Starting phenix.real_space_refine on Tue Aug 4 14:26:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26vb_80904/08_2026/26vb_80904.cif Found real_map, /net/cci-nas-00/data/ceres_data/26vb_80904/08_2026/26vb_80904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/26vb_80904/08_2026/26vb_80904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26vb_80904/08_2026/26vb_80904.map" model { file = "/net/cci-nas-00/data/ceres_data/26vb_80904/08_2026/26vb_80904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26vb_80904/08_2026/26vb_80904.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 2568 2.51 5 N 610 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 3859 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3844 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 22, 'TRANS': 477} Chain breaks: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PAU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.12, per 1000 atoms: 0.29 Number of scatterers: 3859 At special positions: 0 Unit cell: (78.02, 65.57, 73.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 649 8.00 N 610 7.00 C 2568 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: 0.38 Conformation dependent library (CDL) restraints added in 166.9 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 902 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 26 through 49 removed outlier: 3.974A pdb=" N VAL A 30 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 31 " --> pdb=" O MET A 27 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.416A pdb=" N PHE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 97 through 103 removed outlier: 3.520A pdb=" N LEU A 102 " --> pdb=" O TYR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 4.319A pdb=" N LEU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.817A pdb=" N GLU A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 173 removed outlier: 3.687A pdb=" N ARG A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 175 through 195 removed outlier: 3.609A pdb=" N TYR A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 226 Processing helix chain 'A' and resid 226 through 238 removed outlier: 4.073A pdb=" N ARG A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 Processing helix chain 'A' and resid 274 through 283 removed outlier: 5.105A pdb=" N ARG A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 322 removed outlier: 4.055A pdb=" N PHE A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Proline residue: A 299 - end of helix Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 332 through 345 removed outlier: 4.480A pdb=" N VAL A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 382 Processing helix chain 'A' and resid 392 through 417 Processing helix chain 'A' and resid 422 through 434 Processing helix chain 'A' and resid 434 through 446 removed outlier: 3.747A pdb=" N LEU A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 476 Processing helix chain 'A' and resid 528 through 549 removed outlier: 4.589A pdb=" N ALA A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 569 removed outlier: 3.521A pdb=" N LYS A 568 " --> pdb=" O PRO A 564 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 837 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: 0.65 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 566 1.31 - 1.43: 1141 1.43 - 1.56: 2204 1.56 - 1.68: 0 1.68 - 1.81: 51 Bond restraints: 3962 Sorted by residual: bond pdb=" N PAU A 701 " pdb=" C6 PAU A 701 " ideal model delta sigma weight residual 1.332 1.440 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" CB VAL A 538 " pdb=" CG1 VAL A 538 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.80e+00 bond pdb=" C6 PAU A 701 " pdb=" O6' PAU A 701 " ideal model delta sigma weight residual 1.228 1.183 0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" C PRO A 453 " pdb=" N PRO A 454 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.83e+00 bond pdb=" C1 PAU A 701 " pdb=" C5 PAU A 701 " ideal model delta sigma weight residual 1.555 1.522 0.033 2.00e-02 2.50e+03 2.71e+00 ... (remaining 3957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 4951 1.65 - 3.30: 365 3.30 - 4.95: 57 4.95 - 6.59: 14 6.59 - 8.24: 10 Bond angle restraints: 5397 Sorted by residual: angle pdb=" N PRO A 453 " pdb=" CA PRO A 453 " pdb=" C PRO A 453 " ideal model delta sigma weight residual 110.70 115.36 -4.66 1.22e+00 6.72e-01 1.46e+01 angle pdb=" CA PRO A 453 " pdb=" C PRO A 453 " pdb=" N PRO A 454 " ideal model delta sigma weight residual 117.93 122.16 -4.23 1.20e+00 6.94e-01 1.24e+01 angle pdb=" C LEU A 310 " pdb=" N ILE A 311 " pdb=" CA ILE A 311 " ideal model delta sigma weight residual 120.64 115.53 5.11 1.66e+00 3.63e-01 9.48e+00 angle pdb=" CA TYR A 130 " pdb=" CB TYR A 130 " pdb=" CG TYR A 130 " ideal model delta sigma weight residual 113.90 108.84 5.06 1.80e+00 3.09e-01 7.91e+00 angle pdb=" N LEU A 102 " pdb=" CA LEU A 102 " pdb=" C LEU A 102 " ideal model delta sigma weight residual 113.18 109.80 3.38 1.21e+00 6.83e-01 7.79e+00 ... (remaining 5392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 