Starting phenix.real_space_refine on Mon Jan 13 18:55:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcs_38253/01_2025/8xcs_38253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcs_38253/01_2025/8xcs_38253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xcs_38253/01_2025/8xcs_38253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcs_38253/01_2025/8xcs_38253.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcs_38253/01_2025/8xcs_38253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcs_38253/01_2025/8xcs_38253.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 P 3 5.49 5 S 14 5.16 5 C 2121 2.51 5 N 567 2.21 5 O 655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3360 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3281 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 397} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 79 Unusual residues: {'AKG': 1, 'NDP': 1, 'NH4': 1} Classifications: {'undetermined': 3, 'water': 20} Link IDs: {None: 22} Time building chain proxies: 2.93, per 1000 atoms: 0.87 Number of scatterers: 3360 At special positions: 0 Unit cell: (71.44, 69.184, 68.432, 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) S 14 16.00 P 3 15.00 O 655 8.00 N 567 7.00 C 2121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.92 Conformation dependent library (CDL) restraints added in 372.8 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 55.5% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.815A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.919A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.512A pdb=" N ILE A 309 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 344 through 361 removed outlier: 4.472A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 415 removed outlier: 3.762A pdb=" N SER A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.652A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.652A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.471A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 243 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 570 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: 1.00 Time building geometry restraints manager: 1.06 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: 1004 1.34 - 1.45: 483 1.45 - 1.57: 1899 1.57 - 1.69: 2 1.69 - 1.81: 27 Bond restraints: 3415 Sorted by residual: bond pdb=" O1N NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.477 1.550 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.566 0.267 3.80e-02 6.93e+02 4.94e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.559 0.198 3.50e-02 8.16e+02 3.22e+01 bond pdb=" C1 AKG A 502 " pdb=" C2 AKG A 502 " ideal model delta sigma weight residual 1.559 1.461 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C6A NDP A 501 " pdb=" N1A NDP A 501 " ideal model delta sigma weight residual 1.368 1.253 0.115 2.90e-02 1.19e+03 1.58e+01 ... (remaining 3410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 4600 4.42 - 8.85: 23 8.85 - 13.27: 10 13.27 - 17.69: 4 17.69 - 22.12: 1 Bond angle restraints: 4638 Sorted by residual: angle pdb=" C1D NDP A 501 " pdb=" O4D NDP A 501 " pdb=" C4D NDP A 501 " ideal model delta sigma weight residual 105.41 127.53 -22.12 2.71e+00 1.37e-01 6.68e+01 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 119.24 -15.40 1.91e+00 2.73e-01 6.47e+01 angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 122.52 -14.78 1.95e+00 2.62e-01 5.72e+01 angle pdb=" O1X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.46 109.42 8.04 1.17e+00 7.36e-01 4.75e+01 angle pdb=" O2X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.33 108.86 8.47 1.48e+00 4.57e-01 3.28e+01 ... (remaining 4633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.95: 1931 30.95 - 61.89: 84 61.89 - 92.84: 7 92.84 - 123.78: 0 123.78 - 154.73: 1 Dihedral angle restraints: 2023 sinusoidal: 828 harmonic: 1195 Sorted by residual: dihedral pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " ideal model delta sinusoidal sigma weight residual 175.04 20.31 154.73 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB LYS A 304 " pdb=" CG LYS A 304 " pdb=" CD LYS A 304 " pdb=" CE LYS A 304 " ideal model delta sinusoidal sigma weight residual 180.00 121.19 58.81 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 443 0.079 - 0.159: 52 0.159 - 0.238: 3 0.238 - 0.318: 3 0.318 - 0.397: 3 Chirality restraints: 504 Sorted by residual: chirality pdb=" C4D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" C5D NDP A 501 " pdb=" O4D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.32 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C2D NDP A 501 " pdb=" C1D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" O2D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.34 