Starting phenix.real_space_refine on Wed Jul 1 21:54:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ugj_26489/07_2026/7ugj_26489.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugj_26489/07_2026/7ugj_26489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ugj_26489/07_2026/7ugj_26489.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ugj_26489/07_2026/7ugj_26489.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ugj_26489/07_2026/7ugj_26489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugj_26489/07_2026/7ugj_26489.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ugj_26489/07_2026/7ugj_26489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugj_26489/07_2026/7ugj_26489.map" } resolution = 2.81 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= 0.036 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 16 5.16 5 Na 2 4.78 5 C 2035 2.51 5 N 504 2.21 5 O 537 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 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3095 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3076 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 397} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {' NA': 2, 'TB1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 0.58, per 1000 atoms: 0.19 Number of scatterers: 3095 At special positions: 0 Unit cell: (63.9, 79.236, 83.496, 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 16 16.00 Na 2 11.00 F 1 9.00 O 537 8.00 N 504 7.00 C 2035 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: 0.19 Conformation dependent library (CDL) restraints added in 75.8 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 4.251A pdb=" N LYS A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 8 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 10 " --> pdb=" O LYS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 33 Processing helix chain 'A' and resid 35 through 57 removed outlier: 4.197A pdb=" N LYS A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.663A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 73 Processing helix chain 'A' and resid 74 through 108 removed outlier: 3.552A pdb=" N ARG A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.591A pdb=" N LEU A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 170 removed outlier: 3.506A pdb=" N THR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 3.645A pdb=" N GLY A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.858A 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 222 through 226 removed outlier: 3.579A pdb=" N VAL A 225 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLY A 226 " --> pdb=" O HIS A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 222 through 226' Processing helix chain 'A' and resid 227 through 246 removed outlier: 3.719A pdb=" N VAL A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 257 through 265 removed outlier: 3.614A pdb=" N HIS A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 276 removed outlier: 3.551A pdb=" N PHE A 273 " --> pdb=" O MET A 269 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 293 Proline residue: A 283 - end of helix removed outlier: 3.538A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.144A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 3.712A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.759A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.550A pdb=" N VAL A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 370 removed outlier: 4.062A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 387 removed outlier: 3.779A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 417 removed outlier: 3.885A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 735 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: 0.32 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 983 1.37 - 1.55: 2141 1.55 - 1.73: 0 1.73 - 1.92: 30 1.92 - 2.10: 1 Bond restraints: 3155 Sorted by residual: 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=" C EFC A 385 " pdb=" O EFC A 385 " ideal model delta sigma weight residual 1.231 1.185 0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C1 TB1 A 501 " pdb=" C4 TB1 A 501 " ideal model delta sigma weight residual 1.503 1.528 -0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" C2 EFC A 385 " pdb=" F2 EFC A 385 " ideal model delta sigma weight residual 1.388 1.364 0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" C1 EFC A 385 " pdb=" C2 EFC A 385 " ideal model delta sigma weight residual 1.506 1.526 -0.020 2.00e-02 2.50e+03 1.05e+00 ... (remaining 3150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 4254 1.79 - 3.58: 33 3.58 - 5.36: 12 5.36 - 7.15: 3 7.15 - 8.94: 1 Bond angle restraints: 4303 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 101.65 110.59 -8.94 3.00e+00 1.11e-01 8.88e+00 angle pdb=" C LEU A 245 " pdb=" N VAL A 246 " pdb=" CA VAL A 246 " ideal model delta sigma weight residual 122.97 120.65 2.32 9.80e-01 1.04e+00 5.63e+00 angle pdb=" O1 TB1 A 501 " pdb=" C9 TB1 A 501 " pdb=" O5 TB1 A 501 " ideal model delta sigma weight residual 126.71 119.71 7.00 3.00e+00 1.11e-01 5.44e+00 angle pdb=" O3 TB1 A 501 " pdb=" C10 TB1 A 501 " pdb=" O4 TB1 A 501 " ideal model delta sigma weight residual 126.45 119.88 6.57 3.00e+00 1.11e-01 4.80e+00 angle pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " pdb=" C1 EFC A 385 " ideal model delta sigma weight residual 103.98 110.34 -6.36 3.00e+00 