Starting phenix.real_space_refine on Mon Feb 10 22:45:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gsb_34228/02_2025/8gsb_34228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gsb_34228/02_2025/8gsb_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_34228/02_2025/8gsb_34228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gsb_34228/02_2025/8gsb_34228.map" model { file = "/net/cci-nas-00/data/ceres_data/8gsb_34228/02_2025/8gsb_34228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gsb_34228/02_2025/8gsb_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-5592/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: 3.36, per 1000 atoms: 1.06 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: 0.76 Conformation dependent library (CDL) restraints added in 409.7 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: 0.44 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: 0.74 Time building geometry restraints manager: 0.92 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: 2.790 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.490 Find NCS groups from input model: 0.030 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.530 ------------------------------------------------------------------------------- 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 : 0.386 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: 0.2358 time to fit residues: 20.7828 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 : 0.351 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104050 restraints weight = 6558.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104822 restraints weight = 4907.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105773 restraints weight = 4691.563| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.371 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.8296 (m-30) cc_final: 0.8002 (t0) REVERT: H 47 TRP cc_start: 0.8808 (t60) cc_final: 0.8313 (t60) REVERT: H 57 ASN cc_start: 0.8323 (t0) cc_final: 0.7882 (t0) outliers start: 6 outliers final: 1 residues processed: 79 average time/residue: 0.2234 time to fit residues: 20.2097 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 : 0.345 ------------------------------------------------------------------------------- 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 1 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099793 restraints weight = 6602.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099609 restraints weight = 5692.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100924 restraints weight = 5824.003| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 3237 Z= 0.368 Angle : 0.668 8.732 4394 Z= 0.360 Chirality : 0.046 0.149 467 Planarity : 0.005 0.037 569 Dihedral : 5.454 24.963 447 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.21 % Allowed : 12.24 % Favored : 84.55 % 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: -4.18 (0.81), residues: 14 sheet: -0.92 (0.45), residues: 129 loop : -1.22 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 36 HIS 0.003 0.001 HIS A 505 PHE 0.016 0.002 PHE A 400 TYR 0.034 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 73 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8359 (m-30) cc_final: 0.8104 (m-30) REVERT: A 442 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8077 (t0) REVERT: H 47 TRP cc_start: 0.9011 (t60) cc_final: 0.8587 (t60) REVERT: H 57 ASN cc_start: 0.8472 (t0) cc_final: 0.8147 (t0) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.2111 time to fit residues: 17.2357 Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 418 ILE 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 73 THR 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 23 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.101832 restraints weight = 6599.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101442 restraints weight = 5350.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102390 restraints weight = 6387.691| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2829 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= 0.261 Angle : 0.623 8.547 4394 Z= 0.328 Chirality : 0.044 0.138 467 Planarity : 0.004 0.038 569 Dihedral : 5.079 24.107 447 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.37 % Allowed : 13.12 % Favored : 82.51 % 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: -1.82 (0.41), residues: 392 helix: -4.28 (0.80), residues: 15 sheet: -0.92 (0.45), residues: 129 loop : -1.16 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 36 HIS 0.001 0.001 HIS A 505 PHE 0.010 0.001 PHE A 392 TYR 0.025 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 77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8356 (m-30) cc_final: 0.8018 (m-30) REVERT: A 442 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8109 (t0) REVERT: A 474 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7410 (tm-30) REVERT: H 47 TRP cc_start: 0.9026 (t60) cc_final: 0.8607 (t60) REVERT: H 57 ASN cc_start: 0.8424 (t0) cc_final: 0.8096 (t0) outliers start: 15 outliers final: 9 residues processed: 71 average time/residue: 0.1962 time to fit residues: 16.4148 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 : 0.337 ------------------------------------------------------------------------------- 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 393 THR 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 86 LEU Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain K residue 48 LEU 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 2 optimal weight: 0.0770 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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** K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.122348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102451 restraints weight = 6554.