Starting phenix.real_space_refine on Tue Aug 4 21:04:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rqj_54177/08_2026/9rqj_54177.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rqj_54177/08_2026/9rqj_54177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rqj_54177/08_2026/9rqj_54177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rqj_54177/08_2026/9rqj_54177.map" model { file = "/net/cci-nas-00/data/ceres_data/9rqj_54177/08_2026/9rqj_54177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rqj_54177/08_2026/9rqj_54177.cif" } resolution = 3.07 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= 0.009 sd= 0.140 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 22 5.16 5 C 4430 2.51 5 N 1032 2.21 5 O 1108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6594 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3217 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 14, 'TRANS': 381} Chain: "B" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3205 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 14, 'TRANS': 379} Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'LMT': 1, 'PGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'LMT': 1, 'PGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.32, per 1000 atoms: 0.20 Number of scatterers: 6594 At special positions: 0 Unit cell: (93.002, 99.134, 100.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 2 15.00 O 1108 8.00 N 1032 7.00 C 4430 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: 0.45 Conformation dependent library (CDL) restraints added in 292.2 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1474 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.858A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 29 Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 50 through 53 removed outlier: 3.520A pdb=" N TRP A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 50 through 53' Processing helix chain 'A' and resid 54 through 79 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 88 through 110 Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.540A pdb=" N PHE A 115 " --> pdb=" O TRP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 175 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 186 through 205 removed outlier: 3.670A pdb=" N ASP A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 230 removed outlier: 4.079A pdb=" N PHE A 209 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 231 through 237 Proline residue: A 234 - end of helix Processing helix chain 'A' and resid 238 through 287 removed outlier: 3.520A pdb=" N VAL A 244 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Proline residue: A 266 - end of helix Processing helix chain 'A' and resid 294 through 336 removed outlier: 3.687A pdb=" N ARG A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET A 317 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 372 removed outlier: 3.573A pdb=" N SER A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'B' and resid 1 through 5 Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.553A pdb=" N LEU B 14 " --> pdb=" O GLY B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.703A pdb=" N PHE B 52 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 79 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 88 through 110 Processing helix chain 'B' and resid 112 through 125 Processing helix chain 'B' and resid 130 through 175 removed outlier: 4.310A pdb=" N PHE B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 186 through 205 removed outlier: 3.670A pdb=" N ASP B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 229 removed outlier: 4.090A pdb=" N PHE B 209 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 230 through 236 Proline residue: B 234 - end of helix Processing helix chain 'B' and resid 237 through 288 Proline residue: B 266 - end of helix removed outlier: 3.527A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 339 removed outlier: 3.941A pdb=" N MET B 317 " --> pdb=" O TYR B 313 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 372 removed outlier: 3.608A pdb=" N GLN B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N THR B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 372 " --> pdb=" O TYR B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 391 519 hydrogen bonds defined for protein. 