Starting phenix.real_space_refine on Tue Mar 3 13:47:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ugd_26487/03_2026/7ugd_26487.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugd_26487/03_2026/7ugd_26487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ugd_26487/03_2026/7ugd_26487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugd_26487/03_2026/7ugd_26487.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ugd_26487/03_2026/7ugd_26487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugd_26487/03_2026/7ugd_26487.map" } resolution = 2.95 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= 0.003 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2943 atoms to isotropic. 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 3 4.78 5 C 2023 2.51 5 N 501 2.21 5 O 535 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 1 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: 3079 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3076 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 396} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' NA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 0.84, per 1000 atoms: 0.27 Number of scatterers: 3079 At special positions: 0 Unit cell: (71.568, 74.976, 73.272, 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 3 11.00 F 1 9.00 O 535 8.00 N 501 7.00 C 2023 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: 0.30 Conformation dependent library (CDL) restraints added in 105.4 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.833A pdb=" N TYR A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.632A pdb=" N VAL A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.744A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (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 74 removed outlier: 3.697A pdb=" N SER A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 108 removed outlier: 4.123A pdb=" N LYS A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 151 through 170 removed outlier: 3.510A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 218 removed outlier: 3.595A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.519A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 246 removed outlier: 3.841A pdb=" N GLY A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 265 through 276 removed outlier: 3.563A pdb=" N MET A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.548A pdb=" N LYS A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 301 through 310 removed outlier: 4.493A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.535A pdb=" N ALA A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 4.086A pdb=" N VAL A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 370 removed outlier: 4.050A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.530A pdb=" N EFC A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 389 " --> pdb=" O EFC A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 416 removed outlier: 3.854A pdb=" N ARG A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 690 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: 0.29 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 972 1.37 - 1.55: 2133 1.55 - 1.73: 0 1.73 - 1.92: 30 1.92 - 2.10: 1 Bond restraints: 3136 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 5.46e+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 5.40e+00 bond pdb=" C SER A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.79e+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 1.39e+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 1.03e+00 ... (remaining 3131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 4225 1.49 - 2.97: 35 2.97 - 4.46: 10 4.46 - 5.94: 6 5.94 - 7.43: 1 Bond angle restraints: 4277 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 101.65 109.08 -7.43 3.00e+00 1.11e-01 6.13e+00 angle pdb=" CA ARG A 77 " pdb=" CB ARG A 77 " pdb=" CG ARG A 77 " ideal model delta sigma weight residual 114.10 118.52 -4.42 2.00e+00 2.50e-01 4.88e+00 angle pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " pdb=" C1 EFC A 385 " ideal model delta sigma weight residual 103.98 109.40 -5.42 3.00e+00 1.11e-01 3.27e+00 angle pdb=" C ARG A 77 " pdb=" CA ARG A 77 " pdb=" CB ARG A 77 " ideal model delta sigma weight residual 110.67 113.31 -2.64 1.52e+00 4.33e-01 3.02e+00 angle pdb=" CA GLY A 293 " pdb=" C GLY A 293 " pdb=" O GLY A 293 " ideal model delta sigma weight residual 118.86 120.54 -1.68 1.07e+00 8.73e-01 2.48e+00 ... (remaining 4272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.65: 1689 14.65 - 29.31: 108 29.31 - 43.96: 34 43.96 - 58.62: 3 58.62 - 73.27: 5 Dihedral angle restraints: 1839 sinusoidal: 661 harmonic: 1178 Sorted by residual: dihedral pdb=" CA GLU A 416 " pdb=" CB GLU A 416 " pdb=" CG GLU A 416 " pdb=" CD GLU A 416 " ideal model delta sinusoidal sigma weight residual 60.00 106.57 -46.57 3 1.50e+01 4.44e-03 8.36e+00 dihedral pdb=" CB MET A 103 " pdb=" CG MET A 103 " pdb=" SD MET A 103 " pdb=" CE MET A 103 " ideal model delta sinusoidal sigma weight residual 60.00 102.38 -42.38 3 1.50e+01 4.44e-03 7.60e+00 dihedral pdb=" N LEU A 339 " pdb=" CA LEU A 339 " pdb=" CB LEU A 339 " pdb=" CG LEU A 339 " ideal model delta sinusoidal sigma weight residual -60.00 -101.32 41.32 3 1.50e+01 