2123 15.04 - 30.08: 111 30.08 - 45.12: 20 45.12 - 60.15: 4 60.15 - 75.19: 3 Dihedral angle restraints: 2261 sinusoidal: 837 harmonic: 1424 Sorted by residual: dihedral pdb=" CA LEU A 35 " pdb=" C LEU A 35 " pdb=" N LEU A 36 " pdb=" CA LEU A 36 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TYR A 130 " pdb=" C TYR A 130 " pdb=" N GLU A 131 " pdb=" CA GLU A 131 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ALA A 129 " pdb=" C ALA A 129 " pdb=" N TYR A 130 " pdb=" CA TYR A 130 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 2258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 500 0.073 - 0.146: 120 0.146 - 0.219: 7 0.219 - 0.292: 0 0.292 - 0.365: 1 Chirality restraints: 628 Sorted by residual: chirality pdb=" CB ILE A 311 " pdb=" CA ILE A 311 " pdb=" CG1 ILE A 311 " pdb=" CG2 ILE A 311 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB VAL A 377 " pdb=" CA VAL A 377 " pdb=" CG1 VAL A 377 " pdb=" CG2 VAL A 377 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CG LEU A 75 " pdb=" CB LEU A 75 " pdb=" CD1 LEU A 75 " pdb=" CD2 LEU A 75 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 625 not shown) Planarity restraints: 659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 259 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C LEU A 259 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU A 259 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 260 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 538 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C VAL A 538 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL A 538 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 539 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 384 " -0.035 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 385 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " -0.029 5.00e-02 4.00e+02 ... (remaining 656 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 855 2.78 - 3.31: 3674 3.31 - 3.84: 6752 3.84 - 4.37: 7653 4.37 - 4.90: 13466 Nonbonded interactions: 32400 Sorted by model distance: nonbonded pdb=" O LEU A 102 " pdb=" SG CYS A 105 " model vdw 2.244 3.400 nonbonded pdb=" OH TYR A 156 " pdb=" OXT PAU A 701 " model vdw 2.285 3.040 nonbonded pdb=" O ALA A 357 " pdb=" OG SER A 361 " model vdw 2.305 3.040 nonbonded pdb=" O ASP A 203 " pdb=" OG1 THR A 207 " model vdw 2.323 3.040 nonbonded pdb=" O VAL A 545 " pdb=" OG1 THR A 549 " model vdw 2.339 3.040 ... (remaining 32395 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 group one per residue 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.090 Find NCS groups from input model: 0.020 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.008 0.108 3962 Z= 0.325 Angle : 1.004 8.243 5397 Z= 0.541 Chirality : 0.059 0.365 628 Planarity : 0.008 0.051 659 Dihedral : 10.235 75.192 1359 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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: -3.87 (0.27), residues: 496 helix: -2.32 (0.20), residues: 375 sheet: None (None), residues: 0 loop : -2.63 (0.41), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 551 TYR 0.032 0.004 TYR A 106 PHE 0.032 0.003 PHE A 360 TRP 0.020 0.002 TRP A 201 HIS 0.008 0.002 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.32 ( 3962) covalent geometry : angle 1.00387 / 0.54 ( 5397) hydrogen bonds : bond 0.12322 / 8.63 ( 286) hydrogen bonds : angle 6.81912 / 4.65 ( 837) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.078 Fit side-chains REVERT: A 281 TYR cc_start: 0.7522 (m-80) cc_final: 0.7292 (m-10) REVERT: A 295 TYR cc_start: 0.7132 (m-80) cc_final: 0.6645 (m-80) REVERT: A 411 LEU cc_start: 0.7271 (mm) cc_final: 0.6998 (mm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0332 time to fit residues: 2.9802 Evaluate side-chains 52 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.0170 chunk 16 optimal weight: 0.0070 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN A 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.219794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.182625 restraints weight = 4270.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.188660 restraints weight = 2419.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.192846 restraints weight = 1686.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.195418 restraints weight = 1329.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.197369 restraints weight = 1135.913| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3962 Z= 0.140 Angle : 0.594 6.409 5397 Z= 0.309 Chirality : 0.041 0.159 628 Planarity : 0.005 0.039 659 Dihedral : 5.075 37.877 544 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.47 % Allowed : 6.86 % Favored : 91.67 % 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: -1.22 (0.35), residues: 496 helix: -0.37 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -1.85 (0.52), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 280 TYR 0.015 0.002 TYR A 130 PHE 0.013 0.001 PHE A 442 TRP 0.016 0.001 TRP A 469 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 3962) covalent geometry : angle 0.59383 / 0.31 ( 5397) hydrogen bonds : bond 0.04176 / 2.80 ( 286) hydrogen bonds : angle 5.03961 / 3.43 ( 837) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.078 Fit side-chains REVERT: A 552 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6766 (ttt) outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 0.0472 time to fit residues: 3.4910 Evaluate side-chains 54 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 552 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.203300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.167245 restraints weight = 4189.