57 - 5.35: 17 5.35 - 7.14: 2 7.14 - 8.92: 4 Bond angle restraints: 4394 Sorted by residual: angle pdb=" N GLN K 91 " pdb=" CA GLN K 91 " pdb=" C GLN K 91 " ideal model delta sigma weight residual 109.24 100.32 8.92 1.63e+00 3.76e-01 3.00e+01 angle pdb=" N VAL A 341 " pdb=" CA VAL A 341 " pdb=" C VAL A 341 " ideal model delta sigma weight residual 109.34 117.51 -8.17 2.08e+00 2.31e-01 1.54e+01 angle pdb=" N GLY A 476 " pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 113.18 104.87 8.31 2.37e+00 1.78e-01 1.23e+01 angle pdb=" N PHE A 400 " pdb=" CA PHE A 400 " pdb=" C PHE A 400 " ideal model delta sigma weight residual 108.99 114.35 -5.36 1.57e+00 4.06e-01 1.17e+01 angle pdb=" N GLN A 474 " pdb=" CA GLN A 474 " pdb=" C GLN A 474 " ideal model delta sigma weight residual 110.80 118.07 -7.27 2.13e+00 2.20e-01 1.16e+01 ... (remaining 4389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 1655 14.28 - 28.56: 186 28.56 - 42.85: 46 42.85 - 57.13: 16 57.13 - 71.41: 4 Dihedral angle restraints: 1907 sinusoidal: 752 harmonic: 1155 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 154.88 -61.88 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CA ALA A 475 " pdb=" C ALA A 475 " pdb=" N GLY A 476 " pdb=" CA GLY A 476 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CB CYS H 101 " pdb=" SG CYS H 101 " pdb=" SG CYS H 106 " pdb=" CB CYS H 106 " ideal model delta sinusoidal sigma weight residual 93.00 133.22 -40.22 1 1.00e+01 1.00e-02 2.27e+01 ... (remaining 1904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 385 0.052 - 0.104: 61 0.104 - 0.156: 20 0.156 - 0.207: 0 0.207 - 0.259: 1 Chirality restraints: 467 Sorted by residual: chirality pdb=" CA GLN A 474 " pdb=" N GLN A 474 " pdb=" C GLN A 474 " pdb=" CB GLN A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL A 511 " pdb=" N VAL A 511 " pdb=" C VAL A 511 " pdb=" CB VAL A 511 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL H 119 " pdb=" N VAL H 119 " pdb=" C VAL H 119 " pdb=" CB VAL H 119 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 464 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 44 " -0.181 9.50e-02 1.11e+02 8.12e-02 4.43e+00 pdb=" NE ARG H 44 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG H 44 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG H 44 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 44 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER K 7 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO K 8 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 8 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 8 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 492 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C LEU A 492 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU A 492 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 493 " 0.011 2.00e-02 2.50e+03 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1168 2.85 - 3.36: 2819 3.36 - 3.88: 4750 3.88 - 4.39: 5283 4.39 - 4.90: 9213 Nonbonded interactions: 23233 Sorted by model distance: nonbonded pdb=" O GLY H 26 " pdb=" OG1 THR H 30 " model vdw 2.338 3.040 nonbonded pdb=" O GLN A 474 " pdb=" O ASN A 487 " model vdw 2.372 3.040 nonbonded pdb=" O SER A 514 " pdb=" OG SER A 514 " model vdw 2.395 3.040 nonbonded pdb=" O ASP K 61 " pdb=" OD1 ASP K 61 " model vdw 2.406 3.040 nonbonded pdb=" O ASP A 339 " pdb=" OD1 ASP A 339 " model vdw 2.414 3.040 ... (remaining 23228 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.260 Find NCS groups from input model: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.004 0.057 3237 Z= 0.253 Angle : 0.728 8.922 4394 Z= 0.429 Chirality : 0.045 0.259 467 Planarity : 0.005 0.081 569 Dihedral : 13.337 71.409 1158 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.42 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.42), residues: 392 helix: -3.19 (1.17), residues: 8 sheet: -0.89 (0.49), residues: 119 loop : -1.36 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 97 HIS 0.001 0.001 HIS A 505 PHE 0.011 0.001 PHE A 486 TYR 0.027 0.002 TYR K 92 ARG 0.011 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.359 Fit side-chains REVERT: A 474 GLN cc_start: 0.7006 (tp-100) cc_final: 0.6603 (tp-100) REVERT: H 47 TRP cc_start: 0.8813 (t60) cc_final: 0.8193 (t60) REVERT: K 8 PRO cc_start: 0.8518 (Cg_exo) cc_final: 0.8288 (Cg_endo) REVERT: K 33 TYR cc_start: 0.7996 (m-10) cc_final: 0.7765 (m-10) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2365 time to fit residues: 20.7868 Evaluate side-chains 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.004 0.026 3237 Z= 0.237 Angle : 0.627 8.960 4394 Z= 0.334 Chirality : 0.044 0.140 467 Planarity : 0.005 0.042 569 Dihedral : 5.010 24.432 447 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.75 % Allowed : 9.04 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.42), residues: 392 helix: -4.14 (0.86), residues: 14 sheet: -0.73 (0.48), residues: 126 loop : -0.98 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 97 HIS 0.001 0.000 HIS A 505 PHE 0.011 0.002 PHE A 392 TYR 0.026 0.002 TYR K 92 ARG 0.004 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.8337 (m-30) cc_final: 0.8043 (t0) REVERT: H 47 TRP