Starting phenix.real_space_refine on Sat May 10 22:04:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uby_42109/05_2025/8uby_42109_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uby_42109/05_2025/8uby_42109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uby_42109/05_2025/8uby_42109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uby_42109/05_2025/8uby_42109.map" model { file = "/net/cci-nas-00/data/ceres_data/8uby_42109/05_2025/8uby_42109_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uby_42109/05_2025/8uby_42109_trim.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.000 sd= 0.034 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 S 18 5.16 5 C 2262 2.51 5 N 503 2.21 5 O 628 1.98 5 H 3345 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6756 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6598 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 17, 'TRANS': 401} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 158 Unusual residues: {'CHT': 1, 'Y01': 3} Classifications: {'undetermined': 4, 'water': 46} Link IDs: {None: 49} Time building chain proxies: 4.46, per 1000 atoms: 0.66 Number of scatterers: 6756 At special positions: 0 Unit cell: (81.2, 56.55, 65.975, 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 18 16.00 O 628 8.00 N 503 7.00 C 2262 6.00 H 3345 1.00 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: 2.01 Conformation dependent library (CDL) restraints added in 576.3 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 89.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 105 through 131 removed outlier: 3.661A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TYR A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N SER A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.557A pdb=" N ILE A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 5.056A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.779A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 216 removed outlier: 3.547A pdb=" N THR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.079A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.575A pdb=" N ASN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 296 Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.682A pdb=" N ASN A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 363 removed outlier: 5.114A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 396 Processing helix chain 'A' and resid 398 through 418 Processing helix chain 'A' and resid 419 through 423 removed outlier: 3.827A pdb=" N LEU A 422 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG A 423 " --> pdb=" O LEU A 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 419 through 423' Processing helix chain 'A' and resid 424 through 454 Proline residue: A 444 - end of helix Processing helix chain 'A' and resid 458 through 488 removed outlier: 3.506A pdb=" N SER A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.804A pdb=" N GLY A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 816 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: 2.21 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3337 1.03 - 1.23: 11 1.23 - 1.42: 1396 1.42 - 1.61: 2029 1.61 - 1.81: 28 Bond restraints: 6801 Sorted by residual: bond pdb=" N PRO A 303 " pdb=" CA PRO A 303 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.31e-02 5.83e+03 1.08e+00 bond pdb=" CA ILE A 332 " pdb=" CB ILE A 332 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 9.61e-01 bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.474 1.461 0.014 1.57e-02 4.06e+03 7.77e-01 bond pdb=" CB PRO A 304 " pdb=" CG PRO A 304 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.60e-01 bond pdb=" N PRO A 221 " pdb=" CA PRO A 221 " ideal model delta sigma weight residual 1.469 1.478 -0.009 1.28e-02 6.10e+03 4.81e-01 ... (remaining 6796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 11430 1.02 - 2.04: 794 2.04 - 3.06: 38 3.06 - 4.08: 16 4.08 - 5.10: 4 Bond angle restraints: 12282 Sorted by residual: angle pdb=" N VAL A 195 " pdb=" CA VAL A 195 " pdb=" C VAL A 195 " ideal model delta sigma weight residual 106.21 109.71 -3.50 1.07e+00 8.73e-01 1.07e+01 angle pdb=" N LEU A 220 " pdb=" CA LEU A 220 " pdb=" C LEU A 220 " ideal model delta sigma weight residual 109.81 114.91 -5.10 2.21e+00 2.05e-01 5.34e+00 angle pdb=" C VAL A 195 " pdb=" CA VAL A 195 " pdb=" CB VAL A 195 " ideal model delta sigma weight residual 113.22 110.76 2.46 1.12e+00 7.97e-01 4.82e+00 angle pdb=" N TYR A 117 " pdb=" CA TYR A 117 " pdb=" C TYR A 117 " ideal model delta sigma weight residual 113.18 110.57 2.61 1.21e+00 6.83e-01 4.65e+00 angle pdb=" CA LEU A 220 " pdb=" C LEU A 220 " pdb=" N PRO A 221 " ideal model delta sigma weight residual 118.44 121.85 -3.41 1.59e+00 3.96e-01 4.61e+00 ... (remaining 12277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 2963 15.87 - 31.73: 258 31.73 - 47.60: 64 47.60 - 63.46: 80 63.46 - 79.33: 4 Dihedral angle restraints: 3369 sinusoidal: 1889 harmonic: 1480 Sorted by residual: dihedral pdb=" CA TYR A 117 " pdb=" C TYR A 117 " pdb=" N SER A 118 " pdb=" CA SER A 118 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CG ARG A 423 " pdb=" CD ARG A 423 " pdb=" NE ARG A 423 " pdb=" CZ ARG A 423 " ideal model delta sinusoidal sigma weight residual -90.00 -42.14 -47.86 2 1.50e+01 4.44e-03 1.17e+01 dihedral pdb=" N LYS A 330 " pdb=" CA LYS A 330 " pdb=" CB LYS A 330 " pdb=" CG LYS A 330 " ideal model delta sinusoidal sigma weight residual -180.00 -120.78 -59.22 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 