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.172722 restraints weight = 2401.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.176753 restraints weight = 1675.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.179227 restraints weight = 1324.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.180888 restraints weight = 1130.982| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3962 Z= 0.183 Angle : 0.630 9.403 5397 Z= 0.321 Chirality : 0.042 0.170 628 Planarity : 0.004 0.033 659 Dihedral : 4.768 29.302 544 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.45 % Allowed : 9.07 % Favored : 88.48 % 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: -0.40 (0.36), residues: 496 helix: 0.36 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -2.02 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 280 TYR 0.016 0.002 TYR A 93 PHE 0.020 0.002 PHE A 95 TRP 0.014 0.001 TRP A 201 HIS 0.006 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 3962) covalent geometry : angle 0.63034 / 0.32 ( 5397) hydrogen bonds : bond 0.04198 / 2.83 ( 286) hydrogen bonds : angle 4.79199 / 3.26 ( 837) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.135 Fit side-chains REVERT: A 27 MET cc_start: 0.8130 (mmp) cc_final: 0.7765 (mmp) REVERT: A 95 PHE cc_start: 0.8178 (m-80) cc_final: 0.7779 (m-80) outliers start: 10 outliers final: 5 residues processed: 58 average time/residue: 0.0490 time to fit residues: 3.9562 Evaluate side-chains 55 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 450 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4310 r_free = 0.4310 target = 0.209670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.174598 restraints weight = 4153.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.180130 restraints weight = 2358.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.184114 restraints weight = 1637.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.186492 restraints weight = 1289.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.188589 restraints weight = 1098.354| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3962 Z= 0.152 Angle : 0.582 6.040 5397 Z= 0.296 Chirality : 0.041 0.165 628 Planarity : 0.004 0.032 659 Dihedral : 4.572 25.450 544 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.70 % Allowed : 11.03 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.37), residues: 496 helix: 0.70 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.89 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.016 0.001 TYR A 93 PHE 0.013 0.001 PHE A 95 TRP 0.014 0.001 TRP A 469 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 3962) covalent geometry : angle 0.58182 / 0.30 ( 5397) hydrogen bonds : bond 0.04014 / 2.70 ( 286) hydrogen bonds : angle 4.64249 / 3.14 ( 837) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.156 Fit side-chains REVERT: A 27 MET cc_start: 0.8050 (mmp) cc_final: 0.7760 (mmp) REVERT: A 153 MET cc_start: 0.8145 (tpt) cc_final: 0.7846 (tpt) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.0449 time to fit residues: 3.5208 Evaluate side-chains 56 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 539 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.205114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.168931 restraints weight = 4136.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.174546 restraints weight = 2385.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.178634 restraints weight = 1679.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.181260 restraints weight = 1323.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.183094 restraints weight = 1123.426| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3962 Z= 0.161 Angle : 0.582 6.105 5397 Z= 0.296 Chirality : 0.041 0.186 628 Planarity : 0.004 0.032 659 Dihedral : 4.434 21.650 544 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.94 % Allowed : 10.78 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.37), residues: 496 helix: 0.88 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.78 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 551 TYR 0.016 0.001 TYR A 93 PHE 0.011 0.001 PHE A 95 TRP 0.013 0.001 TRP A 469 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 3962) covalent geometry : angle 0.58244 / 0.30 ( 5397) hydrogen bonds : bond 0.03962 / 2.66 ( 286) hydrogen bonds : angle 4.55372 / 3.08 ( 837) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.127 Fit side-chains REVERT: A 27 MET cc_start: 0.8078 (mmp) cc_final: 0.7789 (mmp) REVERT: A 181 LEU cc_start: 0.7813 (tp) cc_final: 0.6970 (mt) REVERT: A 228 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.4304 (mp) outliers start: 12 outliers final: 6 residues processed: 59 average time/residue: 0.0394 time to fit residues: 3.2853 Evaluate side-chains 59 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 539 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 0.0030 chunk 0 optimal weight: 5.