Starting phenix.real_space_refine on Tue Mar 3 11:26:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ugj_26489/03_2026/7ugj_26489.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugj_26489/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ugj_26489/03_2026/7ugj_26489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugj_26489/03_2026/7ugj_26489.map" model { file = "/net/cci-nas-00/data/ceres_data/7ugj_26489/03_2026/7ugj_26489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugj_26489/03_2026/7ugj_26489.cif" } 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-5986/lib/python3.9/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: 0.98, per 1000 atoms: 0.32 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: 0.31 Conformation dependent library (CDL) restraints added in 142.2 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: 0.12 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: 0.34 Time building geometry restraints manager: 0.41 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 - 17.49: 1749 17.49 - 34.98: 82 34.98 - 52.47: 14 52.47 - 69.96: 3 69.96 - 87.46: 2 Dihedral angle restraints: 1850 sinusoidal: 672 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 1847 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: 4.860 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: 5.400 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 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 : 10.716 87.456 1104 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 covalent geometry : bond 0.00234 ( 3155) covalent geometry : angle 0.49811 ( 4303) hydrogen bonds : bond 0.31458 ( 245) hydrogen bonds : angle 6.97724 ( 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 : 0.108 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: 0.5376 time to fit residues: 29.3100 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 : 0.110 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.109287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.073973 restraints weight = 5833.619| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.39 r_work: 0.2935 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2249 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= 0.183 Angle : 0.582 5.454 4303 Z= 0.324 Chirality : 0.040 0.161 537 Planarity : 0.004 0.041 532 Dihedral : 7.492 66.200 459 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.59 % Allowed : 7.30 % Favored : 91.11 % 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: 2.95 (0.39), residues: 411 helix: 2.26 (0.26), residues: 350 sheet: None (None), residues: 0 loop : 0.20 (0.76), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 77 TYR 0.013 0.002 TYR A 299 PHE 0.010 0.001 PHE A 323 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3155) covalent geometry : angle 0.58248 ( 4303) hydrogen bonds : bond 0.09286 ( 245) hydrogen bonds : angle 4.94335 ( 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 46 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.125 Fit side-chains REVERT: A 48 ASP cc_start: 0.8683 (m-30) cc_final: 0.8448 (m-30) outliers start: 5 outliers final: 3 residues processed: 44 average time/residue: 0.5621 time to fit residues: 25.3724 Evaluate side-chains 36 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE 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: 0.6980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.111351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.076885 restraints weight = 5860.619| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.35 r_work: 0.2984 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3155 Z= 0.155 Angle : 0.522 5.420 4303 Z= 0.281 Chirality : 0.038 0.175 537 Planarity : 0.004 0.047 532 Dihedral : 6.910 61.098 459 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.54 % Allowed : 11.43 % Favored : 86.03 % 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: 3.06 (0.40), residues: 411 helix: 2.36 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.00 (0.78), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 5 TYR 0.008 0.001 TYR A 236 PHE 0.007 0.001 PHE A 323 HIS 0.001 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3155) covalent geometry : angle 0.52191 ( 4303) hydrogen bonds : bond 0.07024 ( 245) hydrogen bonds : angle 4.37001 ( 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 51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.123 Fit side-chains REVERT: A 48 ASP cc_start: 0.8602 (m-30) cc_final: 0.8346 (m-30) outliers start: 8 outliers final: 3 residues processed: 48 average time/residue: 0.5230 time to fit residues: 25.8605 Evaluate side-chains 36 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE 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: 2.9990 chunk 35 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.112540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076555 restraints weight = 5824.263| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.41 r_work: 0.2970 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3155 Z= 0.148 Angle : 0.538 6.517 4303 Z= 0.282 Chirality : 0.038 0.191 537 Planarity : 0.004 0.047 532 Dihedral : 6.650 59.419 459 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.22 % Allowed : 13.97 % 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: 3.14 (0.41), residues: 411 helix: 2.48 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.34 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 77 TYR 0.012 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 covalent geometry : bond 0.00305 ( 3155) covalent geometry : angle 0.53836 ( 4303) hydrogen bonds : bond 0.06512 ( 245) hydrogen bonds : angle 4.23070 ( 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 44 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.085 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 42 average time/residue: 0.6222 time to fit residues: 26.7978 Evaluate side-chains 38 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE 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: 2.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3648 r_free = 0.3648 target = 0.111230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075560 restraints weight = 5742.911| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.42 r_work: 0.2911 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3155 Z= 0.145 Angle : 0.530 6.507 4303 Z= 0.272 Chirality : 0.038 0.188 537 Planarity : 0.004 0.046 532 Dihedral : 6.609 59.257 459 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.13 % Allowed : 13.97 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.16 (0.41), residues: 411 helix: 2.50 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.40 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 5 TYR 0.011 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 covalent geometry : bond 0.00303 ( 3155) covalent geometry : angle 0.53003 ( 4303) hydrogen bonds : bond 0.06414 ( 245) hydrogen bonds : angle 4.16109 ( 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 53 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.111 Fit side-chains REVERT: A 334 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8140 (p) outliers start: 13 outliers final: 7 residues processed: 47 average time/residue: 0.5338 time to fit residues: 25.8107 Evaluate side-chains 45 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.111898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.075875 restraints weight = 5753.639| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.38 r_work: 0.2968 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3155 Z= 