1539 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: 0.76 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1021 1.32 - 1.44: 2063 1.44 - 1.56: 3670 1.56 - 1.68: 4 1.68 - 1.80: 42 Bond restraints: 6800 Sorted by residual: bond pdb=" C3' LMT A 502 " pdb=" O3' LMT A 502 " ideal model delta sigma weight residual 1.404 1.359 0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" C6B LMT B 502 " pdb=" O6B LMT B 502 " ideal model delta sigma weight residual 1.407 1.362 0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C2B LMT B 502 " pdb=" O2B LMT B 502 " ideal model delta sigma weight residual 1.410 1.365 0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" C2B LMT A 502 " pdb=" O2B LMT A 502 " ideal model delta sigma weight residual 1.410 1.365 0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" C3' LMT B 502 " pdb=" O3' LMT B 502 " ideal model delta sigma weight residual 1.404 1.360 0.044 2.00e-02 2.50e+03 4.83e+00 ... (remaining 6795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 9109 2.02 - 4.04: 101 4.04 - 6.06: 27 6.06 - 8.07: 3 8.07 - 10.09: 6 Bond angle restraints: 9246 Sorted by residual: angle pdb=" N GLU B 232 " pdb=" CA GLU B 232 " pdb=" C GLU B 232 " ideal model delta sigma weight residual 114.64 108.74 5.90 1.52e+00 4.33e-01 1.51e+01 angle pdb=" C2 LMT B 502 " pdb=" C3 LMT B 502 " pdb=" C4 LMT B 502 " ideal model delta sigma weight residual 117.09 107.00 10.09 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C2 LMT A 502 " pdb=" C3 LMT A 502 " pdb=" C4 LMT A 502 " ideal model delta sigma weight residual 117.09 107.80 9.29 3.00e+00 1.11e-01 9.58e+00 angle pdb=" C10 LMT B 502 " pdb=" C9 LMT B 502 " pdb=" C8 LMT B 502 " ideal model delta sigma weight residual 116.03 106.79 9.24 3.00e+00 1.11e-01 9.49e+00 angle pdb=" N THR A 346 " pdb=" CA THR A 346 " pdb=" C THR A 346 " ideal model delta sigma weight residual 111.28 107.96 3.32 1.09e+00 8.42e-01 9.30e+00 ... (remaining 9241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 3474 17.04 - 34.07: 341 34.07 - 51.11: 85 51.11 - 68.15: 19 68.15 - 85.19: 1 Dihedral angle restraints: 3920 sinusoidal: 1616 harmonic: 2304 Sorted by residual: dihedral pdb=" CA PHE A 339 " pdb=" C PHE A 339 " pdb=" N PRO A 340 " pdb=" CA PRO A 340 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA MET A 352 " pdb=" C MET A 352 " pdb=" N THR A 353 " pdb=" CA THR A 353 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N PRO A 234 " pdb=" CA PRO A 234 " ideal model delta harmonic sigma weight residual -180.00 -162.31 -17.69 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 781 0.042 - 0.084: 210 0.084 - 0.125: 26 0.125 - 0.167: 2 0.167 - 0.209: 6 Chirality restraints: 1025 Sorted by residual: chirality pdb=" C5' LMT B 502 " pdb=" C4' LMT B 502 " pdb=" C6' LMT B 502 " pdb=" O5' LMT B 502 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3B LMT B 502 " pdb=" C2B LMT B 502 " pdb=" C4B LMT B 502 " pdb=" O3B LMT B 502 " both_signs ideal model delta sigma weight residual False 2.50 2.29 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C5' LMT A 502 " pdb=" C4' LMT A 502 " pdb=" C6' LMT A 502 " pdb=" O5' LMT A 502 " both_signs ideal model delta sigma weight residual False -2.51 -2.31 -0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 1022 not shown) Planarity restraints: 1115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 113 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO A 114 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 233 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 234 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 230 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO A 231 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.022 5.00e-02 4.00e+02 ... (remaining 1112 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 391 2.74 - 3.28: 6878 3.28 - 3.82: 10881 3.82 - 4.36: 12849 4.36 - 4.90: 22538 Nonbonded interactions: 53537 Sorted by model distance: nonbonded pdb=" O4P PGT B 501 " pdb=" O6 PGT B 501 " model vdw 2.196 3.040 nonbonded pdb=" O4P PGT A 501 " pdb=" O6 PGT A 501 " model vdw 2.198 3.040 nonbonded pdb=" O LEU B 349 " pdb=" OG1 THR B 353 " model vdw 2.320 3.040 nonbonded pdb=" OE2 GLU A 276 " pdb=" OH TYR A 309 " model vdw 2.334 3.040 nonbonded pdb=" O TRP A 83 " pdb=" OG SER A 87 " model vdw 2.335 3.040 ... (remaining 53532 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 394 or resid 501 through 502)) selection = chain 'B' } 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 5.730 Find NCS groups from input model: 0.060 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.004 0.045 6800 Z= 0.197 Angle : 0.618 10.094 9246 Z= 0.319 Chirality : 0.039 0.209 1025 Planarity : 0.005 0.055 1115 Dihedral : 14.309 85.186 2446 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: 0.27 (0.28), residues: 786 helix: 0.57 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -1.38 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 274 TYR 0.008 0.001 TYR B 162 PHE 0.016 0.001 PHE A 5 TRP 0.008 0.001 TRP B 373 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 ( 6800) covalent geometry : angle 0.61836 / 0.32 ( 9246) hydrogen bonds : bond 0.23047 / 14.87 ( 519) hydrogen bonds : angle 6.57657 / 4.88 ( 1539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.227 Fit side-chains REVERT: A 274 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7930 (mtp-110) REVERT: B 271 LYS cc_start: 0.8748 (mttp) cc_final: 0.8525 (mttp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0840 time to fit residues: 7.1594 Evaluate side-chains 61 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0070 