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C1B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" N9A NDP A 501 " pdb=" O4B NDP A 501 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 501 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 501 " -0.139 2.00e-02 2.50e+03 8.17e-02 8.34e+01 pdb=" C3N NDP A 501 " 0.008 2.00e-02 2.50e+03 pdb=" C4N NDP A 501 " -0.026 2.00e-02 2.50e+03 pdb=" C7N NDP A 501 " 0.058 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 501 " -0.035 2.00e-02 2.50e+03 6.15e-02 3.78e+01 pdb=" C5N NDP A 501 " 0.078 2.00e-02 2.50e+03 pdb=" C6N NDP A 501 " -0.080 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 394 " 0.021 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C HIS A 394 " -0.071 2.00e-02 2.50e+03 pdb=" O HIS A 394 " 0.026 2.00e-02 2.50e+03 pdb=" N MET A 395 " 0.024 2.00e-02 2.50e+03 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1265 2.88 - 3.39: 3295 3.39 - 3.89: 6079 3.89 - 4.40: 7212 4.40 - 4.90: 11655 Nonbonded interactions: 29506 Sorted by model distance: nonbonded pdb=" O HIS A 61 " pdb=" O HOH A 601 " model vdw 2.381 3.040 nonbonded pdb=" O ASP A 145 " pdb=" O HOH A 602 " model vdw 2.445 3.040 nonbonded pdb=" O VAL A 317 " pdb=" ND2 ASN A 344 " model vdw 2.448 3.120 nonbonded pdb=" O ARG A 65 " pdb=" O HOH A 603 " model vdw 2.461 3.040 nonbonded pdb=" O THR A 148 " pdb=" O HOH A 602 " model vdw 2.469 3.040 ... (remaining 29501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.730 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.820 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.009 0.267 3415 Z= 0.517 Angle : 1.096 22.116 4638 Z= 0.584 Chirality : 0.059 0.397 504 Planarity : 0.006 0.082 592 Dihedral : 16.414 154.727 1261 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.69 % Allowed : 3.52 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.43), residues: 416 helix: 0.93 (0.36), residues: 210 sheet: 0.54 (0.74), residues: 60 loop : -0.33 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.408 Fit side-chains REVERT: A 12 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8074 (mptt) outliers start: 16 outliers final: 2 residues processed: 76 average time/residue: 1.6244 time to fit residues: 126.2712 Evaluate side-chains 49 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.106206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.079955 restraints weight = 4250.924| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 1.51 r_work: 0.2654 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3415 Z= 0.247 Angle : 0.523 5.391 4638 Z= 0.278 Chirality : 0.044 0.136 504 Planarity : 0.005 0.043 592 Dihedral : 10.738 154.483 477 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.23 % Allowed : 10.85 % Favored : 85.92 % 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: 1.29 (0.44), residues: 416 helix: 1.77 (0.36), residues: 211 sheet: 0.38 (0.72), residues: 61 loop : -0.24 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 364 HIS 0.006 0.002 HIS A 388 PHE 0.015 0.002 PHE A 341 TYR 0.013 0.002 TYR A 363 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.367 Fit side-chains REVERT: A 16 ARG cc_start: 0.8512 (ttm170) cc_final: 0.8253 (ttm170) REVERT: A 113 LYS cc_start: 0.8986 (mttp) cc_final: 0.8497 (mtpt) REVERT: A 229 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8627 (tttp) REVERT: A 371 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7647 (pt0) outliers start: 11 outliers final: 1 residues processed: 53 average time/residue: 1.7097 time to fit residues: 92.7655 Evaluate side-chains 44 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.106780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.080884 restraints weight = 4172.637| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 1.49 r_work: 0.2691 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3415 Z= 0.189 Angle : 0.474 4.369 4638 Z= 0.249 Chirality : 0.042 0.134 504 Planarity : 0.004 0.044 592 Dihedral : 9.106 143.498 470 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.35 % Allowed : 12.32 % Favored : 85.34 % 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: 1.57 (0.44), residues: 416 helix: 2.05 (0.36), residues: 211 sheet: 0.39 (0.72), residues: 61 loop : -0.11 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 364 HIS 0.004 0.001 HIS A 388 PHE 0.012 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.001 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.395 Fit side-chains REVERT: A 371 GLU cc_start: 0.8038 (pt0) cc_final: 0.7707 (pt0) outliers start: 8 outliers final: 2 residues processed: 47 average time/residue: 1.6168 time to fit residues: 77.8966 Evaluate side-chains 42 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.107287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.081303 