0.142 Angle : 0.544 6.910 4303 Z= 0.277 Chirality : 0.038 0.185 537 Planarity : 0.004 0.046 532 Dihedral : 6.584 59.753 459 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 4.13 % Allowed : 13.97 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.21 (0.41), residues: 411 helix: 2.54 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.39 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 5 TYR 0.008 0.001 TYR A 299 PHE 0.006 0.001 PHE A 323 HIS 0.002 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3155) covalent geometry : angle 0.54369 ( 4303) hydrogen bonds : bond 0.06141 ( 245) hydrogen bonds : angle 4.08836 ( 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 54 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.086 Fit side-chains REVERT: A 334 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8322 (p) outliers start: 13 outliers final: 7 residues processed: 48 average time/residue: 0.5882 time to fit residues: 28.9692 Evaluate side-chains 44 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.0370 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.112448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.076828 restraints weight = 5810.397| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.44 r_work: 0.2959 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3155 Z= 0.136 Angle : 0.547 7.226 4303 Z= 0.277 Chirality : 0.037 0.182 537 Planarity : 0.004 0.043 532 Dihedral : 6.569 59.927 459 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.17 % Allowed : 15.87 % 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: 3.23 (0.41), residues: 411 helix: 2.52 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.31 (0.78), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 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 covalent geometry : bond 0.00278 ( 3155) covalent geometry : angle 0.54678 ( 4303) hydrogen bonds : bond 0.05820 ( 245) hydrogen bonds : angle 4.02964 ( 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 48 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.119 Fit side-chains REVERT: A 334 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8208 (p) outliers start: 10 outliers final: 6 residues processed: 43 average time/residue: 0.5855 time to fit residues: 25.8512 Evaluate side-chains 44 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 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: 0.0270 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.113131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.077415 restraints weight = 5859.366| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.37 r_work: 0.2985 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3155 Z= 0.139 Angle : 0.564 7.285 4303 Z= 0.285 Chirality : 0.038 0.183 537 Planarity : 0.004 0.043 532 Dihedral : 6.548 59.773 459 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.17 % Allowed : 16.51 % 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: 3.20 (0.41), residues: 411 helix: 2.50 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.35 (0.78), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 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 covalent geometry : bond 0.00296 ( 3155) covalent geometry : angle 0.56408 ( 4303) hydrogen bonds : bond 0.05760 ( 245) hydrogen bonds : angle 4.02016 ( 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 49 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.084 Fit side-chains REVERT: A 5 ARG cc_start: 0.8943 (mpt180) cc_final: 0.8646 (mtm180) REVERT: A 334 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8362 (p) outliers start: 10 outliers final: 6 residues processed: 45 average time/residue: 0.5805 time to fit residues: 26.8384 Evaluate side-chains 44 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.112661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.076732 restraints weight = 5865.403| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.46 r_work: 0.2969 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3155 Z= 0.136 Angle : 0.548 7.243 4303 Z= 0.278 Chirality : 0.038 0.180 537 Planarity : 0.004 0.042 532 Dihedral : 6.565 60.487 459 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.86 % Allowed : 17.46 % 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: 3.14 (0.41), residues: 411 helix: 2.45 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.30 (0.78), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 covalent geometry : bond 0.00284 ( 3155) covalent geometry : angle 0.54783 ( 4303) hydrogen bonds : bond 0.05785 ( 245) hydrogen bonds : angle 4.02942 ( 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 48 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.072 Fit side-chains REVERT: A 5 ARG cc_start: 0.8927 (mpt180) cc_final: 0.8616 (mtm180) REVERT: A 334 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8244 (p) outliers start: 9 outliers final: 6 residues processed: 45 average time/residue: 0.5618 time to fit residues: 25.9538 Evaluate side-chains 45 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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 394 ASP 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 25 optimal weight: 0.0020 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.114490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.078840 restraints weight = 5673.743| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.35 r_work: 0.3018 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3155 Z= 0.137 Angle : 0.570 7.134 4303 Z= 0.291 Chirality : 0.038 0.176 537 Planarity : 0.004 0.040 532 Dihedral : 6.618 61.286 459 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.54 % Allowed : 18.10 % Favored : 79.37 % 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: 3.14 (0.41), residues: 411 helix: 2.45 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.27 (0.78), residues: 59 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 covalent geometry : bond 0.00286 ( 3155) covalent geometry : angle 0.57022 ( 4303) hydrogen bonds : bond 0.05516 ( 245) hydrogen bonds : angle 4.05951 ( 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 48 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.139 Fit side-chains REVERT: A 5 ARG cc_start: 0.8946 (mpt180) cc_final: 0.8597 (mtm180) REVERT: A 334 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8378 (p) outliers start: 8 outliers final: 4 residues processed: 44 average time/residue: 0.5727 time to fit residues: 25.8996 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 : 0.081 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.0270 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.113311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077515 restraints weight = 5783.384| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.45 r_work: 0.2948 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3155 Z= 0.138 Angle : 0.559 7.431 4303 Z= 0.285 Chirality : 0.038 0.175 537 Planarity : 0.004 0.038 532 Dihedral : 6.622 61.416 459 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.22 % Allowed : 18.73 % Favored : 79.05 % 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: 3.11 (0.41), residues: 411 helix: 2.42 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.27 (0.79), residues: 59 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 covalent geometry : bond 0.00297 ( 3155) covalent geometry : angle 0.55893 ( 4303) hydrogen bonds : bond 0.05716 ( 245) hydrogen bonds : angle 4.07072 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1556.16 seconds wall clock time: 27 minutes 5.27 seconds (1625.27 seconds total)