Starting phenix.real_space_refine on Fri Dec 27 12:41:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bw7_16280/12_2024/8bw7_16280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bw7_16280/12_2024/8bw7_16280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bw7_16280/12_2024/8bw7_16280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bw7_16280/12_2024/8bw7_16280.map" model { file = "/net/cci-nas-00/data/ceres_data/8bw7_16280/12_2024/8bw7_16280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bw7_16280/12_2024/8bw7_16280.cif" } resolution = 3.53 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= -0.001 sd= 0.060 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: 5 Type Number sf(0) Gaussians S 35 5.16 5 Cl 1 4.86 5 C 3069 2.51 5 N 804 2.21 5 O 839 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4748 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3842 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 25, 'TRANS': 471} Chain breaks: 2 Chain: "B" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 895 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CL': 1, 'AKG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.61, per 1000 atoms: 0.76 Number of scatterers: 4748 At special positions: 0 Unit cell: (118.144, 69.888, 80.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 35 16.00 O 839 8.00 N 804 7.00 C 3069 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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: 1.16 Conformation dependent library (CDL) restraints added in 567.8 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 4 sheets defined 67.2% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.726A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 25 Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 132 through 160 removed outlier: 3.868A pdb=" N PHE A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 181 Processing helix chain 'A' and resid 184 through 214 removed outlier: 3.547A pdb=" N TYR A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 244 removed outlier: 3.867A pdb=" N ALA A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 265 removed outlier: 3.849A pdb=" N LEU A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Proline residue: A 257 - end of helix removed outlier: 3.675A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.564A pdb=" N TYR A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 326 through 332 removed outlier: 3.501A pdb=" N LEU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 358 Processing helix chain 'A' and resid 366 through 392 removed outlier: 3.563A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 394 through 415 removed outlier: 4.098A pdb=" N LEU A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 449 removed outlier: 3.882A pdb=" N GLU A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 484 through 501 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 502 through 504 No H-bonds generated for 'chain 'A' and resid 502 through 504' Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.509A pdb=" N ARG A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 56 Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.257A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.539A pdb=" N SER B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.631A pdb=" N THR B 109 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 93 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 39 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1309 1.34 - 1.46: 928 1.46 - 1.58: 2568 1.58 - 1.70: 0 1.70 - 1.82: 55 Bond restraints: 4860 Sorted by residual: bond pdb=" C1 AKG A 601 " pdb=" O2 AKG A 601 " ideal model delta sigma weight residual 1.239 1.308 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C5 AKG A 601 " pdb=" O3 AKG A 601 " ideal model delta sigma weight residual 1.247 1.309 -0.062 2.00e-02 2.50e+03 9.48e+00 bond pdb=" C4 AKG A 601 " pdb=" C5 AKG A 601 " ideal model delta sigma weight residual 1.540 1.500 0.040 2.00e-02 2.50e+03 3.97e+00 bond pdb=" C VAL A 493 " pdb=" N PRO A 494 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.36e-02 5.41e+03 3.35e+00 bond pdb=" C5 AKG A 601 " pdb=" O4 AKG A 601 " ideal model delta sigma weight residual 1.249 1.214 0.035 2.00e-02 2.50e+03 3.02e+00 ... (remaining 4855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 6475 1.86 - 3.71: 102 3.71 - 5.57: 20 5.57 - 7.43: 8 7.43 - 9.28: 2 Bond angle restraints: 6607 Sorted by residual: angle pdb=" C CYS A 128 " pdb=" CA CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sigma weight residual 117.23 110.12 7.11 1.36e+00 5.41e-01 2.74e+01 angle pdb=" O SER B 114 " pdb=" C SER B 114 " pdb=" N ALA B 115 " ideal model delta sigma weight residual 121.20 114.21 6.99 1.61e+00 3.86e-01 1.88e+01 angle pdb=" CA CYS A 128 " pdb=" C