Starting phenix.real_space_refine on Wed Mar 5 18:24:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ug0_26482/03_2025/7ug0_26482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ug0_26482/03_2025/7ug0_26482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ug0_26482/03_2025/7ug0_26482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ug0_26482/03_2025/7ug0_26482.map" model { file = "/net/cci-nas-00/data/ceres_data/7ug0_26482/03_2025/7ug0_26482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ug0_26482/03_2025/7ug0_26482.cif" } resolution = 2.55 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= 0.033 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: 6 Type Number sf(0) Gaussians S 17 5.16 5 Na 2 4.78 5 C 2050 2.51 5 N 507 2.21 5 O 549 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 3126 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3103 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 18, 'TRANS': 399} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 23 Unusual residues: {' NA': 2, 'TB1': 1} Classifications: {'undetermined': 3, 'water': 4} Link IDs: {None: 6} Time building chain proxies: 4.06, per 1000 atoms: 1.30 Number of scatterers: 3126 At special positions: 0 Unit cell: (67.308, 78.384, 70.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 17 16.00 Na 2 11.00 F 1 9.00 O 549 8.00 N 507 7.00 C 2050 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: 0.83 Conformation dependent library (CDL) restraints added in 412.0 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.637A pdb=" N ILE A 8 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.625A pdb=" N TYR A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 57 removed outlier: 4.088A pdb=" N LYS A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.542A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 73 removed outlier: 3.637A pdb=" N ILE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 107 Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.590A pdb=" N THR A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 220 removed outlier: 3.514A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 224 through 246 Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 257 through 276 removed outlier: 5.198A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.521A pdb=" N GLY A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.501A pdb=" N TYR A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 3.993A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.581A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 349 removed outlier: 3.516A pdb=" N SER A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 4.252A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 4.108A pdb=" N ILE A 389 " --> pdb=" O EFC A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 418 removed outlier: 4.182A pdb=" N ARG A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.85 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 987 1.37 - 1.55: 2162 1.55 - 1.73: 0 1.73 - 1.92: 32 1.92 - 2.10: 1 Bond restraints: 3182 Sorted by residual: bond pdb=" C EFC A 385 " pdb=" O EFC A 385 " ideal model delta sigma weight residual 1.231 1.184 0.047 2.00e-02 2.50e+03 5.59e+00 bond pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 2.054 2.101 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C1 TB1 A 501 " pdb=" C4 TB1 A 501 " ideal model delta sigma weight residual 1.503 1.529 -0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" C2 EFC A 385 " pdb=" F2 EFC A 385 " ideal model delta sigma weight residual 1.388 1.365 0.023 2.00e-02 2.50e+03 1.38e+00 bond pdb=" C10 TB1 A 501 " pdb=" C7 TB1 A 501 " ideal model delta sigma weight residual 1.548 1.526 0.022 2.00e-02 2.50e+03 1.20e+00 ... (remaining 3177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 4287 1.45 - 2.90: 34 2.90 - 4.35: 5 4.35 - 5.80: 8 5.80 - 7.25: 3 Bond angle restraints: 4337 Sorted by residual: angle pdb=" CB EFC A 385 " pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 101.65 108.90 -7.25 3.00e+00 1.11e-01 5.83e+00 angle pdb=" O1 TB1 A 501 " pdb=" C9 TB1 A 501 " pdb=" O5 TB1 A 501 " ideal model delta sigma weight residual 126.71 119.70 7.01 3.00e+00 1.11e-01 5.47e+00 angle pdb=" O3 TB1 A 501 " pdb=" C10 TB1 A 501 " pdb=" O4 TB1 A 501 " ideal model delta sigma weight residual 126.45 120.01 6.44 3.00e+00 1.11e-01 4.61e+00 angle pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " pdb=" C1 EFC A 385 " ideal model delta sigma weight residual 103.98 109.54 -5.56 3.00e+00 1.11e-01 3.44e+00 angle pdb=" C11 TB1 A 501 " pdb=" C9 TB1 A 501 " pdb=" O5 TB1 A 501 " ideal model delta sigma weight residual 115.01 120.10 -5.09 3.00e+00 1.11e-01 2.88e+00 ... (remaining 4332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.74: 1682 12.74 - 25.49: 131 25.49 - 38.23: 39 38.23 - 50.98: 9 50.98 - 63.72: 9 Dihedral angle restraints: 1870 sinusoidal: 686 harmonic: 1184 Sorted