cc_start: 0.8704 (t60) cc_final: 0.8159 (t60) REVERT: H 57 ASN cc_start: 0.8322 (t0) cc_final: 0.7837 (t0) REVERT: K 106 GLU cc_start: 0.6709 (pm20) cc_final: 0.6506 (pm20) outliers start: 6 outliers final: 1 residues processed: 79 average time/residue: 0.2251 time to fit residues: 20.4954 Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3237 Z= 0.306 Angle : 0.632 8.211 4394 Z= 0.340 Chirality : 0.045 0.143 467 Planarity : 0.005 0.037 569 Dihedral : 5.201 25.500 447 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.62 % Allowed : 11.95 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.41), residues: 392 helix: -4.14 (0.85), residues: 14 sheet: -0.84 (0.45), residues: 129 loop : -1.16 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.002 0.001 HIS A 505 PHE 0.012 0.002 PHE A 400 TYR 0.032 0.002 TYR K 92 ARG 0.005 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8430 (m-30) cc_final: 0.8075 (m-30) REVERT: A 442 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8143 (t0) REVERT: H 47 TRP cc_start: 0.8850 (t60) cc_final: 0.8357 (t60) REVERT: H 57 ASN cc_start: 0.8428 (t0) cc_final: 0.8029 (t0) REVERT: K 43 GLN cc_start: 0.8780 (mp10) cc_final: 0.8559 (mp10) outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.2092 time to fit residues: 16.7945 Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3237 Z= 0.323 Angle : 0.652 8.701 4394 Z= 0.345 Chirality : 0.045 0.144 467 Planarity : 0.004 0.038 569 Dihedral : 5.255 23.829 447 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.08 % Allowed : 13.70 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.41), residues: 392 helix: -4.26 (0.82), residues: 15 sheet: -0.94 (0.45), residues: 129 loop : -1.18 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.001 0.001 HIS H 100 PHE 0.016 0.002 PHE A 400 TYR 0.027 0.002 TYR K 92 ARG 0.006 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8454 (m-30) cc_final: 0.8018 (m-30) REVERT: A 442 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8149 (t0) REVERT: A 474 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7311 (tm-30) REVERT: H 47 TRP cc_start: 0.8978 (t60) cc_final: 0.8511 (t60) REVERT: H 57 ASN cc_start: 0.8411 (t0) cc_final: 0.8095 (t0) REVERT: K 43 GLN cc_start: 0.8857 (mp10) cc_final: 0.8623 (mp10) REVERT: K 80 GLU cc_start: 0.8307 (mp0) cc_final: 0.8103 (mp0) outliers start: 14 outliers final: 9 residues processed: 74 average time/residue: 0.1974 time to fit residues: 17.1495 Evaluate side-chains 72 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN K 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3237 Z= 0.204 Angle : 0.605 8.550 4394 Z= 0.314 Chirality : 0.044 0.132 467 Planarity : 0.004 0.037 569 Dihedral : 4.916 24.337 447 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.08 % Allowed : 14.29 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.41), residues: 392 helix: -4.22 (0.86), residues: 15 sheet: -0.87 (0.46), residues: 129 loop : -1.13 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.000 HIS A 505 PHE 0.008 0.001 PHE A 400 TYR 0.020 0.002 TYR K 92 ARG 0.006 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8386 (m-30) cc_final: 0.7948 (m-30) REVERT: A 442 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8215 (t0) REVERT: A 474 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7320 (tm-30) REVERT: H 10 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: H 47 TRP cc_start: 0.8885 (t60) cc_final: 0.8394 (t60) REVERT: H 57 ASN cc_start: 0.8322 (t0) cc_final: 0.7996 (t0) REVERT: K 39 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7994 (tt0) outliers start: 14 outliers final: 10 residues processed: 78 average time/residue: 0.2010 time to fit residues: 18.4477 Evaluate side-chains 74 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3237 Z= 0.215 Angle : 0.613 8.094 4394 Z= 0.320 Chirality : 0.044 0.134 467 Planarity : 0.004 0.038 569 Dihedral : 4.838 23.974 447 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.50 % Allowed : 16.62 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.41), residues: 392 helix: -4.31 (0.78), residues: 15 sheet: -0.83 (0.46), residues: 129 loop : -1.14 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 36 HIS 0.001 0.000 HIS A 505 PHE 0.010 0.001 PHE A 400 TYR 0.020 0.001 TYR K 92 ARG 0.007 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8403 (m-30) cc_final: 0.7945 (m-30) REVERT: A 442 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8197 (t0) REVERT: A 474 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7281 (tm-30) REVERT: H 10 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: H 47 TRP cc_start: 0.8905 (t60) cc_final: 0.8398 (t60) REVERT: H 57 ASN cc_start: 0.8289 (t0) cc_final: 0.8011 (t0) outliers start: 12 outliers final: 10 residues processed: 77 average time/residue: 0.2143 time to fit residues: 19.0845 Evaluate side-chains 75 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3237 Z= 0.215 Angle : 0.611 8.029 4394 Z= 0.321 Chirality : 0.043 0.135 467 Planarity : 0.004 0.039 569 Dihedral : 4.854 24.100 447 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.66 % Allowed : 15.16 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.41), residues: 