CYS A 128 " pdb=" N SER A 129 " ideal model delta sigma weight residual 119.98 116.68 3.30 8.50e-01 1.38e+00 1.51e+01 angle pdb=" N VAL B 64 " pdb=" CA VAL B 64 " pdb=" C VAL B 64 " ideal model delta sigma weight residual 113.53 109.77 3.76 9.80e-01 1.04e+00 1.47e+01 angle pdb=" CA GLN A 314 " pdb=" CB GLN A 314 " pdb=" CG GLN A 314 " ideal model delta sigma weight residual 114.10 120.89 -6.79 2.00e+00 2.50e-01 1.15e+01 ... (remaining 6602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2429 17.94 - 35.88: 319 35.88 - 53.83: 93 53.83 - 71.77: 10 71.77 - 89.71: 8 Dihedral angle restraints: 2859 sinusoidal: 1101 harmonic: 1758 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual -86.00 -162.65 76.65 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual -86.00 -135.89 49.89 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CA PRO A 215 " pdb=" C PRO A 215 " pdb=" N ILE A 216 " pdb=" CA ILE A 216 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 2856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 512 0.034 - 0.067: 173 0.067 - 0.101: 53 0.101 - 0.135: 15 0.135 - 0.169: 2 Chirality restraints: 755 Sorted by residual: chirality pdb=" CG LEU A 199 " pdb=" CB LEU A 199 " pdb=" CD1 LEU A 199 " pdb=" CD2 LEU A 199 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CA ASN A 125 " pdb=" N ASN A 125 " pdb=" C ASN A 125 " pdb=" CB ASN A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 752 not shown) Planarity restraints: 827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " 0.039 2.00e-02 2.50e+03 7.29e-02 5.32e+01 pdb=" C SER B 114 " -0.126 2.00e-02 2.50e+03 pdb=" O SER B 114 " 0.046 2.00e-02 2.50e+03 pdb=" N ALA B 115 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 493 " -0.044 5.00e-02 4.00e+02 6.77e-02 7.32e+00 pdb=" N PRO A 494 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 494 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 494 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 214 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 215 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " -0.022 5.00e-02 4.00e+02 ... (remaining 824 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 150 2.71 - 3.26: 4849 3.26 - 3.81: 8060 3.81 - 4.35: 9223 4.35 - 4.90: 16054 Nonbonded interactions: 38336 Sorted by model distance: nonbonded pdb=" O PHE A 133 " pdb=" OH TYR A 185 " model vdw 2.164 3.040 nonbonded pdb=" OG SER A 175 " pdb=" O PHE A 191 " model vdw 2.271 3.040 nonbonded pdb=" O ASP A 70 " pdb=" NH2 ARG B 59 " model vdw 2.273 3.120 nonbonded pdb=" N GLN A 455 " pdb=" OE1 GLN A 455 " model vdw 2.290 3.120 nonbonded pdb=" OE1 GLU A 212 " pdb=" OG SER A 271 " model vdw 2.297 3.040 ... (remaining 38331 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.430 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4860 Z= 0.214 Angle : 0.622 9.283 6607 Z= 0.324 Chirality : 0.039 0.169 755 Planarity : 0.005 0.073 827 Dihedral : 17.605 89.709 1726 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 34.58 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.36), residues: 604 helix: 1.55 (0.29), residues: 357 sheet: -1.79 (0.69), residues: 44 loop : -0.69 (0.47), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 346 HIS 0.002 0.001 HIS A 34 PHE 0.008 0.001 PHE A 191 TYR 0.008 0.001 TYR A 169 ARG 0.003 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.511 Fit side-chains REVERT: A 31 MET cc_start: 0.7041 (tpt) cc_final: 0.6324 (tpt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1283 time to fit residues: 14.5384 Evaluate side-chains 77 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0030 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4860 Z= 0.187 Angle : 0.571 6.943 6607 Z= 0.291 Chirality : 0.039 0.155 755 Planarity : 0.004 0.056 827 Dihedral : 4.308 47.804 671 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.14 % Allowed : 33.20 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.36), residues: 604 helix: 1.49 (0.28), residues: 364 sheet: -1.89 (0.69), residues: 44 loop : -0.84 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 247 HIS 0.003 0.001 HIS A 48 PHE 0.010 0.001 PHE A 351 TYR 0.010 0.001 TYR A 185 ARG 0.005 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.522 Fit side-chains REVERT: A 31 MET cc_start: 0.7068 (tpt) cc_final: 0.6328 (tpt) outliers start: 16 outliers final: 10 residues processed: 88 average time/residue: 0.1134 time to fit residues: 14.1485 Evaluate side-chains 89 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 493 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4860 Z= 0.186 Angle : 0.550 6.584 6607 Z= 0.280 Chirality : 0.039 0.157 755 Planarity : 0.004 0.052 827 Dihedral : 4.271 44.966 671 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.52 % Allowed : 33.20 % Favored : 62.