by residual: dihedral pdb=" CB MET A 194 " pdb=" CG MET A 194 " pdb=" SD MET A 194 " pdb=" CE MET A 194 " ideal model delta sinusoidal sigma weight residual 180.00 122.68 57.32 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CB MET A 292 " pdb=" CG MET A 292 " pdb=" SD MET A 292 " pdb=" CE MET A 292 " ideal model delta sinusoidal sigma weight residual -60.00 -113.78 53.78 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CG ARG A 80 " pdb=" CD ARG A 80 " pdb=" NE ARG A 80 " pdb=" CZ ARG A 80 " ideal model delta sinusoidal sigma weight residual -90.00 -129.22 39.22 2 1.50e+01 4.44e-03 8.53e+00 ... (remaining 1867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 387 0.033 - 0.066: 120 0.066 - 0.098: 26 0.098 - 0.131: 8 0.131 - 0.164: 1 Chirality restraints: 542 Sorted by residual: chirality pdb=" C7 TB1 A 501 " pdb=" N TB1 A 501 " pdb=" C10 TB1 A 501 " pdb=" C11 TB1 A 501 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA VAL A 355 " pdb=" N VAL A 355 " pdb=" C VAL A 355 " pdb=" CB VAL A 355 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.09e-01 chirality pdb=" CA MET A 59 " pdb=" N MET A 59 " pdb=" C MET A 59 " pdb=" CB MET A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 539 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 45 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 152 " -0.015 5.00e-02 4.00e+02 2.27e-02 8.26e-01 pdb=" N PRO A 153 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 376 " 0.014 5.00e-02 4.00e+02 2.16e-02 7.48e-01 pdb=" N PRO A 377 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.012 5.00e-02 4.00e+02 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 851 2.81 - 3.33: 3175 3.33 - 3.85: 4814 3.85 - 4.38: 5623 4.38 - 4.90: 9868 Nonbonded interactions: 24331 Sorted by model distance: nonbonded pdb=" OG SER A 278 " pdb=" O3 TB1 A 501 " model vdw 2.287 3.040 nonbonded pdb=" O HOH A 601 " pdb=" O HOH A 604 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.341 3.040 nonbonded pdb=" OD2 ASP A 405 " pdb=" O HOH A 601 " model vdw 2.359 3.040 nonbonded pdb=" N TB1 A 501 " pdb=" O1 TB1 A 501 " model vdw 2.361 3.120 ... (remaining 24326 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: 0.010 Normalize map: mean=0, sd=1: 5.940 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 : 0.002 0.047 3182 Z= 0.153 Angle : 0.451 7.246 4337 Z= 0.208 Chirality : 0.036 0.164 542 Planarity : 0.003 0.031 534 Dihedral : 11.574 63.720 1120 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.39), residues: 413 helix: 1.50 (0.26), residues: 336 sheet: None (None), residues: 0 loop : 0.91 (0.78), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.005 0.001 PHE A 210 TYR 0.013 0.001 TYR A 299 ARG 0.001 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.314 Fit side-chains REVERT: A 174 GLU cc_start: 0.7990 (tp30) cc_final: 0.7645 (tp30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 1.5558 time to fit residues: 63.7484 Evaluate side-chains 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.092632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.069321 restraints weight = 5575.670| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.40 r_work: 0.2783 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3182 Z= 0.225 Angle : 0.493 4.689 4337 Z= 0.269 Chirality : 0.038 0.128 542 Planarity : 0.004 0.029 534 Dihedral : 6.614 57.593 461 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.23 % Allowed : 4.01 % Favored : 94.75 % 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: 3.44 (0.40), residues: 413 helix: 2.60 (0.27), residues: 343 sheet: None (None), residues: 0 loop : 0.63 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 219 PHE 0.009 0.001 PHE A 323 TYR 0.023 0.001 TYR A 299 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.311 Fit side-chains REVERT: A 296 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 311 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7761 (mtp) REVERT: A 390 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7903 (m-30) outliers start: 4 outliers final: 0 residues processed: 37 average time/residue: 1.5485 time to fit residues: 58.7588 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.094242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.071151 restraints weight = 5487.120| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.33 r_work: 0.2804 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3182 Z= 0.182 Angle : 0.447 4.671 4337 Z= 0.240 Chirality : 0.037 0.128 542 Planarity : 0.004 0.029 534 Dihedral : 5.557 45.356 461 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.54 % Allowed : 4.94 % Favored : 93.52 % 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: 3.88 (0.41), residues: 413 helix: 3.00 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.36 (0.69), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.023 0.001 TYR A 299 ARG 0.001 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.701 