4.44e-03 7.39e+00 ... (remaining 1836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 301 0.025 - 0.050: 144 0.050 - 0.074: 71 0.074 - 0.099: 17 0.099 - 0.124: 5 Chirality restraints: 538 Sorted by residual: chirality pdb=" CA VAL A 355 " pdb=" N VAL A 355 " pdb=" C VAL A 355 " pdb=" CB VAL A 355 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA MET A 59 " pdb=" N MET A 59 " pdb=" C MET A 59 " pdb=" CB MET A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA SER A 74 " pdb=" N SER A 74 " pdb=" C SER A 74 " pdb=" CB SER A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 535 not shown) Planarity restraints: 526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 45 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 376 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO A 377 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 77 " 0.005 2.00e-02 2.50e+03 9.71e-03 9.43e-01 pdb=" C ARG A 77 " -0.017 2.00e-02 2.50e+03 pdb=" O ARG A 77 " 0.006 2.00e-02 2.50e+03 pdb=" N LEU A 78 " 0.006 2.00e-02 2.50e+03 ... (remaining 523 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 21 2.58 - 3.16: 2549 3.16 - 3.74: 4669 3.74 - 4.32: 6149 4.32 - 4.90: 10397 Nonbonded interactions: 23785 Sorted by model distance: nonbonded pdb=" O ASN A 310 " pdb="NA NA A 502 " model vdw 2.005 2.470 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.258 3.040 nonbonded pdb=" OE1 GLU A 296 " pdb=" OH TYR A 299 " model vdw 2.308 3.040 nonbonded pdb=" O GLN A 150 " pdb=" OG1 THR A 154 " model vdw 2.372 3.040 nonbonded pdb=" OG SER A 93 " pdb="NA NA A 504 " model vdw 2.372 2.470 ... (remaining 23780 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: 3.050 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 0.000 Process input model: 4.790 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 3136 Z= 0.104 Angle : 0.450 7.431 4277 Z= 0.221 Chirality : 0.036 0.124 538 Planarity : 0.003 0.027 526 Dihedral : 11.383 73.274 1091 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.39), residues: 409 helix: 0.73 (0.28), residues: 317 sheet: None (None), residues: 0 loop : -1.32 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 397 TYR 0.010 0.001 TYR A 299 PHE 0.004 0.001 PHE A 273 HIS 0.001 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 3136) covalent geometry : angle 0.45018 ( 4277) hydrogen bonds : bond 0.29737 ( 230) hydrogen bonds : angle 6.82216 ( 690) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.133 Fit side-chains REVERT: A 174 GLU cc_start: 0.7975 (tp30) cc_final: 0.7490 (tm-30) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.5412 time to fit residues: 24.5088 Evaluate side-chains 38 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.097 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.098391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.073278 restraints weight = 6163.944| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.46 r_work: 0.2834 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3136 Z= 0.163 Angle : 0.546 6.354 4277 Z= 0.289 Chirality : 0.039 0.151 538 Planarity : 0.004 0.045 526 Dihedral : 3.650 22.421 442 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.31 % Allowed : 10.94 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.09 (0.41), residues: 409 helix: 2.03 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -1.22 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 77 TYR 0.022 0.001 TYR A 299 PHE 0.008 0.001 PHE A 143 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3136) covalent geometry : angle 0.54597 ( 4277) hydrogen bonds : bond 0.06704 ( 230) hydrogen bonds : angle 4.50096 ( 690) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.111 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.5708 time to fit residues: 24.6133 Evaluate side-chains 36 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.0570 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.101195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.076055 restraints weight = 6048.328| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.45 r_work: 0.2882 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3136 Z= 0.130 Angle : 0.510 5.526 4277 Z= 0.261 Chirality : 0.037 0.124 538 Planarity : 0.004 0.041 526 Dihedral : 3.505 20.218 442 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.31 % Allowed : 13.75 % Favored : 85.94 % 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: 2.62 (0.42), residues: 409 helix: 2.39 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.06 (0.67), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 395 TYR 0.019 0.001 TYR A 299 PHE 0.007 0.001 PHE A 301 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3136) covalent geometry : angle 0.51048 ( 4277) hydrogen bonds : bond 0.05401 ( 230) hydrogen bonds : angle 4.08629 ( 690) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.068 Fit side-chains REVERT: A 294 ILE cc_start: 0.8432 (mm) cc_final: 0.8191 (mm) REVERT: A 298 ILE cc_start: 0.8994 (mt) cc_final: 0.8605 (tt) outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.4945 time to fit residues: 22.8832 Evaluate side-chains 37 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.0030 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.100605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.075567 