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.189326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135185 restraints weight = 6970.127| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.03 r_work: 0.3310 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6800 Z= 0.177 Angle : 0.563 7.983 9246 Z= 0.303 Chirality : 0.039 0.146 1025 Planarity : 0.005 0.054 1115 Dihedral : 8.333 59.838 1056 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.75 % Allowed : 4.06 % Favored : 95.19 % 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: 1.99 (0.30), residues: 786 helix: 1.92 (0.20), residues: 643 sheet: None (None), residues: 0 loop : -1.46 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 274 TYR 0.016 0.001 TYR B 162 PHE 0.014 0.002 PHE B 157 TRP 0.009 0.001 TRP B 53 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 6800) covalent geometry : angle 0.56304 / 0.30 ( 9246) hydrogen bonds : bond 0.06885 / 4.52 ( 519) hydrogen bonds : angle 3.96986 / 2.88 ( 1539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.137 Fit side-chains REVERT: B 269 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8233 (mt-10) REVERT: B 335 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6365 (mm) outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 0.0742 time to fit residues: 7.1340 Evaluate side-chains 73 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 335 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.188176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139042 restraints weight = 6741.504| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.40 r_work: 0.3360 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6800 Z= 0.158 Angle : 0.526 7.180 9246 Z= 0.281 Chirality : 0.038 0.145 1025 Planarity : 0.004 0.049 1115 Dihedral : 7.915 55.529 1056 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.35 % Allowed : 8.42 % Favored : 90.23 % 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: 2.37 (0.30), residues: 786 helix: 2.18 (0.20), residues: 649 sheet: None (None), residues: 0 loop : -1.54 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 323 TYR 0.014 0.001 TYR B 162 PHE 0.015 0.002 PHE B 157 TRP 0.011 0.001 TRP A 75 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 6800) covalent geometry : angle 0.52575 / 0.28 ( 9246) hydrogen bonds : bond 0.05940 / 3.88 ( 519) hydrogen bonds : angle 3.68564 / 2.66 ( 1539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.217 Fit side-chains REVERT: A 233 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7773 (mt) REVERT: A 311 ARG cc_start: 0.8064 (ttm-80) cc_final: 0.7645 (ttp80) REVERT: B 335 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6499 (mm) outliers start: 9 outliers final: 5 residues processed: 74 average time/residue: 0.0777 time to fit residues: 7.5663 Evaluate side-chains 76 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 74 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.189612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.136717 restraints weight = 6850.805| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.26 r_work: 0.3331 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6800 Z= 0.140 Angle : 0.500 6.873 9246 Z= 0.266 Chirality : 0.037 0.139 1025 Planarity : 0.004 0.052 1115 Dihedral : 7.737 53.665 1056 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.65 % Allowed : 9.47 % Favored : 88.87 % 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: 2.58 (0.30), residues: 786 helix: 2.36 (0.20), residues: 647 sheet: None (None), residues: 0 loop : -1.60 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 323 TYR 0.013 0.001 TYR B 326 PHE 0.013 0.001 PHE A 52 TRP 0.011 0.001 TRP B 53 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 6800) covalent geometry : angle 0.50036 / 0.27 ( 9246) hydrogen bonds : bond 0.05367 / 3.51 ( 519) hydrogen bonds : angle 3.58269 / 2.59 ( 1539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.223 Fit side-chains REVERT: A 311 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7661 (ttp80) REVERT: A 370 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8320 (mt) REVERT: B 269 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8221 (mm-30) REVERT: B 335 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6539 (mm) REVERT: B 370 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8276 (mt) outliers start: 11 outliers final: 5 residues processed: 76 average time/residue: 0.0726 time to fit residues: 7.2769 Evaluate side-chains 80 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.187802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137379 restraints weight = 6877.552| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.71 r_work: 0.3322 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6800 Z= 0.163 Angle : 0.519 6.849 9246 Z= 0.277 Chirality : 0.038 0.142 1025 Planarity : 0.004 0.050 1115 Dihedral : 7.809 55.904 1056 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.95 % Allowed : 10.23 % Favored : 87.82 % 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: 2.51 (0.30), residues: 786 helix: 2.32 (0.20), residues: 647 sheet: None (None), residues: 0 loop : -1.65 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 323 TYR 0.016 0.001 TYR B 162 PHE 0.016 0.002 PHE A 157 TRP 0.011 0.001 TRP A 75 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 6800) covalent geometry : angle 0.51914 / 0.28 ( 9246) hydrogen bonds : bond 0.05627 / 3.70 ( 519) hydrogen bonds : angle 3.57960 / 2.59 ( 1539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.222 Fit side-chains REVERT: A 233 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7973 (mt) REVERT: A 370 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8417 (mt) REVERT: B 269 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8387 (mm-30) REVERT: B 335 LEU cc_start: 0.6845 (mm) cc_final: 0.6633 (mm) REVERT: B 370 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8416 (mt) outliers start: 13 outliers final: 7 residues processed: 77 average time/residue: 0.0765 time to fit residues: 7.6337 Evaluate side-chains 79 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.186472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134720 restraints weight = 6883.235| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.24 r_work: 0.3312 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6800 Z= 0.183 Angle : 0.533 6.666 9246 Z= 0.285 Chirality : 0.039 0.146 1025 Planarity : 0.005 0.052 1115 Dihedral : 7.924 58.250 1056 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.26 % Allowed : 10.98 % Favored : 86.77 % 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: 2.44 (0.30), residues: 786 helix: 2.27 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.67 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 306 TYR 0.017 0.002 TYR B 162 PHE 0.016 0.002 PHE A 157 TRP 0.011 0.001 TRP A 75 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 6800) covalent geometry : angle 0.53307 / 0.29 ( 9246) hydrogen bonds : bond 0.05814 / 3.82 ( 519) hydrogen bonds : angle 3.60878 / 2.61 ( 1539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.145 Fit side-chains REVERT: A 1 MET cc_start: 0.6091 (ttm) cc_final: 0.5890 (ttp) REVERT: A 211 ASN cc_start: 0.8209 (t0) cc_final: 0.8000 (t0) REVERT: A 233 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7858 (mt) REVERT: A 370 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8478 (mt) REVERT: B 211 ASN cc_start: 0.8223 (t0) cc_final: 0.8002 (t0) REVERT: B 269 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8358 (mm-30) REVERT: B 370 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8534 (mt) outliers start: 15 outliers final: 9 residues processed: 77 average time/residue: 0.0749 time to fit residues: 7.6658 Evaluate side-chains 82 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.188073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138734 restraints weight = 6785.708| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.42 r_work: 0.3355 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6800 Z= 0.151 Angle : 0.506 6.583 9246 Z= 0.270 Chirality : 0.038 0.141 1025 Planarity : 0.004 0.052 1115 Dihedral : 7.797 56.410 1056 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.80 % Allowed : 11.43 % Favored : 86.77 % 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: 2.63 (0.30), residues: 786 helix: 2.39 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -1.62 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 306 TYR 0.014 0.001 TYR B 326 PHE 0.014 0.001 PHE B 157 TRP 0.011 0.001 TRP A 75 HIS 0.004 0.000 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 6800) covalent geometry : angle 0.50599 / 0.27 ( 9246) hydrogen bonds : bond 0.05417 / 3.55 ( 519) hydrogen bonds : angle 3.54862 / 2.56 ( 1539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.138 Fit side-chains REVERT: A 233 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7716 (mt) REVERT: A 370 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8458 (mt) REVERT: B 211 ASN cc_start: 0.8190 (t0) cc_final: 0.7973 (t0) REVERT: B 370 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8447 (mt) outliers start: 12 outliers final: 9 residues processed: 76 average time/residue: 0.0764 time to fit residues: 7.7088 Evaluate side-chains 83 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 29 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.189538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.140753 restraints weight = 6868.125| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.39 r_work: 0.3399 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6800 Z= 0.134 Angle : 0.493 6.824 9246 Z= 0.262 Chirality : 0.037 0.139 1025 Planarity : 0.004 0.053 1115 Dihedral : 7.706 54.690 1056 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.80 % Allowed : 11.58 % Favored : 86.62 % 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: 