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.36), residues: 604 helix: 1.47 (0.28), residues: 364 sheet: -1.76 (0.64), residues: 50 loop : -0.82 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 48 PHE 0.012 0.001 PHE A 351 TYR 0.012 0.001 TYR A 264 ARG 0.003 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.496 Fit side-chains REVERT: A 31 MET cc_start: 0.7033 (tpt) cc_final: 0.6272 (tpt) REVERT: B 84 ASN cc_start: 0.4887 (p0) cc_final: 0.3709 (m-40) outliers start: 23 outliers final: 14 residues processed: 96 average time/residue: 0.1163 time to fit residues: 15.8103 Evaluate side-chains 96 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 54 optimal weight: 0.2980 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4860 Z= 0.172 Angle : 0.550 6.711 6607 Z= 0.278 Chirality : 0.039 0.164 755 Planarity : 0.004 0.055 827 Dihedral : 4.199 42.482 671 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.93 % Allowed : 33.99 % Favored : 62.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.36), residues: 604 helix: 1.51 (0.28), residues: 364 sheet: -1.71 (0.64), residues: 50 loop : -0.84 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.001 HIS A 34 PHE 0.009 0.001 PHE A 351 TYR 0.011 0.001 TYR A 264 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.515 Fit side-chains REVERT: A 31 MET cc_start: 0.6991 (tpt) cc_final: 0.6313 (tpt) REVERT: A 212 GLU cc_start: 0.7679 (tt0) cc_final: 0.7456 (mt-10) REVERT: B 84 ASN cc_start: 0.4929 (p0) cc_final: 0.3825 (m-40) outliers start: 20 outliers final: 14 residues processed: 101 average time/residue: 0.1186 time to fit residues: 16.7858 Evaluate side-chains 96 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4860 Z= 0.182 Angle : 0.566 7.618 6607 Z= 0.284 Chirality : 0.039 0.162 755 Planarity : 0.004 0.056 827 Dihedral : 4.189 41.430 671 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.73 % Allowed : 34.38 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.36), residues: 604 helix: 1.52 (0.28), residues: 364 sheet: -1.67 (0.64), residues: 50 loop : -0.81 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.003 0.001 HIS A 34 PHE 0.010 0.001 PHE A 351 TYR 0.011 0.001 TYR A 264 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.503 Fit side-chains REVERT: A 31 MET cc_start: 0.6968 (tpt) cc_final: 0.6309 (tpt) REVERT: A 212 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: B 84 ASN cc_start: 0.4982 (p0) cc_final: 0.3881 (m-40) outliers start: 19 outliers final: 16 residues processed: 97 average time/residue: 0.1160 time to fit residues: 15.8679 Evaluate side-chains 97 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4860 Z= 0.190 Angle : 0.555 6.805 6607 Z= 0.280 Chirality : 0.039 0.163 755 Planarity : 0.004 0.056 827 Dihedral : 4.165 40.664 671 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.72 % Allowed : 33.60 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.36), residues: 604 helix: 1.51 (0.28), residues: 364 sheet: -1.58 (0.65), residues: 50 loop : -0.76 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 48 PHE 0.011 0.001 PHE A 351 TYR 0.011 0.001 TYR A 264 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.603 Fit side-chains REVERT: A 5 ASP cc_start: 0.8166 (t0) cc_final: 0.7899 (t0) REVERT: A 112 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7837 (p0) REVERT: A 212 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: B 84 ASN cc_start: 0.5016 (p0) cc_final: 0.3956 (m-40) outliers start: 24 outliers final: 17 residues processed: 102 average time/residue: 0.1238 time to fit residues: 17.6839 Evaluate side-chains 100 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.0270 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4860 Z= 0.180 Angle : 0.561 6.838 6607 Z= 0.281 Chirality : 0.039 0.164 755 Planarity : 0.004 0.057 827 Dihedral : 4.175 39.576 671 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.72 % Allowed : 33.40 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.36), residues: 604 helix: 1.49 (0.28), residues: 370 sheet: -1.76 (0.70), residues: 44 loop : -0.84 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.001 HIS A 34 PHE 0.010 0.001 PHE A 351 TYR 0.011 0.001 TYR A 264 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.399 Fit side-chains REVERT: A 5 ASP cc_start: 0.8174 (t0) cc_final: 0.7918 (t0) REVERT: A 31 MET cc_start: 0.6950 (tpt) cc_final: 0.6322 (tpt) REVERT: A 206 CYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7758 (t) REVERT: B 84 ASN cc_start: 0.4950 (p0) cc_final: 0.3891 (m-40) outliers start: 24 outliers final: 17 residues processed: 98 average time/residue: 0.1237 time to fit residues: 16.5716 Evaluate side-chains 95 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.0010 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4860 Z= 0.172 Angle : 0.561 6.838 6607 Z= 0.279 Chirality : 0.039 0.165 755 Planarity : 0.004 0.057 827 Dihedral : 4.127 38.235 671 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.13 % Allowed : 33.79 % Favored : 62.