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102581 restraints weight = 5329.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.103134 restraints weight = 5018.026| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3237 Z= 0.202 Angle : 0.601 8.353 4394 Z= 0.313 Chirality : 0.043 0.133 467 Planarity : 0.004 0.039 569 Dihedral : 4.821 23.778 447 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.08 % Allowed : 13.41 % Favored : 82.51 % 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: -4.21 (0.87), residues: 15 sheet: -0.77 (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 392 TYR 0.021 0.001 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 85 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8284 (m-30) cc_final: 0.7961 (m-30) REVERT: A 442 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8131 (t0) REVERT: A 474 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7384 (tm-30) REVERT: H 47 TRP cc_start: 0.8979 (t60) cc_final: 0.8568 (t60) REVERT: H 57 ASN cc_start: 0.8356 (t0) cc_final: 0.8020 (t0) REVERT: K 39 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7958 (tt0) outliers start: 14 outliers final: 11 residues processed: 80 average time/residue: 0.1945 time to fit residues: 18.2173 Evaluate side-chains 79 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 393 THR 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 27 PHE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 48 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 6 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 = 0.3612 r_free = 0.3612 target = 0.121724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102483 restraints weight = 6796.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.102182 restraints weight = 5921.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.103412 restraints weight = 5472.836| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3237 Z= 0.238 Angle : 0.610 8.031 4394 Z= 0.320 Chirality : 0.044 0.138 467 Planarity : 0.004 0.037 569 Dihedral : 4.871 24.303 447 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.79 % Allowed : 15.16 % 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: -1.77 (0.41), residues: 392 helix: -4.32 (0.76), residues: 15 sheet: -0.84 (0.46), residues: 129 loop : -1.16 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 36 HIS 0.001 0.001 HIS A 505 PHE 0.013 0.001 PHE A 400 TYR 0.021 0.002 TYR K 92 ARG 0.006 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 83 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8263 (m-30) cc_final: 0.7946 (m-30) REVERT: A 442 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8107 (t0) REVERT: A 474 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7425 (tm-30) REVERT: H 57 ASN cc_start: 0.8356 (t0) cc_final: 0.8127 (t0) REVERT: K 61 ASP cc_start: 0.7211 (t0) cc_final: 0.6910 (t0) outliers start: 13 outliers final: 11 residues processed: 79 average time/residue: 0.1984 time to fit residues: 18.4327 Evaluate side-chains 72 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 393 THR 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 27 PHE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 CYS 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 29 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** K 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.101148 restraints weight = 6560.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101056 restraints weight = 5254.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.101788 restraints weight = 5544.063| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3237 Z= 0.212 Angle : 0.611 8.044 4394 Z= 0.322 Chirality : 0.044 0.134 467 Planarity : 0.004 0.038 569 Dihedral : 4.892 24.305 447 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.37 % Allowed : 15.16 % 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: -1.71 (0.41), residues: 392 helix: -4.35 (0.74), residues: 15 sheet: -0.72 (0.46), residues: 129 loop : -1.16 (0.39), 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 0.010 0.001 PHE A 400 TYR 0.018 0.001 TYR K 92 ARG 0.007 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 81 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 442 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8126 (t0) REVERT: A 474 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7527 (tm-30) REVERT: H 57 ASN cc_start: 0.8340 (t0) cc_final: 0.8066 (t0) REVERT: K 39 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: K 61 ASP cc_start: 0.7382 (t0) cc_final: 0.7109 (t0) outliers start: 15 outliers final: 12 residues processed: 77 average time/residue: 0.2112 time to fit residues: 18.8207 Evaluate side-chains 76 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 393 THR 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 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 62 ARG 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 4 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102012 restraints weight = 6707.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101782 restraints weight = 5796.