restraints weight = 6099.780| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.46 r_work: 0.2867 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3136 Z= 0.129 Angle : 0.487 4.956 4277 Z= 0.252 Chirality : 0.038 0.175 538 Planarity : 0.004 0.041 526 Dihedral : 3.480 20.057 442 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.25 % Allowed : 16.56 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.77 (0.42), residues: 409 helix: 2.46 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -0.90 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 395 TYR 0.019 0.001 TYR A 299 PHE 0.009 0.001 PHE A 301 HIS 0.001 0.000 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3136) covalent geometry : angle 0.48701 ( 4277) hydrogen bonds : bond 0.05143 ( 230) hydrogen bonds : angle 3.93608 ( 690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.108 Fit side-chains REVERT: A 294 ILE cc_start: 0.8375 (mm) cc_final: 0.8143 (mm) REVERT: A 298 ILE cc_start: 0.9032 (mt) cc_final: 0.8641 (tt) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.4869 time to fit residues: 20.5623 Evaluate side-chains 38 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.0370 chunk 13 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.101047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075977 restraints weight = 6093.753| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.46 r_work: 0.2878 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3136 Z= 0.125 Angle : 0.483 4.904 4277 Z= 0.251 Chirality : 0.037 0.123 538 Planarity : 0.004 0.039 526 Dihedral : 3.441 19.684 442 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.56 % Allowed : 16.25 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.84 (0.42), residues: 409 helix: 2.51 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -0.85 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 77 TYR 0.018 0.001 TYR A 299 PHE 0.007 0.001 PHE A 301 HIS 0.001 0.000 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3136) covalent geometry : angle 0.48308 ( 4277) hydrogen bonds : bond 0.04913 ( 230) hydrogen bonds : angle 3.89887 ( 690) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.110 Fit side-chains REVERT: A 294 ILE cc_start: 0.8339 (mm) cc_final: 0.8129 (mm) REVERT: A 298 ILE cc_start: 0.9022 (mt) cc_final: 0.8627 (tt) outliers start: 5 outliers final: 1 residues processed: 41 average time/residue: 0.4927 time to fit residues: 20.8185 Evaluate side-chains 39 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.098209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.072951 restraints weight = 5975.900| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.43 r_work: 0.2830 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3136 Z= 0.145 Angle : 0.509 5.112 4277 Z= 0.261 Chirality : 0.038 0.159 538 Planarity : 0.004 0.039 526 Dihedral : 3.533 19.850 442 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.56 % Allowed : 17.50 % Favored : 80.94 % 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: 2.83 (0.43), residues: 409 helix: 2.51 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -0.92 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 77 TYR 0.019 0.001 TYR A 299 PHE 0.010 0.001 PHE A 301 HIS 0.002 0.000 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 3136) covalent geometry : angle 0.50921 ( 4277) hydrogen bonds : bond 0.05558 ( 230) hydrogen bonds : angle 3.94017 ( 690) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.100 Fit side-chains REVERT: A 281 THR cc_start: 0.7646 (OUTLIER) cc_final: 0.7394 (m) REVERT: A 294 ILE cc_start: 0.8334 (mm) cc_final: 0.8104 (mm) REVERT: A 298 ILE cc_start: 0.9023 (mt) cc_final: 0.8627 (tt) outliers start: 5 outliers final: 1 residues processed: 41 average time/residue: 0.4556 time to fit residues: 19.2269 Evaluate side-chains 40 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 281 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.100322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.075284 restraints weight = 6040.688| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.40 r_work: 0.2875 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3136 Z= 0.124 Angle : 0.491 5.469 4277 Z= 0.253 Chirality : 0.037 0.165 538 Planarity : 0.004 0.039 526 Dihedral : 3.549 19.789 442 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.88 % Allowed : 16.88 % Favored : 81.25 % 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: 2.93 (0.43), residues: 409 helix: 2.59 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -0.91 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 77 TYR 0.018 0.001 TYR A 299 PHE 0.007 0.001 PHE A 301 HIS 0.002 0.000 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3136) covalent geometry : angle 0.49123 ( 4277) hydrogen bonds : bond 0.04801 ( 230) hydrogen bonds : angle 3.84879 ( 690) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.074 Fit side-chains REVERT: A 281 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7485 (m) REVERT: A 294 ILE cc_start: 0.8341 (mm) cc_final: 0.8138 (mm) REVERT: A 298 ILE cc_start: 0.9044 (mt) cc_final: 0.8659 (tt) outliers start: 6 outliers final: 2 residues processed: 43 average time/residue: 0.4411 time to fit residues: 19.6053 Evaluate side-chains 