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.36), residues: 604 helix: 1.52 (0.28), residues: 369 sheet: -1.73 (0.70), residues: 44 loop : -0.82 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.001 HIS A 48 PHE 0.009 0.001 PHE A 351 TYR 0.011 0.001 TYR A 264 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.496 Fit side-chains REVERT: A 5 ASP cc_start: 0.8214 (t0) cc_final: 0.7926 (t0) REVERT: A 31 MET cc_start: 0.6970 (tpt) cc_final: 0.6355 (tpt) REVERT: A 64 GLU cc_start: 0.6478 (tm-30) cc_final: 0.5845 (mp0) REVERT: A 206 CYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7757 (t) REVERT: B 84 ASN cc_start: 0.4834 (p0) cc_final: 0.3821 (m-40) outliers start: 21 outliers final: 19 residues processed: 100 average time/residue: 0.1156 time to fit residues: 16.3440 Evaluate side-chains 103 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4860 Z= 0.163 Angle : 0.585 7.493 6607 Z= 0.291 Chirality : 0.039 0.163 755 Planarity : 0.004 0.057 827 Dihedral : 4.085 36.370 671 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.52 % Allowed : 34.18 % Favored : 61.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.36), residues: 604 helix: 1.63 (0.28), residues: 367 sheet: -1.71 (0.71), residues: 44 loop : -0.84 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.002 0.001 HIS A 34 PHE 0.008 0.001 PHE A 191 TYR 0.010 0.001 TYR A 264 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.528 Fit side-chains REVERT: A 5 ASP cc_start: 0.8186 (t0) cc_final: 0.7941 (t0) REVERT: A 31 MET cc_start: 0.6926 (tpt) cc_final: 0.6325 (tpt) REVERT: A 64 GLU cc_start: 0.6409 (tm-30) cc_final: 0.5819 (mp0) REVERT: A 206 CYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7764 (t) REVERT: A 512 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5926 (mt) REVERT: B 80 TYR cc_start: 0.6146 (m-80) cc_final: 0.5938 (m-80) REVERT: B 84 ASN cc_start: 0.4845 (p0) cc_final: 0.3857 (m-40) outliers start: 23 outliers final: 19 residues processed: 107 average time/residue: 0.1151 time to fit residues: 17.3685 Evaluate side-chains 106 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.0370 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4860 Z= 0.170 Angle : 0.584 7.856 6607 Z= 0.289 Chirality : 0.039 0.166 755 Planarity : 0.004 0.057 827 Dihedral : 4.078 35.348 671 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.32 % Allowed : 34.97 % Favored : 60.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.36), residues: 604 helix: 1.58 (0.28), residues: 369 sheet: -1.72 (0.71), residues: 44 loop : -0.76 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.002 0.001 HIS A 34 PHE 0.009 0.001 PHE A 351 TYR 0.011 0.001 TYR A 264 ARG 0.003 0.000 ARG A 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.511 Fit side-chains REVERT: A 5 ASP cc_start: 0.8194 (t0) cc_final: 0.7952 (t0) REVERT: A 31 MET cc_start: 0.6937 (tpt) cc_final: 0.6321 (tpt) REVERT: A 64 GLU cc_start: 0.6456 (tm-30) cc_final: 0.5871 (mp0) REVERT: A 206 CYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7768 (t) REVERT: A 512 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5885 (mt) REVERT: B 80 TYR cc_start: 0.6121 (m-80) cc_final: 0.5916 (m-80) REVERT: B 84 ASN cc_start: 0.4835 (p0) cc_final: 0.3875 (m-40) outliers start: 22 outliers final: 20 residues processed: 105 average time/residue: 0.1234 time to fit residues: 17.9013 Evaluate side-chains 107 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.0570 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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 = 0.4681 r_free = 0.4681 target = 0.232559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.194320 restraints weight = 6107.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.198471 restraints weight = 3822.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.201326 restraints weight = 2835.077| |-----------------------------------------------------------------------------| r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4860 Z= 0.166 Angle : 0.586 8.799 6607 Z= 0.288 Chirality : 0.039 0.164 755 Planarity : 0.004 0.057 827 Dihedral : 4.055 34.605 671 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.32 % Allowed : 35.17 % Favored : 60.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.36), residues: 604 helix: 1.61 (0.28), residues: 369 sheet: -1.67 (0.77), residues: 41 loop : -0.71 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 52 HIS 0.002 0.000 HIS A 34 PHE 0.008 0.001 PHE A 351 TYR 0.011 0.001 TYR A 264 ARG 0.003 0.000 ARG A 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1364.48 seconds wall clock time: 25 minutes 32.92 seconds (1532.92 seconds total)