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.103632 restraints weight = 5540.020| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3237 Z= 0.229 Angle : 0.618 7.998 4394 Z= 0.327 Chirality : 0.044 0.134 467 Planarity : 0.004 0.036 569 Dihedral : 4.874 24.162 447 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.37 % Allowed : 15.16 % 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: -1.66 (0.42), residues: 392 helix: -4.28 (0.81), residues: 15 sheet: -0.61 (0.47), residues: 129 loop : -1.16 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 36 HIS 0.001 0.000 HIS A 505 PHE 0.012 0.001 PHE A 400 TYR 0.017 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 79 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8288 (m-30) cc_final: 0.8041 (m-30) REVERT: A 442 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8103 (t0) REVERT: A 474 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7571 (tm-30) REVERT: H 57 ASN cc_start: 0.8361 (t0) cc_final: 0.8159 (t0) REVERT: K 61 ASP cc_start: 0.7409 (t0) cc_final: 0.7092 (t0) outliers start: 15 outliers final: 13 residues processed: 73 average time/residue: 0.2159 time to fit residues: 18.2726 Evaluate side-chains 77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 393 THR 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 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 48 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.0270 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.121734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.101039 restraints weight = 6631.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.100840 restraints weight = 5243.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.101468 restraints weight = 5482.507| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3237 Z= 0.202 Angle : 0.623 8.895 4394 Z= 0.327 Chirality : 0.043 0.131 467 Planarity : 0.004 0.036 569 Dihedral : 4.699 24.016 447 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % 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: -1.57 (0.42), residues: 392 helix: -4.29 (0.81), residues: 15 sheet: -0.51 (0.47), residues: 129 loop : -1.14 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 36 HIS 0.001 0.000 HIS A 505 PHE 0.009 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 81 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8317 (m-30) cc_final: 0.8070 (m-30) REVERT: A 442 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8113 (t0) REVERT: A 474 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7635 (tm-30) REVERT: K 39 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: K 61 ASP cc_start: 0.7506 (t0) cc_final: 0.7192 (t0) outliers start: 16 outliers final: 13 residues processed: 76 average time/residue: 0.2148 time to fit residues: 18.9403 Evaluate side-chains 77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 393 THR 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 27 PHE Chi-restraints excluded: chain H residue 34 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** K 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.120796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100287 restraints weight = 6548.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100177 restraints weight = 5518.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.100605 restraints weight = 5638.936| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3237 Z= 0.230 Angle : 0.644 8.982 4394 Z= 0.341 Chirality : 0.043 0.134 467 Planarity : 0.004 0.034 569 Dihedral : 4.754 23.065 447 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.37 % Allowed : 15.16 % 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: -1.59 (0.42), residues: 392 helix: -4.30 (0.79), residues: 15 sheet: -0.51 (0.47), residues: 129 loop : -1.15 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.001 0.000 HIS A 505 PHE 0.013 0.001 PHE A 400 TYR 0.016 0.001 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 78 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8284 (m-30) cc_final: 0.8048 (m-30) REVERT: A 442 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8106 (t0) REVERT: A 474 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7609 (tm-30) REVERT: K 39 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: K 61 ASP cc_start: 0.7491 (t0) cc_final: 0.7198 (t0) outliers start: 15 outliers final: 13 residues processed: 74 average time/residue: 0.2099 time to fit residues: 18.2289 Evaluate side-chains 77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 393 THR 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 27 PHE Chi-restraints excluded: chain H residue 34 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.101087 restraints weight = 6547.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.100819 restraints weight = 5534.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.102586 restraints weight = 5347.823| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3754 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= 0.224 Angle : 0.637 8.545 4394 Z= 0.337 Chirality : 0.043 0.133 467 Planarity : 0.004 0.034 569 Dihedral : 4.769 23.019 447 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.08 % Allowed : 15.45 % 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: -1.54 (0.42), residues: 392 helix: -4.31 (0.79), residues: 15 sheet: -0.48 (0.47), residues: 129 loop : -1.12 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.001 0.000 HIS A 505 PHE 0.012 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: 1462.80 seconds wall clock time: 26 minutes 54.12 seconds (1614.12 seconds total)