1.11e-01 4.50e+00 ... (remaining 4298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.85: 1711 12.85 - 25.70: 80 25.70 - 38.55: 35 38.55 - 51.40: 6 51.40 - 64.25: 3 Dihedral angle restraints: 1835 sinusoidal: 657 harmonic: 1178 Sorted by residual: dihedral pdb=" CB MET A 59 " pdb=" CG MET A 59 " pdb=" SD MET A 59 " pdb=" CE MET A 59 " ideal model delta sinusoidal sigma weight residual 180.00 122.19 57.81 3 1.50e+01 4.44e-03 9.45e+00 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 180.00 123.09 56.91 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA ARG A 105 " pdb=" CB ARG A 105 " pdb=" CG ARG A 105 " pdb=" CD ARG A 105 " ideal model delta sinusoidal sigma weight residual -180.00 -135.03 -44.97 3 1.50e+01 4.44e-03 8.09e+00 ... (remaining 1832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 344 0.028 - 0.055: 127 0.055 - 0.083: 45 0.083 - 0.111: 19 0.111 - 0.138: 2 Chirality restraints: 537 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 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA PRO A 45 " pdb=" N PRO A 45 " pdb=" C PRO A 45 " pdb=" CB PRO A 45 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.13e-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 2.41 0.10 2.00e-01 2.50e+01 2.66e-01 ... (remaining 534 not shown) Planarity restraints: 532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 45 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.015 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 VAL A 355 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 356 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 376 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.04e-01 pdb=" N PRO A 377 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.013 5.00e-02 4.00e+02 ... (remaining 529 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 824 2.81 - 3.33: 3277 3.33 - 3.85: 4667 3.85 - 4.38: 5570 4.38 - 4.90: 9580 Nonbonded interactions: 23918 Sorted by model distance: nonbonded pdb=" N TB1 A 501 " pdb=" O1 TB1 A 501 " model vdw 2.285 3.120 nonbonded pdb=" OG1 THR A 92 " pdb="NA NA A 503 " model vdw 2.348 2.470 nonbonded pdb=" OD1 ASN A 378 " pdb=" N VAL A 379 " model vdw 2.414 3.120 nonbonded pdb=" O VAL A 346 " pdb=" OG SER A 349 " model vdw 2.444 3.040 nonbonded pdb=" O ASN A 401 " pdb="NA NA A 502 " model vdw 2.463 2.470 ... (remaining 23913 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: 4.820 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: 0.000 Set scattering table: 0.010 Process input model: 3.420 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:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 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 3155 Z= 0.113 Angle : 0.498 8.940 4303 Z= 0.234 Chirality : 0.035 0.138 537 Planarity : 0.003 0.030 532 Dihedral : 9.696 64.251 1089 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 2.01 (0.39), residues: 411 helix: 1.51 (0.26), residues: 331 sheet: None (None), residues: 0 loop : 0.92 (0.75), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.008 0.001 TYR A 7 PHE 0.005 0.001 PHE A 261 HIS 0.001 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 3155) covalent geometry : angle 0.49811 / 0.23 ( 4303) hydrogen bonds : bond 0.31458 / 20.64 ( 245) hydrogen bonds : angle 6.97724 / 5.22 ( 735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.117 Fit side-chains REVERT: A 108 ASN cc_start: 0.8987 (t0) cc_final: 0.8729 (t0) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.4440 time to fit residues: 24.2608 Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.075 ------------------------------------------------------------------------------- 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: 0.8980 chunk 26 optimal weight: 0.0370 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.110354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.075869 restraints weight = 5859.469| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.33 r_work: 0.2938 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3155 Z= 0.188 Angle : 0.589 4.791 4303 Z= 0.328 Chirality : 0.040 0.160 537 Planarity : 0.005 0.045 532 Dihedral : 5.016 60.840 444 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.59 % Allowed : 6.98 % Favored : 91.43 % 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: 3.02 (0.40), residues: 411 helix: 2.31 (0.26), residues: 350 sheet: None (None), residues: 0 loop : 0.19 (0.76), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 77 TYR 0.013 0.002 TYR A 89 PHE 0.009 0.001 PHE A 323 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.19 ( 3155) covalent geometry : angle 0.58893 / 0.33 ( 4303) hydrogen bonds : bond 0.09079 / 6.03 ( 245) hydrogen bonds : angle 4.94050 / 3.67 ( 735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.091 Fit side-chains REVERT: A 48 ASP cc_start: 0.8659 (m-30) cc_final: 0.8420 (m-30) outliers start: 5 outliers final: 2 residues processed: 45 average time/residue: 0.3900 time to fit residues: 18.0273 Evaluate side-chains 36 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 0.0000 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.111856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.077466 restraints weight = 5847.645| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.35 r_work: 0.2996 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3155 Z= 0.150 Angle : 0.533 6.621 4303 Z= 0.280 Chirality : 0.038 0.143 537 Planarity : 0.004 0.050 532 Dihedral : 4.510 52.115 444 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 2.54 % Allowed : 12.38 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.08 (0.41), residues: 411 helix: 2.33 (0.27), residues: 357 sheet: None (None), residues: 0 loop : 0.11 (0.85), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 77 TYR 0.010 0.001 TYR A 299 PHE 0.009 0.001 PHE A 323 HIS 0.001 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 ( 3155) covalent geometry : angle 0.53332 / 0.28 ( 4303) hydrogen bonds : bond 0.06866 / 4.57 ( 245) hydrogen bonds : angle 4.35862 / 3.27 ( 735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.125 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.5202 time to fit residues: 25.0904 Evaluate side-chains 40 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.111344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.074975 restraints weight = 5789.774| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.39 r_work: 0.2941 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3155 Z= 0.155 Angle : 0.534 6.576 4303 Z= 0.279 Chirality : 0.038 0.152 537 Planarity : 0.004 0.048 532 Dihedral : 4.241 46.594 444 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.86 % Allowed : 13.33 % Favored : 83.81 % 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: 3.10 (0.41), residues: 411 helix: 2.44 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.31 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 77 TYR 0.010 0.001 TYR A 299 PHE 0.006 0.001 PHE A 301 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 3155) covalent geometry : angle 0.53447 / 0.28 ( 4303) hydrogen bonds : bond 0.06861 / 4.60 ( 245) hydrogen bonds : angle 4.28721 / 3.23 ( 735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.078 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 44 average time/residue: 0.6038 time to fit residues: 27.1984 Evaluate side-chains 42 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS A 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.110734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.074885 restraints weight = 5735.176| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.43 r_work: 0.2922 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3155 Z= 0.146 Angle : 0.512 6.218 4303 Z= 0.267 Chirality : 0.037 0.142 537 Planarity : 0.004 0.047 532 Dihedral : 4.128 40.941 444 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 4.13 % Allowed : 14.60 % Favored : 81.27 % 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: 3.03 (0.41), residues: 411 helix: 2.34 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -0.23 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 77 TYR 0.009 0.001 TYR A 299 PHE 0.006 0.001 PHE A 323 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 3155) covalent geometry : angle 0.51247 / 0.27 ( 4303) hydrogen bonds : bond 0.06513 / 4.36 ( 245) hydrogen bonds : angle 4.19082 / 3.15 ( 735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.128 Fit side-chains REVERT: A 334 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8145 (p) outliers start: 13 outliers final: 8 residues processed: 46 average time/residue: 0.5519 time to fit residues: 26.1238 Evaluate side-chains 44 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.112168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.076236 restraints weight = 5734.189| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.34 r_work: 0.2969 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3155 Z= 0.138 Angle : 0.518 6.495 4303 Z= 0.269 Chirality : 0.037 0.134 537 Planarity : 0.004 0.046 532 Dihedral : 4.041 37.252 444 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.81 % Allowed : 15.24 % Favored : 80.95 % 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: 3.09 (0.41), residues: 411 helix: 2.39 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -0.24 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 77 TYR 0.010 0.001 TYR A 299 PHE 0.006 0.001 PHE A 323 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 3155) covalent geometry : angle 0.51780 / 0.27 ( 4303) hydrogen bonds : bond 0.06095 / 4.08 ( 245) hydrogen bonds : angle 4.09242 / 3.09 ( 735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.075 Fit side-chains REVERT: A 334 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8410 (p) outliers start: 12 outliers final: 6 residues processed: 46 average time/residue: 0.5429 time to fit residues: 25.5670 Evaluate side-chains 42 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.111153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.075255 restraints weight = 5812.802| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.44 r_work: 0.2927 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3155 Z= 0.145 Angle : 0.530 6.475 4303 Z= 0.277 Chirality : 0.037 0.133 537 Planarity : 0.004 0.045 532 Dihedral : 3.967 33.547 444 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.81 % Allowed : 15.87 % Favored : 80.32 % 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: 3.02 (0.41), residues: 411 helix: 2.30 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.13 (0.85), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 287 TYR 0.011 0.001 TYR A 299 PHE 0.005 0.001 PHE A 156 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 3155) covalent geometry : angle 0.53017 / 0.28 ( 4303) hydrogen bonds : bond 0.06235 / 4.18 ( 