Starting phenix.real_space_refine on Wed Mar 5 17:52:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ex7_28653/03_2025/8ex7_28653.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ex7_28653/03_2025/8ex7_28653.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/8ex7_28653/03_2025/8ex7_28653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ex7_28653/03_2025/8ex7_28653.map" model { file = "/net/cci-nas-00/data/ceres_data/8ex7_28653/03_2025/8ex7_28653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ex7_28653/03_2025/8ex7_28653.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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2090 2.51 5 N 524 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3177 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3177 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 12, 'TRANS': 401} Chain breaks: 2 Time building chain proxies: 3.94, per 1000 atoms: 1.24 Number of scatterers: 3177 At special positions: 0 Unit cell: (68.145, 65.549, 76.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 546 8.00 N 524 7.00 C 2090 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: 0.86 Conformation dependent library (CDL) restraints added in 444.3 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 92.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 99 through 118 Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.717A pdb=" N VAL A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.577A pdb=" N GLY A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 165 removed outlier: 4.129A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 166 through 187 removed outlier: 3.619A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 212 removed outlier: 3.552A pdb=" N ALA A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TYR A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 222 removed outlier: 3.561A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 256 removed outlier: 4.185A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 4.280A pdb=" N TYR A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 281 removed outlier: 4.703A pdb=" N SER A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 302 through 311 removed outlier: 3.583A pdb=" N ILE A 310 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 348 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 361 through 389 Processing helix chain 'A' and resid 394 through 420 removed outlier: 3.800A pdb=" N VAL A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA A 401 " --> pdb=" O PRO A 397 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 removed outlier: 4.028A pdb=" N PHE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.575A pdb=" N ALA A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 Processing helix chain 'A' and resid 474 through 490 removed outlier: 3.568A pdb=" N LEU A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 539 removed outlier: 4.084A pdb=" N PHE A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) 263 hydrogen bonds defined for protein. 789 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: 1.03 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: 967 1.34 - 1.46: 641 1.46 - 1.57: 1617 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3251 Sorted by residual: bond pdb=" C TRP A 178 " pdb=" N SER A 179 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.36e-02 5.41e+03 1.19e+01 bond pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.33e-02 5.65e+03 6.17e+00 bond pdb=" N PHE A 177 " pdb=" CA PHE A 177 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.62e+00 bond pdb=" N PHE A 176 " pdb=" CA PHE A 176 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.71e+00 bond pdb=" N SER A 179 " pdb=" CA SER A 179 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.49e+00 ... (remaining 3246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 4205 1.40 - 2.80: 172 2.80 - 4.20: 27 4.20 - 5.60: 9 5.60 - 7.00: 3 Bond angle restraints: 4416 Sorted by residual: angle pdb=" N VAL A 125 " pdb=" CA VAL A 125 " pdb=" C VAL A 125 " ideal model delta sigma weight residual 111.88 108.10 3.78 1.06e+00 8.90e-01 1.27e+01 angle pdb=" C TRP A 178 " pdb=" N SER A 179 " pdb=" CA SER A 179 " ideal model delta sigma weight residual 120.29 115.80 4.49 1.42e+00 4.96e-01 9.98e+00 angle pdb=" C MET A 334 " pdb=" N TRP A 335 " pdb=" CA TRP A 335 " ideal model delta sigma weight residual 122.42 117.09 5.33 1.77e+00 3.19e-01 9.06e+00 angle pdb=" N VAL A 122 " pdb=" CA VAL A 122 " pdb=" C VAL A 122 " ideal model delta sigma weight residual 112.98 109.31 3.67 1.25e+00 6.40e-01 8.60e+00 angle pdb=" CA PRO A 239 " pdb=" N PRO A 239 " pdb=" CD PRO A 239 " ideal model delta sigma weight residual 112.00 108.05 3.95 1.40e+00 5.10e-01 7.96e+00 ... (remaining 4411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 1661 15.95 - 31.90: 170 31.90 - 47.84: 37 47.84 - 63.79: 2 63.79 - 79.74: 2 Dihedral angle restraints: 