restraints weight = 4281.818| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 1.52 r_work: 0.2696 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3415 Z= 0.167 Angle : 0.455 4.928 4638 Z= 0.240 Chirality : 0.042 0.130 504 Planarity : 0.004 0.044 592 Dihedral : 8.471 124.901 470 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.93 % Allowed : 12.02 % Favored : 85.04 % 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: 1.69 (0.44), residues: 416 helix: 2.17 (0.36), residues: 211 sheet: 0.44 (0.73), residues: 61 loop : -0.09 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.004 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.343 Fit side-chains REVERT: A 4 ILE cc_start: 0.8211 (tp) cc_final: 0.7932 (tt) REVERT: A 246 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7653 (mtt180) REVERT: A 371 GLU cc_start: 0.8062 (pt0) cc_final: 0.7751 (pt0) REVERT: A 388 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.7953 (t70) outliers start: 10 outliers final: 2 residues processed: 52 average time/residue: 1.6245 time to fit residues: 86.6234 Evaluate side-chains 47 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.104947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.078820 restraints weight = 4246.385| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 1.51 r_work: 0.2649 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3415 Z= 0.231 Angle : 0.487 4.469 4638 Z= 0.258 Chirality : 0.043 0.134 504 Planarity : 0.004 0.045 592 Dihedral : 8.082 102.683 470 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.23 % Allowed : 11.73 % Favored : 85.04 % 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: 1.60 (0.44), residues: 416 helix: 2.11 (0.36), residues: 211 sheet: 0.37 (0.72), residues: 61 loop : -0.16 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.006 0.001 HIS A 388 PHE 0.017 0.002 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.390 Fit side-chains REVERT: A 4 ILE cc_start: 0.8195 (tp) cc_final: 0.7880 (tt) REVERT: A 19 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: A 246 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7609 (mtt180) REVERT: A 371 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7782 (pt0) outliers start: 11 outliers final: 2 residues processed: 50 average time/residue: 1.6561 time to fit residues: 84.8542 Evaluate side-chains 46 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 9 optimal weight: 0.0060 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.107482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.081985 restraints weight = 4458.547| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 1.50 r_work: 0.2678 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3415 Z= 0.151 Angle : 0.450 4.640 4638 Z= 0.238 Chirality : 0.042 0.129 504 Planarity : 0.004 0.045 592 Dihedral : 7.621 98.486 470 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.64 % Allowed : 12.90 % Favored : 84.46 % 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: 1.68 (0.44), residues: 416 helix: 2.20 (0.36), residues: 211 sheet: 0.37 (0.72), residues: 61 loop : -0.13 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.383 Fit side-chains REVERT: A 4 ILE cc_start: 0.8130 (tp) cc_final: 0.7808 (tt) REVERT: A 246 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7500 (mtt180) REVERT: A 371 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7730 (pt0) REVERT: A 388 HIS cc_start: 0.8888 (OUTLIER) cc_final: 0.8042 (t70) outliers start: 9 outliers final: 2 residues processed: 51 average time/residue: 1.6334 time to fit residues: 85.3019 Evaluate side-chains 47 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.104258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.078974 restraints weight = 4289.609| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 1.42 r_work: 0.2605 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3415 Z= 0.275 Angle : 0.522 4.812 4638 Z= 0.277 Chirality : 0.044 0.139 504 Planarity : 0.004 0.046 592 Dihedral : 7.659 98.515 470 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.64 % Allowed : 13.49 % Favored : 83.87 % 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: 1.55 (0.44), residues: 416 helix: 2.22 (0.35), residues: 206 sheet: 0.36 (0.72), residues: 61 loop : -0.34 (0.57), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.007 0.001 HIS A 388 PHE 0.019 0.002 PHE A 341 TYR 0.014 0.002 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.463 Fit side-chains REVERT: A 4 ILE cc_start: 0.8210 (tp) cc_final: 0.7869 (tt) REVERT: A 246 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7539 (mtt180) REVERT: A 371 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7801 (pt0) outliers start: 9 outliers final: 2 