392 helix: -4.36 (0.73), residues: 15 sheet: -0.74 (0.46), residues: 129 loop : -1.13 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 36 HIS 0.001 0.001 HIS A 505 PHE 0.011 0.001 PHE A 400 TYR 0.018 0.001 TYR K 92 ARG 0.006 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8406 (m-30) cc_final: 0.7931 (m-30) REVERT: A 442 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8201 (t0) REVERT: A 474 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7363 (tm-30) REVERT: H 10 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: K 39 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: K 61 ASP cc_start: 0.7457 (t0) cc_final: 0.7190 (t0) outliers start: 16 outliers final: 10 residues processed: 76 average time/residue: 0.2214 time to fit residues: 19.4717 Evaluate side-chains 74 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.0010 chunk 31 optimal weight: 6.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3237 Z= 0.170 Angle : 0.610 7.935 4394 Z= 0.319 Chirality : 0.043 0.129 467 Planarity : 0.004 0.039 569 Dihedral : 4.583 23.109 447 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.92 % Allowed : 16.33 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.42), residues: 392 helix: -4.34 (0.76), residues: 15 sheet: -0.51 (0.46), residues: 129 loop : -1.07 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.001 0.000 HIS A 505 PHE 0.007 0.001 PHE A 392 TYR 0.015 0.001 TYR K 92 ARG 0.007 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8377 (m-30) cc_final: 0.7937 (m-30) REVERT: A 442 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8205 (t0) REVERT: A 474 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7198 (tm-30) REVERT: H 10 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: K 61 ASP cc_start: 0.7449 (t0) cc_final: 0.7134 (t0) REVERT: K 92 TYR cc_start: 0.8929 (p90) cc_final: 0.8668 (p90) outliers start: 10 outliers final: 7 residues processed: 70 average time/residue: 0.2000 time to fit residues: 16.3348 Evaluate side-chains 75 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.0060 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3237 Z= 0.197 Angle : 0.638 9.137 4394 Z= 0.333 Chirality : 0.043 0.131 467 Planarity : 0.004 0.036 569 Dihedral : 4.609 23.352 447 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.21 % Allowed : 15.74 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.42), residues: 392 helix: -4.36 (0.73), residues: 15 sheet: -0.32 (0.48), residues: 129 loop : -1.02 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 36 HIS 0.001 0.000 HIS A 505 PHE 0.010 0.001 PHE A 400 TYR 0.015 0.001 TYR K 92 ARG 0.007 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8368 (m-30) cc_final: 0.7915 (m-30) REVERT: A 442 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8184 (t0) REVERT: A 474 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7381 (tm-30) REVERT: H 10 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: K 61 ASP cc_start: 0.7418 (t0) cc_final: 0.7149 (t0) outliers start: 11 outliers final: 9 residues processed: 74 average time/residue: 0.2159 time to fit residues: 18.6087 Evaluate side-chains 72 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3237 Z= 0.265 Angle : 0.675 8.981 4394 Z= 0.356 Chirality : 0.044 0.138 467 Planarity : 0.004 0.035 569 Dihedral : 4.954 23.968 447 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.79 % Allowed : 15.74 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.42), residues: 392 helix: -4.42 (0.67), residues: 15 sheet: -0.38 (0.48), residues: 129 loop : -1.10 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.001 0.001 HIS H 100 PHE 0.015 0.002 PHE A 400 TYR 0.019 0.002 TYR K 92 ARG 0.007 0.001 ARG H 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.7790 (m-10) cc_final: 0.7568 (m-10) REVERT: A 442 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8203 (t0) REVERT: A 474 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7474 (tm-30) REVERT: H 10 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: K 61 ASP cc_start: 0.7453 (t0) cc_final: 0.7148 (t0) outliers start: 13 outliers final: 9 residues processed: 72 average time/residue: 0.2358 time to fit residues: 19.4362 Evaluate side-chains 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.100147 restraints weight = 6499.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100188 restraints weight = 5470.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102076 restraints weight = 4747.207| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3237 Z= 0.248 Angle : 0.668 8.525 4394 Z= 0.352 Chirality : 0.044 0.134 467 Planarity : 0.004 0.042 569 Dihedral : 4.948 23.638 447 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.21 % Allowed : 17.49 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.42), residues: 392 helix: -4.34 (0.75), residues: 15 sheet: -0.39 (0.48), residues: 129 loop : -1.12 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 36 HIS 0.001 0.001 HIS A 505 PHE 0.013 0.001 PHE A 400 TYR 0.017 0.001 TYR K 92 ARG 0.007 0.001 ARG H 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1270.34 seconds wall clock time: 23 minutes 37.64 seconds (1417.64 seconds total)