Starting phenix.real_space_refine on Tue Mar 3 11:27:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ug0_26482/03_2026/7ug0_26482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ug0_26482/03_2026/7ug0_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ug0_26482/03_2026/7ug0_26482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ug0_26482/03_2026/7ug0_26482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ug0_26482/03_2026/7ug0_26482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ug0_26482/03_2026/7ug0_26482.map" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.92, per 1000 atoms: 0.29 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: 0.31 Conformation dependent library (CDL) restraints added in 272.1 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: 0.09 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: 0.56 Time building geometry restraints manager: 0.42 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: 0.000 Normalize map: mean=0, sd=1: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.020 Find NCS groups from input model: 0.010 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.640 ------------------------------------------------------------------------------- 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= 0.112 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG A 395 TYR 0.013 0.001 TYR A 299 PHE 0.005 0.001 PHE A 210 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3182) covalent geometry : angle 0.45145 ( 4337) hydrogen bonds : bond 0.28026 ( 250) hydrogen bonds : angle 6.14949 ( 750) *********************** 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 : 0.117 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: 0.7131 time to fit residues: 29.1410 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 : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.093717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.070290 restraints weight = 5613.749| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.42 r_work: 0.2785 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3182 Z= 0.149 Angle : 0.477 4.675 4337 Z= 0.261 Chirality : 0.038 0.127 542 Planarity : 0.004 0.029 534 Dihedral : 6.605 56.648 461 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.23 % Allowed : 3.70 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.56 (0.40), residues: 413 helix: 2.68 (0.27), residues: 343 sheet: None (None), residues: 0 loop : 0.69 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.022 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.003 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3182) covalent geometry : angle 0.47694 ( 4337) hydrogen bonds : bond 0.07128 ( 250) hydrogen bonds : angle 3.82549 ( 750) *********************** 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 : 0.069 Fit side-chains REVERT: A 296 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7680 (tm-30) REVERT: A 311 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7685 (mtp) REVERT: A 390 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7773 (m-30) outliers start: 4 outliers final: 0 residues processed: 37 average time/residue: 0.7079 time to fit residues: 26.7596 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 : 0.114 ------------------------------------------------------------------------------- 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 0 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.092932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.069714 restraints weight = 5607.627| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.36 r_work: 0.2805 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3182 Z= 0.146 Angle : 0.459 4.673 4337 Z= 0.247 Chirality : 0.037 0.130 542 Planarity : 0.004 0.029 534 Dihedral : 5.585 46.179 461 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.85 (0.41), residues: 413 helix: 2.97 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.40 (0.69), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 80 TYR 0.023 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3182) covalent geometry : angle 0.45903 ( 4337) hydrogen bonds : bond 0.06787 ( 250) hydrogen bonds : angle 3.63331 ( 750) *********************** 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 40 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.119 Fit side-chains REVERT: A 296 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7500 (tm-30) outliers start: 5 outliers final: 1 residues processed: 37 average time/residue: 0.7921 time to fit residues: 29.9543 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 : 0.115 ------------------------------------------------------------------------------- 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 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.093480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.070458 restraints weight = 5544.094| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.33 r_work: 0.2819 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2523 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= 0.139 Angle : 0.463 4.651 4337 Z= 0.248 Chirality : 0.037 0.129 542 Planarity : 0.004 0.031 534 Dihedral : 5.043 39.098 461 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.23 % Allowed : 6.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.95 (0.41), residues: 413 helix: 3.05 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.35 (0.69), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 287 TYR 0.022 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3182) covalent geometry : angle 0.46325 ( 4337) hydrogen bonds : bond 0.06238 ( 250) hydrogen bonds : angle 3.51289 ( 750) *********************** 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 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.109 Fit side-chains REVERT: A 9 GLU cc_start: 0.8605 (mp0) cc_final: 0.8275 (mp0) REVERT: A 291 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8324 (mt-10) REVERT: A 296 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7437 (tm-30) outliers start: 4 outliers final: 1 residues processed: 36 average time/residue: 0.7182 time to fit residues: 26.5516 Evaluate side-chains 34 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 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 = 0.3326 r_free = 0.3326 target = 0.093009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.069809 restraints weight = 5587.042| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.41 r_work: 0.2773 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2559 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= 0.139 Angle : 0.462 4.641 4337 Z= 0.246 Chirality : 0.037 0.128 542 Planarity : 0.004 0.029 534 Dihedral : 4.652 34.438 461 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.62 % Allowed : 8.02 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.94 (0.41), residues: 413 helix: 3.03 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.40 (0.70), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 287 TYR 0.021 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3182) covalent geometry : angle 0.46159 ( 4337) hydrogen bonds : bond 0.06242 ( 250) hydrogen bonds : angle 3.47825 ( 750) *********************** 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 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.181 Fit side-chains REVERT: A 9 GLU cc_start: 0.8646 (mp0) cc_final: 0.8219 (mp0) REVERT: A 291 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8283 (mt-10) REVERT: A 296 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7468 (tm-30) outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 0.7918 time to fit residues: 28.3779 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 : 0.114 ------------------------------------------------------------------------------- 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 32 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.095378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.072440 restraints weight = 5553.392| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.35 r_work: 0.2852 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3182 Z= 0.122 Angle : 0.436 4.625 4337 Z= 0.231 Chirality : 0.036 0.125 542 Planarity : 0.004 0.030 534 Dihedral : 4.295 29.262 461 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.54 % Allowed : 8.