42 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 281 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.074596 restraints weight = 6175.096| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.43 r_work: 0.2860 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3136 Z= 0.130 Angle : 0.496 6.454 4277 Z= 0.256 Chirality : 0.037 0.168 538 Planarity : 0.004 0.038 526 Dihedral : 3.539 19.554 442 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.56 % Allowed : 17.50 % Favored : 80.94 % 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: 2.93 (0.43), residues: 409 helix: 2.57 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -0.84 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 77 TYR 0.018 0.001 TYR A 299 PHE 0.006 0.001 PHE A 210 HIS 0.002 0.000 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3136) covalent geometry : angle 0.49624 ( 4277) hydrogen bonds : bond 0.05010 ( 230) hydrogen bonds : angle 3.85058 ( 690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.081 Fit side-chains REVERT: A 281 THR cc_start: 0.7738 (OUTLIER) cc_final: 0.7477 (m) REVERT: A 291 GLU cc_start: 0.8726 (pm20) cc_final: 0.8343 (pm20) REVERT: A 298 ILE cc_start: 0.9052 (mt) cc_final: 0.8668 (tt) outliers start: 5 outliers final: 2 residues processed: 43 average time/residue: 0.5021 time to fit residues: 22.2449 Evaluate side-chains 42 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 281 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.100338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.075160 restraints weight = 6119.352| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.42 r_work: 0.2873 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3136 Z= 0.125 Angle : 0.510 7.443 4277 Z= 0.258 Chirality : 0.037 0.148 538 Planarity : 0.004 0.038 526 Dihedral : 3.534 19.645 442 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.88 % Allowed : 17.50 % Favored : 80.62 % 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 (0.43), residues: 409 helix: 2.61 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -0.69 (0.70), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 77 TYR 0.019 0.001 TYR A 299 PHE 0.006 0.001 PHE A 210 HIS 0.002 0.000 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3136) covalent geometry : angle 0.51030 ( 4277) hydrogen bonds : bond 0.04818 ( 230) hydrogen bonds : angle 3.79596 ( 690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.109 Fit side-chains REVERT: A 245 LEU cc_start: 0.8183 (mp) cc_final: 0.7927 (tt) REVERT: A 281 THR cc_start: 0.7738 (OUTLIER) cc_final: 0.7479 (m) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.5018 time to fit residues: 22.2201 Evaluate side-chains 44 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.100250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.074816 restraints weight = 6038.509| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.46 r_work: 0.2864 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3136 Z= 0.130 Angle : 0.503 7.144 4277 Z= 0.260 Chirality : 0.037 0.146 538 Planarity : 0.004 0.038 526 Dihedral : 3.598 19.587 442 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.88 % Allowed : 17.81 % Favored : 80.31 % 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: 2.97 (0.43), residues: 409 helix: 2.57 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -0.68 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 77 TYR 0.021 0.001 TYR A 299 PHE 0.006 0.001 PHE A 210 HIS 0.002 0.000 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3136) covalent geometry : angle 0.50332 ( 4277) hydrogen bonds : bond 0.04958 ( 230) hydrogen bonds : angle 3.79926 ( 690) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.115 Fit side-chains REVERT: A 245 LEU cc_start: 0.8162 (mp) cc_final: 0.7917 (tt) REVERT: A 281 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7445 (m) REVERT: A 291 GLU cc_start: 0.8699 (pm20) cc_final: 0.8311 (pm20) outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.5311 time to fit residues: 22.9874 Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 37 optimal weight: 0.5980 chunk 35 optimal weight: 0.0030 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.3348 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.102639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.077773 restraints weight = 6080.978| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.43 r_work: 0.2920 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3136 Z= 0.117 Angle : 0.509 7.660 4277 Z= 0.257 Chirality : 0.037 0.145 538 Planarity : 0.004 0.038 526 Dihedral : 3.553 20.171 442 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.88 % Allowed : 17.50 % Favored : 80.62 % 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 (0.43), residues: 409 helix: 2.68 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -0.59 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 77 TYR 0.024 0.001 TYR A 299 PHE 0.007 0.001 PHE A 210 HIS 0.002 0.000 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3136) covalent geometry : angle 0.50928 ( 4277) hydrogen bonds : bond 0.04239 ( 230) hydrogen bonds : angle 3.67846 ( 690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1059.46 seconds wall clock time: 18 minutes 42.38 seconds (1122.38 seconds total)