1872 sinusoidal: 692 harmonic: 1180 Sorted by residual: dihedral pdb=" CA PHE A 187 " pdb=" C PHE A 187 " pdb=" N ILE A 188 " pdb=" CA ILE A 188 " ideal model delta harmonic sigma weight residual 180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA TYR A 235 " pdb=" C TYR A 235 " pdb=" N PHE A 236 " pdb=" CA PHE A 236 " ideal model delta harmonic sigma weight residual 180.00 159.84 20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PHE A 165 " pdb=" C PHE A 165 " pdb=" N ASN A 166 " pdb=" CA ASN A 166 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 1869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 442 0.059 - 0.118: 74 0.118 - 0.177: 4 0.177 - 0.236: 0 0.236 - 0.295: 1 Chirality restraints: 521 Sorted by residual: chirality pdb=" CA TRP A 178 " pdb=" N TRP A 178 " pdb=" C TRP A 178 " pdb=" CB TRP A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA MET A 334 " pdb=" N MET A 334 " pdb=" C MET A 334 " pdb=" CB MET A 334 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CB VAL A 135 " pdb=" CA VAL A 135 " pdb=" CG1 VAL A 135 " pdb=" CG2 VAL A 135 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 518 not shown) Planarity restraints: 539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 238 " 0.061 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO A 239 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 176 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C PHE A 176 " -0.033 2.00e-02 2.50e+03 pdb=" O PHE A 176 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 177 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 409 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C ILE A 409 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE A 409 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE A 410 " -0.009 2.00e-02 2.50e+03 ... (remaining 536 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 421 2.75 - 3.29: 3351 3.29 - 3.82: 5464 3.82 - 4.36: 6168 4.36 - 4.90: 10789 Nonbonded interactions: 26193 Sorted by model distance: nonbonded pdb=" O LEU A 117 " pdb=" OG1 THR A 121 " model vdw 2.211 3.040 nonbonded pdb=" O LEU A 229 " pdb=" OG SER A 232 " model vdw 2.233 3.040 nonbonded pdb=" O ALA A 208 " pdb=" OG1 THR A 212 " model vdw 2.250 3.040 nonbonded pdb=" O MET A 404 " pdb=" OG SER A 407 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP A 163 " pdb=" OG1 THR A 458 " model vdw 2.284 3.040 ... (remaining 26188 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.710 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3251 Z= 0.286 Angle : 0.687 6.996 4416 Z= 0.420 Chirality : 0.044 0.295 521 Planarity : 0.006 0.091 539 Dihedral : 13.308 79.739 1116 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 0.68 (0.42), residues: 408 helix: 0.67 (0.27), residues: 356 sheet: None (None), residues: 0 loop : -0.31 (1.05), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 178 HIS 0.003 0.001 HIS A 468 PHE 0.014 0.002 PHE A 234 TYR 0.020 0.002 TYR A 116 ARG 0.002 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.344 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1435 time to fit residues: 6.5662 Evaluate side-chains 31 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.199705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.179964 restraints weight = 3518.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.181976 restraints weight = 2627.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.183625 restraints weight = 2170.922| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3251 Z= 0.269 Angle : 0.615 7.725 4416 Z= 0.332 Chirality : 0.043 0.216 521 Planarity : 0.005 0.055 539 Dihedral : 4.729 25.589 444 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.99 % Allowed : 5.97 % Favored : 91.04 % 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: 1.02 (0.43), residues: 408 helix: 0.85 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 0.06 (1.13), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 178 HIS 0.002 0.001 HIS A 341 PHE 0.013 0.002 PHE A 410 TYR 0.016 0.002 TYR A 116 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.348 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 36 average time/residue: 0.1288 time to fit residues: 6.1870 Evaluate side-chains 35 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 26 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.202696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.183003 restraints weight = 3525.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.185373 restraints weight = 2618.