2.85 (0.30), residues: 786 helix: 2.55 (0.20), residues: 645 sheet: None (None), residues: 0 loop : -1.46 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 323 TYR 0.014 0.001 TYR B 326 PHE 0.012 0.001 PHE B 157 TRP 0.011 0.001 TRP B 53 HIS 0.003 0.000 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 6800) covalent geometry : angle 0.49329 / 0.26 ( 9246) hydrogen bonds : bond 0.05097 / 3.35 ( 519) hydrogen bonds : angle 3.49907 / 2.53 ( 1539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.141 Fit side-chains REVERT: A 233 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7678 (mt) REVERT: A 370 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8375 (mt) REVERT: B 370 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8394 (mt) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.0785 time to fit residues: 7.7296 Evaluate side-chains 82 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.189039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139599 restraints weight = 6876.959| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.44 r_work: 0.3377 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6800 Z= 0.142 Angle : 0.499 7.197 9246 Z= 0.265 Chirality : 0.037 0.141 1025 Planarity : 0.004 0.052 1115 Dihedral : 7.729 55.794 1056 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.95 % Allowed : 11.43 % Favored : 86.62 % 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: 2.85 (0.30), residues: 786 helix: 2.55 (0.20), residues: 645 sheet: None (None), residues: 0 loop : -1.47 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 323 TYR 0.014 0.001 TYR B 162 PHE 0.014 0.001 PHE A 157 TRP 0.011 0.001 TRP A 75 HIS 0.003 0.000 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 6800) covalent geometry : angle 0.49858 / 0.26 ( 9246) hydrogen bonds : bond 0.05199 / 3.42 ( 519) hydrogen bonds : angle 3.49281 / 2.52 ( 1539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.168 Fit side-chains REVERT: A 233 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7633 (mt) REVERT: A 370 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8327 (mt) REVERT: B 370 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8386 (mt) outliers start: 13 outliers final: 9 residues processed: 78 average time/residue: 0.0693 time to fit residues: 7.2094 Evaluate side-chains 83 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.0970 chunk 3 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.190159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135164 restraints weight = 6815.910| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.21 r_work: 0.3339 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6800 Z= 0.142 Angle : 0.498 6.908 9246 Z= 0.265 Chirality : 0.037 0.144 1025 Planarity : 0.004 0.054 1115 Dihedral : 7.747 58.903 1056 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.80 % Allowed : 12.18 % Favored : 86.02 % 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: 2.89 (0.30), residues: 786 helix: 2.55 (0.20), residues: 650 sheet: None (None), residues: 0 loop : -1.41 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 323 TYR 0.014 0.001 TYR B 162 PHE 0.013 0.001 PHE B 157 TRP 0.011 0.001 TRP A 75 HIS 0.003 0.000 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6800) covalent geometry : angle 0.49756 / 0.26 ( 9246) hydrogen bonds : bond 0.05190 / 3.41 ( 519) hydrogen bonds : angle 3.48398 / 2.52 ( 1539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.128 Fit side-chains REVERT: A 233 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7687 (mt) REVERT: A 370 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8217 (mt) REVERT: B 370 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8283 (mt) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.0738 time to fit residues: 7.2576 Evaluate side-chains 82 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.188743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.139787 restraints weight = 6780.937| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.39 r_work: 0.3372 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6800 Z= 0.144 Angle : 0.498 7.217 9246 Z= 0.265 Chirality : 0.037 0.143 1025 Planarity : 0.004 0.052 1115 Dihedral : 7.689 56.280 1056 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.95 % Allowed : 12.18 % Favored : 85.86 % 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: 2.87 (0.30), residues: 786 helix: 2.53 (0.20), residues: 650 sheet: None (None), residues: 0 loop : -1.43 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 306 TYR 0.014 0.001 TYR B 162 PHE 0.014 0.001 PHE B 157 TRP 0.011 0.001 TRP A 75 HIS 0.003 0.000 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6800) covalent geometry : angle 0.49781 / 0.27 ( 9246) hydrogen bonds : bond 0.05215 / 3.43 ( 519) hydrogen bonds : angle 3.48534 / 2.52 ( 1539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.60 seconds wall clock time: 26 minutes 29.69 seconds (1589.69 seconds total)