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.211514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.175845 restraints weight = 4223.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.181635 restraints weight = 2382.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.185737 restraints weight = 1649.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.188269 restraints weight = 1288.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.190028 restraints weight = 1095.550| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3962 Z= 0.137 Angle : 0.556 6.234 5397 Z= 0.283 Chirality : 0.039 0.136 628 Planarity : 0.004 0.034 659 Dihedral : 4.323 20.353 544 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.21 % Allowed : 12.01 % Favored : 85.78 % 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: 0.65 (0.37), residues: 496 helix: 1.10 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.66 (0.52), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 280 TYR 0.019 0.001 TYR A 93 PHE 0.009 0.001 PHE A 390 TRP 0.013 0.001 TRP A 469 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 3962) covalent geometry : angle 0.55592 / 0.28 ( 5397) hydrogen bonds : bond 0.03844 / 2.58 ( 286) hydrogen bonds : angle 4.49154 / 3.02 ( 837) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.080 Fit side-chains REVERT: A 27 MET cc_start: 0.8051 (mmp) cc_final: 0.7755 (mmp) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.0545 time to fit residues: 3.4710 Evaluate side-chains 44 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 552 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.0000 chunk 32 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 = 0.4386 r_free = 0.4386 target = 0.221251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.183802 restraints weight = 4261.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.189593 restraints weight = 2419.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.193520 restraints weight = 1678.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.196416 restraints weight = 1315.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.198357 restraints weight = 1104.634| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3962 Z= 0.132 Angle : 0.573 8.121 5397 Z= 0.286 Chirality : 0.039 0.134 628 Planarity : 0.004 0.037 659 Dihedral : 4.251 20.253 544 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.96 % Allowed : 12.75 % Favored : 85.29 % 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: 0.92 (0.38), residues: 496 helix: 1.28 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -1.58 (0.54), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 553 TYR 0.019 0.001 TYR A 93 PHE 0.010 0.001 PHE A 390 TRP 0.013 0.001 TRP A 469 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 3962) covalent geometry : angle 0.57315 / 0.29 ( 5397) hydrogen bonds : bond 0.03824 / 2.60 ( 286) hydrogen bonds : angle 4.44680 / 2.99 ( 837) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.077 Fit side-chains REVERT: A 27 MET cc_start: 0.8052 (mmp) cc_final: 0.7802 (mmp) REVERT: A 153 MET cc_start: 0.8116 (tpt) cc_final: 0.7858 (tpt) outliers start: 8 outliers final: 5 residues processed: 43 average time/residue: 0.0343 time to fit residues: 2.0352 Evaluate side-chains 43 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 552 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 0.0050 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN A 214 GLN A 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.214628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.179270 restraints weight = 4146.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.185161 restraints weight = 2334.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.189292 restraints weight = 1616.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.191812 restraints weight = 1264.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.193769 restraints weight = 1073.113| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3962 Z= 0.139 Angle : 0.574 7.737 5397 Z= 0.287 Chirality : 0.040 0.132 628 Planarity : 0.004 0.038 659 Dihedral : 4.207 20.484 544 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.70 % Allowed : 11.27 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.38), residues: 496 helix: 1.35 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -1.39 (0.54), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 553 TYR 0.017 0.001 TYR A 93 PHE 0.009 0.001 PHE A 390 TRP 0.012 0.001 TRP A 469 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 3962) covalent geometry : angle 0.57448 / 0.29 ( 5397) hydrogen bonds : bond 0.03805 / 2.58 ( 286) hydrogen bonds : angle 4.42097 / 2.97 ( 837) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.077 Fit side-chains REVERT: A 27 MET cc_start: 0.8065 (mmp) cc_final: 0.7810 (mmp) outliers start: 11 outliers final: 7 residues processed: 48 average time/residue: 0.0377 time to fit residues: 2.4151 Evaluate side-chains 45 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 552 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN A 152 GLN A 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.212669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.176644 restraints weight = 4213.