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.186957 restraints weight = 2139.839| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3251 Z= 0.208 Angle : 0.558 6.776 4416 Z= 0.301 Chirality : 0.040 0.191 521 Planarity : 0.004 0.042 539 Dihedral : 4.457 23.397 444 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.39 % Allowed : 11.04 % Favored : 86.57 % 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: 1.54 (0.43), residues: 408 helix: 1.21 (0.28), residues: 358 sheet: None (None), residues: 0 loop : 0.22 (1.08), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 178 HIS 0.001 0.001 HIS A 468 PHE 0.010 0.001 PHE A 410 TYR 0.014 0.001 TYR A 116 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.344 Fit side-chains REVERT: A 183 PHE cc_start: 0.7719 (t80) cc_final: 0.7498 (t80) outliers start: 8 outliers final: 6 residues processed: 34 average time/residue: 0.0943 time to fit residues: 4.6820 Evaluate side-chains 34 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.201531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.181989 restraints weight = 3561.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.184340 restraints weight = 2645.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.185694 restraints weight = 2165.735| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3251 Z= 0.232 Angle : 0.569 6.996 4416 Z= 0.305 Chirality : 0.041 0.195 521 Planarity : 0.004 0.033 539 Dihedral : 4.439 23.215 444 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.99 % Allowed : 11.94 % Favored : 85.07 % 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: 1.64 (0.43), residues: 408 helix: 1.26 (0.27), residues: 358 sheet: None (None), residues: 0 loop : 0.39 (1.10), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 178 HIS 0.001 0.001 HIS A 341 PHE 0.012 0.001 PHE A 498 TYR 0.013 0.001 TYR A 116 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.312 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 36 average time/residue: 0.1177 time to fit residues: 5.7046 Evaluate side-chains 38 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.200697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.181126 restraints weight = 3517.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.183116 restraints weight = 2605.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.184802 restraints weight = 2150.375| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3251 Z= 0.262 Angle : 0.587 6.966 4416 Z= 0.313 Chirality : 0.041 0.191 521 Planarity : 0.004 0.030 539 Dihedral : 4.458 23.739 444 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.99 % Allowed : 14.33 % Favored : 82.69 % 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: 1.62 (0.43), residues: 408 helix: 1.26 (0.27), residues: 358 sheet: None (None), residues: 0 loop : 0.29 (1.09), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 178 HIS 0.001 0.001 HIS A 341 PHE 0.013 0.001 PHE A 410 TYR 0.013 0.001 TYR A 116 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.351 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 39 average time/residue: 0.1219 time to fit residues: 6.3311 Evaluate side-chains 37 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.203847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.184884 restraints weight = 3584.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.187152 restraints weight = 2591.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.188967 restraints weight = 2090.853| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3251 Z= 0.209 Angle : 0.555 6.686 4416 Z= 0.297 Chirality : 0.040 0.172 521 Planarity : 0.004 0.029 539 Dihedral : 4.279 21.489 444 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.88 % Allowed : 14.93 % Favored : 81.19 % 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: 1.92 (0.43), residues: 408 helix: 1.45 (0.27), residues: 358 sheet: None (None), residues: 0 loop : 0.45 (1.10), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 178 HIS 0.001 0.000 HIS A 468 PHE 0.009 0.001 PHE A 410 TYR 0.012 0.001 TYR A 116 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.277 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 36 average time/residue: 0.1128 time to fit residues: 5.5525 Evaluate side-chains 38 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 30 optimal weight: 0.0870 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.205198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.185025 restraints weight = 3603.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.187256 restraints weight = 2619.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.189110 restraints weight = 2121.741| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3251 Z= 0.232 Angle : 0.580 7.009 4416 Z= 0.310 Chirality : 0.041 0.173 521 Planarity : 0.004 0.029 539 Dihedral : 4.331 22.036 444 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.58 % Allowed : 15.52 % Favored : 80.90 % 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: 1.87 (0.43), residues: 408 helix: 1.42 (0.27), residues: 359 sheet: None (None), residues: 0 loop : 0.33 (1.11), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 178 HIS 0.001 0.000 HIS A 341 PHE 0.011 0.001 PHE A 498 TYR 0.011 0.001 TYR A 116 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.363 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 39 average time/residue: 0.1307 time to fit residues: 6.7933 Evaluate side-chains 41 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.203190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.184430 restraints weight = 3478.