residues processed: 44 average time/residue: 1.7830 time to fit residues: 80.3414 Evaluate side-chains 44 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 8.9990 chunk 23 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.107060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.081557 restraints weight = 4363.064| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 1.48 r_work: 0.2680 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3415 Z= 0.162 Angle : 0.465 4.381 4638 Z= 0.245 Chirality : 0.042 0.132 504 Planarity : 0.004 0.047 592 Dihedral : 7.243 96.297 470 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.35 % Allowed : 13.20 % Favored : 84.46 % 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: 1.68 (0.44), residues: 416 helix: 2.21 (0.35), residues: 211 sheet: 0.32 (0.72), residues: 61 loop : -0.12 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.004 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.369 Fit side-chains REVERT: A 4 ILE cc_start: 0.8124 (tp) cc_final: 0.7799 (tt) REVERT: A 78 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: A 371 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7729 (pt0) REVERT: A 388 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.8084 (t70) outliers start: 8 outliers final: 1 residues processed: 47 average time/residue: 1.7322 time to fit residues: 83.3031 Evaluate side-chains 46 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.106362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.080766 restraints weight = 4348.971| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 1.48 r_work: 0.2662 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3415 Z= 0.185 Angle : 0.479 4.869 4638 Z= 0.252 Chirality : 0.042 0.134 504 Planarity : 0.004 0.046 592 Dihedral : 7.255 95.573 470 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.35 % Allowed : 13.49 % Favored : 84.16 % 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: 1.70 (0.44), residues: 416 helix: 2.23 (0.35), residues: 211 sheet: 0.35 (0.72), residues: 61 loop : -0.13 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.005 0.001 HIS A 388 PHE 0.013 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.387 Fit side-chains REVERT: A 4 ILE cc_start: 0.8101 (tp) cc_final: 0.7777 (tt) REVERT: A 78 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: A 246 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7516 (mtt180) REVERT: A 371 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7736 (pt0) REVERT: A 388 HIS cc_start: 0.8950 (OUTLIER) cc_final: 0.7985 (t70) outliers start: 8 outliers final: 1 residues processed: 45 average time/residue: 1.7694 time to fit residues: 81.5990 Evaluate side-chains 46 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.104180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.078938 restraints weight = 4346.763| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 1.42 r_work: 0.2618 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3415 Z= 0.286 Angle : 0.524 5.250 4638 Z= 0.277 Chirality : 0.045 0.141 504 Planarity : 0.004 0.046 592 Dihedral : 7.573 96.764 470 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.35 % Allowed : 13.49 % Favored : 84.16 % 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: 1.57 (0.44), residues: 416 helix: 2.24 (0.35), residues: 206 sheet: 0.32 (0.72), residues: 61 loop : -0.32 (0.57), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.007 0.001 HIS A 388 PHE 0.019 0.002 PHE A 341 TYR 0.014 0.002 TYR A 363 ARG 0.002 0.000 ARG A 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.363 Fit side-chains REVERT: A 4 ILE cc_start: 0.8252 (tp) cc_final: 0.7916 (tt) REVERT: A 78 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: A 246 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7585 (mtt180) REVERT: A 371 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7839 (pt0) outliers start: 8 outliers final: 2 residues processed: 44 average time/residue: 1.7764 time to fit residues: 80.0419 Evaluate side-chains 45 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.082920 restraints weight = 4364.165| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.48 r_work: 0.2719 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3415 Z= 0.143 Angle : 0.457 5.087 4638 Z= 0.239 Chirality : 0.041 0.131 504 Planarity : 0.004 0.047 592 Dihedral : 7.080 94.155 470 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.35 % Allowed : 13.49 % Favored : 84.16 % 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: 1.71 (0.44), residues: 416 helix: 2.23 (0.36), residues: 211 sheet: 0.35 (0.72), residues: 61 loop : -0.10 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2702.64 seconds wall clock time: 48 minutes 25.87 seconds (2905.87 seconds total)