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.182497 restraints weight = 2376.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.186642 restraints weight = 1655.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.189240 restraints weight = 1297.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.191137 restraints weight = 1102.346| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3962 Z= 0.160 Angle : 0.594 8.123 5397 Z= 0.298 Chirality : 0.041 0.140 628 Planarity : 0.004 0.042 659 Dihedral : 4.329 20.885 544 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.96 % Allowed : 12.50 % Favored : 85.54 % 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: 1.07 (0.38), residues: 496 helix: 1.36 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -1.38 (0.54), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 551 TYR 0.023 0.001 TYR A 93 PHE 0.018 0.001 PHE A 95 TRP 0.011 0.001 TRP A 469 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 3962) covalent geometry : angle 0.59427 / 0.30 ( 5397) hydrogen bonds : bond 0.03835 / 2.60 ( 286) hydrogen bonds : angle 4.43913 / 2.98 ( 837) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.126 Fit side-chains REVERT: A 153 MET cc_start: 0.8187 (tpt) cc_final: 0.7869 (tpt) outliers start: 8 outliers final: 7 residues processed: 43 average time/residue: 0.0511 time to fit residues: 3.0142 Evaluate side-chains 45 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 552 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.223785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.186661 restraints weight = 4237.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.192649 restraints weight = 2355.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.196738 restraints weight = 1615.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.199446 restraints weight = 1255.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.201403 restraints weight = 1063.939| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3962 Z= 0.140 Angle : 0.599 9.197 5397 Z= 0.295 Chirality : 0.040 0.133 628 Planarity : 0.004 0.038 659 Dihedral : 4.324 20.140 544 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.23 % Allowed : 13.48 % Favored : 85.29 % 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: 1.24 (0.38), residues: 496 helix: 1.47 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.26 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 551 TYR 0.022 0.001 TYR A 93 PHE 0.009 0.001 PHE A 390 TRP 0.012 0.001 TRP A 469 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 3962) covalent geometry : angle 0.59865 / 0.30 ( 5397) hydrogen bonds : bond 0.03762 / 2.55 ( 286) hydrogen bonds : angle 4.40931 / 2.95 ( 837) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.134 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 38 average time/residue: 0.0558 time to fit residues: 2.9095 Evaluate side-chains 39 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 539 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.0170 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.0470 chunk 23 optimal weight: 0.5980 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.209561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.174258 restraints weight = 4251.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.180323 restraints weight = 2370.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.184501 restraints weight = 1613.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.187135 restraints weight = 1245.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.189199 restraints weight = 1048.270| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3962 Z= 0.128 Angle : 0.583 9.319 5397 Z= 0.288 Chirality : 0.039 0.123 628 Planarity : 0.004 0.042 659 Dihedral : 4.327 20.117 544 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.72 % Allowed : 13.24 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.39), residues: 496 helix: 1.56 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.05 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 551 TYR 0.020 0.001 TYR A 93 PHE 0.019 0.001 PHE A 95 TRP 0.012 0.001 TRP A 469 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 3962) covalent geometry : angle 0.58304 / 0.29 ( 5397) hydrogen bonds : bond 0.03655 / 2.47 ( 286) hydrogen bonds : angle 4.35002 / 2.91 ( 837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 697.22 seconds wall clock time: 12 minutes 41.74 seconds (761.74 seconds total)