Fit side-chains REVERT: A 296 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7461 (tm-30) outliers start: 5 outliers final: 1 residues processed: 35 average time/residue: 1.7520 time to fit residues: 62.8413 Evaluate side-chains 32 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.093448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.070314 restraints weight = 5665.639| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.36 r_work: 0.2792 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3182 Z= 0.191 Angle : 0.454 4.642 4337 Z= 0.243 Chirality : 0.037 0.128 542 Planarity : 0.004 0.029 534 Dihedral : 5.102 39.852 461 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.93 % Allowed : 6.79 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.41), residues: 413 helix: 3.06 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.38 (0.69), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.021 0.001 TYR A 299 ARG 0.006 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.377 Fit side-chains REVERT: A 9 GLU cc_start: 0.8829 (mp0) cc_final: 0.8402 (mp0) REVERT: A 291 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8296 (mt-10) REVERT: A 296 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7425 (tm-30) outliers start: 3 outliers final: 1 residues processed: 35 average time/residue: 1.7692 time to fit residues: 63.4192 Evaluate side-chains 33 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 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 = 0.3329 r_free = 0.3329 target = 0.093347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.070358 restraints weight = 5543.841| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.34 r_work: 0.2788 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3182 Z= 0.189 Angle : 0.453 4.653 4337 Z= 0.241 Chirality : 0.037 0.128 542 Planarity : 0.004 0.030 534 Dihedral : 4.672 34.585 461 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.62 % Allowed : 7.72 % Favored : 91.67 % 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: 3.96 (0.41), residues: 413 helix: 3.05 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.42 (0.70), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.021 0.001 TYR A 299 ARG 0.007 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.308 Fit side-chains REVERT: A 5 ARG cc_start: 0.8199 (tpp-160) cc_final: 0.7540 (tpp-160) REVERT: A 9 GLU cc_start: 0.8861 (mp0) cc_final: 0.8509 (mp0) REVERT: A 291 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8306 (mt-10) REVERT: A 296 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7435 (tm-30) outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 1.5796 time to fit residues: 55.0401 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.093043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.069758 restraints weight = 5726.865| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.38 r_work: 0.2781 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3182 Z= 0.191 Angle : 0.451 4.644 4337 Z= 0.241 Chirality : 0.037 0.127 542 Planarity : 0.004 0.030 534 Dihedral : 4.458 32.014 461 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.93 % Allowed : 9.26 % Favored : 89.81 % 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: 3.99 (0.41), residues: 413 helix: 3.08 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.38 (0.70), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.021 0.001 TYR A 299 ARG 0.006 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.341 Fit side-chains REVERT: A 5 ARG cc_start: 0.8193 (tpp-160) cc_final: 0.7425 (tpp-160) REVERT: A 9 GLU cc_start: 0.8897 (mp0) cc_final: 0.8482 (mp0) REVERT: A 291 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8270 (mt-10) REVERT: A 296 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7445 (tm-30) outliers start: 3 outliers final: 1 residues processed: 35 average time/residue: 1.7001 time to fit residues: 61.0538 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.094621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.071641 restraints weight = 5491.200| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.33 r_work: 0.2813 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3182 Z= 0.169 Angle : 0.441 5.137 4337 Z= 0.234 Chirality : 0.036 0.125 542 Planarity : 0.004 0.030 534 Dihedral : 4.241 28.674 461 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.93 % Allowed : 8.95 % Favored : 90.12 % 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: 4.08 (0.41), residues: 413 helix: 3.14 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.42 (0.71), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.020 0.001 TYR A 299 ARG 0.006 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.342 Fit side-chains REVERT: A 5 ARG cc_start: 0.8191 (tpp-160) cc_final: 0.7382 (tpp-160) REVERT: A 9 GLU cc_start: 0.8907 (mp0) cc_final: 0.8466 (mp0) REVERT: A 291 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8264 (mt-10) REVERT: A 296 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7389 (tm-30) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 1.6157 time to fit residues: 59.6699 Evaluate side-chains 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 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 = 0.3326 r_free = 0.3326 target = 0.092909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.069742 restraints weight = 5567.352| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.39 r_work: 0.2801 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.003 0.033 3182 Z= 0.196 Angle : 0.462 5.393 4337 Z= 0.245 Chirality : 0.037 0.127 542 Planarity : 0.004 0.030 534 Dihedral : 4.273 29.676 461 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.31 % Allowed : 10.49 % Favored : 89.20 % 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: 4.02 (0.41), residues: 413 helix: 3.09 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.44 (0.72), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.020 0.001 TYR A 299 ARG 0.005 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.360 Fit side-chains REVERT: A 5 ARG cc_start: 0.8227 (tpp-160) cc_final: 0.7387 (tpp-160) REVERT: A 9 GLU cc_start: 0.8926 (mp0) cc_final: 0.8459 (mp0) REVERT: A 291 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8287 (mt-10) REVERT: A 296 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7467 (tm-30) outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 1.6677 time to fit residues: 59.8429 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 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 = 0.3327 r_free = 0.3327 target = 0.092950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.069835 restraints weight = 5549.946| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.34 r_work: 0.2785 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3182 Z= 0.199 Angle : 0.466 6.480 4337 Z= 0.248 Chirality : 0.037 0.127 542 Planarity : 0.004 0.030 534 Dihedral : 4.239 29.064 461 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.62 % Allowed : 10.19 % Favored : 89.20 % 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: 4.02 (0.41), residues: 413 helix: 3.10 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.41 (0.72), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.020 0.001 TYR A 299 ARG 0.005 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.352 Fit side-chains REVERT: A 5 ARG cc_start: 0.8202 (tpp-160) cc_final: 0.7229 (tpp-160) REVERT: A 9 GLU cc_start: 0.8925 (mp0) cc_final: 0.8214 (mp0) REVERT: A 291 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 296 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7428 (tm-30) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 1.5838 time to fit residues: 56.8486 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.093920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.070982 restraints weight = 5500.846| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.33 r_work: 0.2823 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3182 Z= 0.176 Angle : 0.453 6.075 4337 Z= 0.240 Chirality : 0.036 0.125 542 Planarity : 0.004 0.030 534 Dihedral : 4.155 27.589 461 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.31 % Allowed : 10.49 % Favored : 89.20 % 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: 4.07 (0.41), residues: 413 helix: 3.13 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.41 (0.72), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.020 0.001 TYR A 299 ARG 0.005 0.001 ARG A 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.303 Fit side-chains REVERT: A 5 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.7195 (tpp-160) REVERT: A 9 GLU cc_start: 0.8904 (mp0) cc_final: 0.8231 (mp0) REVERT: A 291 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8236 (mt-10) REVERT: A 296 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7397 (tm-30) outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 1.5664 time to fit residues: 57.8209 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.092226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.069121 restraints weight = 5599.277| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.34 r_work: 0.2771 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3182 Z= 0.209 Angle : 0.479 6.832 4337 Z= 0.254 Chirality : 0.037 0.128 542 Planarity : 0.004 0.030 534 Dihedral : 4.226 29.036 461 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.31 % Allowed : 10.80 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.00 (0.41), residues: 413 helix: 3.12 (0.28), residues: 338 sheet: None (None), residues: 0 loop : 0.29 (0.69), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.008 0.001 PHE A 156 TYR 0.021 0.001 TYR A 299 ARG 0.005 0.001 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2912.39 seconds wall clock time: 50 minutes 27.54 seconds (3027.54 seconds total)