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.186447 restraints weight = 2537.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.188286 restraints weight = 2082.207| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3251 Z= 0.221 Angle : 0.568 7.388 4416 Z= 0.303 Chirality : 0.040 0.165 521 Planarity : 0.004 0.029 539 Dihedral : 4.283 21.280 444 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.58 % Allowed : 16.12 % Favored : 80.30 % 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: 2.00 (0.43), residues: 408 helix: 1.50 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 0.41 (1.13), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 178 HIS 0.001 0.000 HIS A 468 PHE 0.010 0.001 PHE A 410 TYR 0.011 0.001 TYR A 116 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.336 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 37 average time/residue: 0.1231 time to fit residues: 6.1174 Evaluate side-chains 38 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 429 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.0000 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 overall best weight: 0.3582 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.202638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.183169 restraints weight = 3518.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.185416 restraints weight = 2581.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.187151 restraints weight = 2070.757| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3251 Z= 0.188 Angle : 0.537 7.794 4416 Z= 0.288 Chirality : 0.039 0.144 521 Planarity : 0.004 0.029 539 Dihedral : 4.104 19.348 444 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.58 % Allowed : 16.12 % Favored : 80.30 % 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: 2.26 (0.43), residues: 408 helix: 1.68 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 0.45 (1.13), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 178 HIS 0.001 0.000 HIS A 341 PHE 0.009 0.001 PHE A 410 TYR 0.012 0.001 TYR A 116 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.329 Fit side-chains REVERT: A 116 TYR cc_start: 0.7616 (m-80) cc_final: 0.6644 (m-80) REVERT: A 366 PHE cc_start: 0.5818 (t80) cc_final: 0.5316 (t80) outliers start: 12 outliers final: 8 residues processed: 40 average time/residue: 0.1322 time to fit residues: 6.9644 Evaluate side-chains 36 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 0.0980 chunk 29 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.204553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.184881 restraints weight = 3486.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.187521 restraints weight = 2664.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.189253 restraints weight = 2150.139| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3251 Z= 0.210 Angle : 0.576 8.105 4416 Z= 0.303 Chirality : 0.040 0.153 521 Planarity : 0.004 0.028 539 Dihedral : 4.166 19.891 444 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.99 % Allowed : 17.61 % Favored : 79.40 % 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: 2.18 (0.42), residues: 408 helix: 1.63 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 0.41 (1.14), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 178 HIS 0.001 0.000 HIS A 341 PHE 0.010 0.001 PHE A 410 TYR 0.010 0.001 TYR A 160 ARG 0.002 0.000 ARG A 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.353 Fit side-chains REVERT: A 116 TYR cc_start: 0.7726 (m-80) cc_final: 0.6665 (m-80) outliers start: 10 outliers final: 10 residues processed: 38 average time/residue: 0.1322 time to fit residues: 6.5579 Evaluate side-chains 40 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.203930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.183597 restraints weight = 3549.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.185949 restraints weight = 2605.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.187609 restraints weight = 2113.510| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3251 Z= 0.259 Angle : 0.609 7.730 4416 Z= 0.322 Chirality : 0.041 0.169 521 Planarity : 0.004 0.029 539 Dihedral : 4.337 22.214 444 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.58 % Allowed : 17.31 % Favored : 79.10 % 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: 1.95 (0.42), residues: 408 helix: 1.47 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 0.37 (1.12), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 178 HIS 0.001 0.001 HIS A 341 PHE 0.013 0.002 PHE A 498 TYR 0.011 0.001 TYR A 160 ARG 0.002 0.000 ARG A 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1410.73 seconds wall clock time: 25 minutes 14.66 seconds (1514.66 seconds total)