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.09 (0.41), residues: 413 helix: 3.13 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.46 (0.71), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 287 TYR 0.020 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 3182) covalent geometry : angle 0.43572 ( 4337) hydrogen bonds : bond 0.05399 ( 250) hydrogen bonds : angle 3.34194 ( 750) *********************** 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 39 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.169 Fit side-chains REVERT: A 9 GLU cc_start: 0.8670 (mp0) cc_final: 0.8138 (mp0) REVERT: A 291 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8250 (mt-10) REVERT: A 296 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7405 (tm-30) outliers start: 5 outliers final: 2 residues processed: 35 average time/residue: 0.6946 time to fit residues: 24.8988 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 : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.0670 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.094626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.071713 restraints weight = 5546.341| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.34 r_work: 0.2823 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2780 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= 0.125 Angle : 0.439 4.644 4337 Z= 0.232 Chirality : 0.036 0.126 542 Planarity : 0.004 0.030 534 Dihedral : 4.217 28.473 461 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.31 % Allowed : 9.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.04 (0.41), residues: 413 helix: 3.12 (0.28), residues: 341 sheet: None (None), residues: 0 loop : 0.31 (0.71), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.020 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3182) covalent geometry : angle 0.43920 ( 4337) hydrogen bonds : bond 0.05648 ( 250) hydrogen bonds : angle 3.35096 ( 750) *********************** 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 34 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.114 Fit side-chains REVERT: A 9 GLU cc_start: 0.8683 (mp0) cc_final: 0.8121 (mp0) REVERT: A 291 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 296 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7390 (tm-30) outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.7963 time to fit residues: 27.6955 Evaluate side-chains 34 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 11 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.092047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.069047 restraints weight = 5711.657| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.35 r_work: 0.2773 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3182 Z= 0.148 Angle : 0.460 4.683 4337 Z= 0.245 Chirality : 0.037 0.129 542 Planarity : 0.004 0.030 534 Dihedral : 4.325 30.397 461 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.93 % Allowed : 9.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.94 (0.41), residues: 413 helix: 3.07 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.19 (0.70), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.021 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3182) covalent geometry : angle 0.45974 ( 4337) hydrogen bonds : bond 0.06561 ( 250) hydrogen bonds : angle 3.48517 ( 750) *********************** 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 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8279 (mt-10) REVERT: A 296 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7491 (tm-30) outliers start: 3 outliers final: 1 residues processed: 35 average time/residue: 0.7911 time to fit residues: 28.2785 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 : 0.114 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.0370 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.093860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.070943 restraints weight = 5613.816| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.36 r_work: 0.2807 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3182 Z= 0.130 Angle : 0.458 6.312 4337 Z= 0.242 Chirality : 0.036 0.126 542 Planarity : 0.004 0.030 534 Dihedral : 4.162 27.495 461 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.41), residues: 413 helix: 3.12 (0.28), residues: 341 sheet: None (None), residues: 0 loop : 0.22 (0.71), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.020 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3182) covalent geometry : angle 0.45778 ( 4337) hydrogen bonds : bond 0.05694 ( 250) hydrogen bonds : angle 3.36864 ( 750) *********************** 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 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8252 (mt-10) REVERT: A 296 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7411 (tm-30) outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.7931 time to fit residues: 28.3694 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 : 0.120 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 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 = 0.3326 r_free = 0.3326 target = 0.092907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.069981 restraints weight = 5570.176| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.35 r_work: 0.2785 rms_B_bonded: 3.00 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: 0.8378 moved from start: 0.2721 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= 0.137 Angle : 0.467 6.140 4337 Z= 0.247 Chirality : 0.037 0.127 542 Planarity : 0.004 0.030 534 Dihedral : 4.184 28.141 461 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.62 % Allowed : 10.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.00 (0.41), residues: 413 helix: 3.10 (0.28), residues: 341 sheet: None (None), residues: 0 loop : 0.20 (0.71), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.020 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3182) covalent geometry : angle 0.46677 ( 4337) hydrogen bonds : bond 0.06047 ( 250) hydrogen bonds : angle 3.40094 ( 750) ********************** 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: 2 poor density : 34 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 296 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7437 (tm-30) outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 0.7892 time to fit residues: 29.0435 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 : 0.116 ------------------------------------------------------------------------------- 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 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.093228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.070320 restraints weight = 5608.518| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.35 r_work: 0.2792 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2724 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= 0.135 Angle : 0.468 6.846 4337 Z= 0.247 Chirality : 0.036 0.127 542 Planarity : 0.004 0.030 534 Dihedral : 4.143 27.460 461 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.62 % Allowed : 10.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.01 (0.41), residues: 413 helix: 3.12 (0.28), residues: 341 sheet: None (None), residues: 0 loop : 0.17 (0.71), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.020 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3182) covalent geometry : angle 0.46785 ( 4337) hydrogen bonds : bond 0.05914 ( 250) hydrogen bonds : angle 3.38619 ( 750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1424.13 seconds wall clock time: 24 minutes 55.04 seconds (1495.04 seconds total)