245) hydrogen bonds : angle 4.10675 / 3.09 ( 735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.074 Fit side-chains REVERT: A 334 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8181 (p) outliers start: 12 outliers final: 7 residues processed: 42 average time/residue: 0.4405 time to fit residues: 19.0155 Evaluate side-chains 43 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.111994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.075696 restraints weight = 5851.862| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.40 r_work: 0.2963 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3155 Z= 0.141 Angle : 0.536 6.818 4303 Z= 0.280 Chirality : 0.037 0.131 537 Planarity : 0.004 0.043 532 Dihedral : 3.953 31.597 444 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.44 % Allowed : 15.87 % Favored : 79.68 % 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: 3.01 (0.41), residues: 411 helix: 2.30 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.16 (0.85), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 287 TYR 0.010 0.001 TYR A 299 PHE 0.006 0.001 PHE A 156 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 3155) covalent geometry : angle 0.53568 / 0.28 ( 4303) hydrogen bonds : bond 0.06011 / 4.03 ( 245) hydrogen bonds : angle 4.07935 / 3.07 ( 735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.119 Fit side-chains REVERT: A 334 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8340 (p) outliers start: 14 outliers final: 9 residues processed: 42 average time/residue: 0.4181 time to fit residues: 18.0630 Evaluate side-chains 45 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.0470 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.0270 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.113244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.077727 restraints weight = 5843.881| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.46 r_work: 0.2953 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3155 Z= 0.129 Angle : 0.518 6.983 4303 Z= 0.269 Chirality : 0.036 0.121 537 Planarity : 0.004 0.040 532 Dihedral : 3.898 28.771 444 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.17 % Allowed : 16.83 % Favored : 80.00 % 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: 3.15 (0.41), residues: 411 helix: 2.45 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.25 (0.78), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 287 TYR 0.008 0.001 TYR A 299 PHE 0.006 0.001 PHE A 156 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 3155) covalent geometry : angle 0.51842 / 0.27 ( 4303) hydrogen bonds : bond 0.05437 / 3.65 ( 245) hydrogen bonds : angle 3.99490 / 3.01 ( 735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.071 Fit side-chains REVERT: A 334 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8201 (p) outliers start: 10 outliers final: 4 residues processed: 43 average time/residue: 0.4931 time to fit residues: 21.7514 Evaluate side-chains 43 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.0170 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.113414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.077464 restraints weight = 5688.773| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.34 r_work: 0.2994 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3155 Z= 0.137 Angle : 0.546 7.057 4303 Z= 0.284 Chirality : 0.036 0.122 537 Planarity : 0.004 0.039 532 Dihedral : 3.859 26.419 444 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.54 % Allowed : 18.73 % Favored : 78.73 % 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: 3.08 (0.41), residues: 411 helix: 2.34 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.07 (0.85), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 287 TYR 0.009 0.001 TYR A 299 PHE 0.006 0.001 PHE A 156 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 3155) covalent geometry : angle 0.54637 / 0.28 ( 4303) hydrogen bonds : bond 0.05632 / 3.78 ( 245) hydrogen bonds : angle 4.00724 / 3.02 ( 735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.123 Fit side-chains REVERT: A 334 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8359 (p) outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 0.5558 time to fit residues: 23.9623 Evaluate side-chains 44 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.0870 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.109144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.072443 restraints weight = 5803.246| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.42 r_work: 0.2890 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3155 Z= 0.179 Angle : 0.564 6.598 4303 Z= 0.297 Chirality : 0.038 0.143 537 Planarity : 0.004 0.039 532 Dihedral : 3.890 24.250 444 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.54 % Allowed : 18.73 % Favored : 78.73 % 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: 2.79 (0.41), residues: 411 helix: 2.16 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -0.23 (0.85), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 287 TYR 0.012 0.001 TYR A 299 PHE 0.008 0.001 PHE A 301 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 3155) covalent geometry : angle 0.56368 / 0.30 ( 4303) hydrogen bonds : bond 0.07193 / 4.83 ( 245) hydrogen bonds : angle 4.25510 / 3.19 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1214.64 seconds wall clock time: 21 minutes 24.46 seconds (1284.46 seconds total)