358 0.021 - 0.042: 117 0.042 - 0.063: 33 0.063 - 0.084: 50 0.084 - 0.104: 11 Chirality restraints: 569 Sorted by residual: chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.73e-01 chirality pdb=" CA ILE A 131 " pdb=" N ILE A 131 " pdb=" C ILE A 131 " pdb=" CB ILE A 131 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.45e-01 chirality pdb=" CA PRO A 304 " pdb=" N PRO A 304 " pdb=" C PRO A 304 " pdb=" CB PRO A 304 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.34e-01 ... (remaining 566 not shown) Planarity restraints: 959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 256 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO A 257 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 423 " -0.163 9.50e-02 1.11e+02 5.47e-02 3.48e+00 pdb=" NE ARG A 423 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 423 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 423 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 423 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 423 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 423 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 423 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 423 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 114 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C PHE A 114 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE A 114 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 115 " 0.009 2.00e-02 2.50e+03 ... (remaining 956 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.34: 1996 2.34 - 2.90: 15817 2.90 - 3.47: 19065 3.47 - 4.03: 25376 4.03 - 4.60: 38501 Nonbonded interactions: 100755 Sorted by model distance: nonbonded pdb="HD21 ASN A 356 " pdb=" O HOH A 705 " model vdw 1.772 2.450 nonbonded pdb=" O MET A 382 " pdb=" HG SER A 385 " model vdw 1.786 2.450 nonbonded pdb=" O SER A 104 " pdb=" HE ARG A 107 " model vdw 1.799 2.450 nonbonded pdb=" HG2 ARG A 423 " pdb="HH11 ARG A 423 " model vdw 1.810 2.270 nonbonded pdb=" O GLY A 474 " pdb=" HG1 THR A 478 " model vdw 1.814 2.450 ... (remaining 100750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.250 Find NCS groups from input model: 0.040 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:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3456 Z= 0.115 Angle : 0.474 5.105 4731 Z= 0.270 Chirality : 0.032 0.104 569 Planarity : 0.006 0.073 558 Dihedral : 14.527 79.329 1370 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.56 % Allowed : 13.28 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.72 (0.42), residues: 417 helix: 3.06 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -0.97 (0.74), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.001 0.000 HIS A 145 PHE 0.010 0.001 PHE A 496 TYR 0.012 0.001 TYR A 117 ARG 0.007 0.001 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.12146 ( 272) hydrogen bonds : angle 5.41640 ( 816) covalent geometry : bond 0.00215 ( 3456) covalent geometry : angle 0.47441 ( 4731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 512 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7550 (tppt) outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 2.2275 time to fit residues: 131.7121 Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 404 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.102100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.083168 restraints weight = 15235.735| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.98 r_work: 0.2904 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3456 Z= 0.165 Angle : 0.520 5.588 4731 Z= 0.279 Chirality : 0.034 0.116 569 Planarity : 0.005 0.059 558 Dihedral : 5.855 56.152 666 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.85 % Allowed : 16.95 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.41), residues: 417 helix: 3.09 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.68 (0.75), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.006 0.002 HIS A 145 PHE 0.012 0.001 PHE A 496 TYR 0.021 0.001 TYR A 117 ARG 0.005 0.001 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.05448 ( 272) hydrogen bonds : angle 4.20573 ( 816) covalent geometry : bond 0.00357 ( 3456) covalent geometry : angle 0.52020 ( 4731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8400 (mmm160) cc_final: 0.8195 (mmm160) REVERT: A 452 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7516 (tp30) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 2.4683 time to fit residues: 92.1670 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 452 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.087126 restraints weight = 15565.520| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.99 r_work: 0.3022 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3456 Z= 0.139 Angle : 0.474 5.134 4731 Z= 0.254 Chirality : 0.034 0.113 569 Planarity : 0.004 0.051 558 Dihedral : 5.595 55.305 666 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.41 % Allowed : 14.41 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.41), residues: 417 helix: 3.10 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.88 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.001 0.001 HIS A 145 PHE 0.011 0.001 PHE A 114 TYR 0.019 0.001 TYR A 117 ARG 0.003 0.001 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.05168 ( 272) hydrogen bonds : angle 4.03465 ( 816) covalent geometry : bond 0.00296 ( 3456) covalent geometry : angle 0.47444 ( 4731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8586 (mptm) REVERT: A 452 GLU cc_start: 0.7929 (tp30) cc_final: 0.7662 (tp30) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 2.2163 time to fit residues: 85.1943 Evaluate side-chains 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 350 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.079907 restraints weight = 15633.584| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.98 r_work: 0.2854 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3456 Z= 0.154 Angle : 0.485 5.145 4731 Z= 0.261 Chirality : 0.034 0.117 569 Planarity : 0.004 0.050 558 Dihedral : 5.577 55.125 664 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.98 % Allowed : 14.41 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.41), residues: 417 helix: 3.11 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.74 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.002 0.001 HIS A 145 PHE 0.012 0.001 PHE A 114 TYR 0.021 0.001 TYR A 117 ARG 0.002 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.05087 ( 272) hydrogen bonds : angle 4.02419 ( 816) covalent geometry : bond 0.00339 ( 3456) covalent geometry : angle 0.48505 ( 4731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8547 (mptm) REVERT: A 452 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7597 (tp30) outliers start: 7 outliers final: 3 residues processed: 36 average time/residue: 2.2571 time to fit residues: 84.9779 Evaluate side-chains 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 452 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 20 optimal weight: 0.0060 chunk 2 optimal weight: 0.5980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.100206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.081566 restraints weight = 15300.959| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.97 r_work: 0.2883 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3456 Z= 0.118 Angle : 0.456 5.163 4731 Z= 0.244 Chirality : 0.033 0.110 569 Planarity : 0.004 0.048 558 Dihedral : 5.433 54.286 664 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.13 % Allowed : 15.25 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.41), residues: 417 helix: 3.14 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.82 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.002 0.001 HIS A 145 PHE 0.009 0.001 PHE A 496 TYR 0.018 0.001 TYR A 117 ARG 0.002 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 272) hydrogen bonds : angle 3.90332 ( 816) covalent geometry : bond 0.00239 ( 3456) covalent geometry : angle 0.45644 ( 4731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8812 (mm) cc_final: 0.8610 (mt) REVERT: A 330 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8554 (mptm) REVERT: A 452 GLU cc_start: 0.7876 (tp30) cc_final: 0.7533 (tp30) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 2.2008 time to fit residues: 82.2890 Evaluate side-chains 33 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 350 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.098056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.079292 restraints weight = 15437.425| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.97 r_work: 0.2849 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3456 Z= 0.154 Angle : 0.479 5.261 4731 Z= 0.258 Chirality : 0.034 0.117 569 Planarity : 0.004 0.048 558 Dihedral : 5.599 54.263 664 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.26 % Allowed : 14.12 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.41), residues: 417 helix: 3.08 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.74 (0.74), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.002 0.001 HIS A 145 PHE 0.012 0.001 PHE A 114 TYR 0.020 0.001 TYR A 117 ARG 0.002 0.000 ARG A 174 Details of bonding type rmsd hydrogen bonds : bond 0.04993 ( 272) hydrogen bonds : angle 3.96957 ( 816) covalent geometry : bond 0.00338 ( 3456) covalent geometry : angle 0.47913 ( 4731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 259 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8483 (mp) REVERT: A 330 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8557 (mptm) REVERT: A 452 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7650 (tp30) outliers start: 8 outliers final: 3 residues processed: 37 average time/residue: 2.0353 time to fit residues: 78.5147 Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 452 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.083541 restraints weight = 15884.156| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.96 r_work: 0.2968 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3456 Z= 0.156 Angle : 0.485 5.255 4731 Z= 0.261 Chirality : 0.034 0.124 569 Planarity : 0.004 0.048 558 Dihedral : 5.817 54.510 664 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.98 % Allowed : 13.84 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.41), residues: 417 helix: 3.01 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.75 (0.74), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.002 0.001 HIS A 145 PHE 0.012 0.001 PHE A 114 TYR 0.020 0.001 TYR A 117 ARG 0.002 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.05084 ( 272) hydrogen bonds : angle 3.97972 ( 816) covalent geometry : bond 0.00346 ( 3456) covalent geometry : angle 0.48503 ( 4731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 259 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 330 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8608 (mptm) REVERT: A 452 GLU cc_start: 0.7984 (tp30) cc_final: 0.7709 (tp30) outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 2.1514 time to fit residues: 80.8150 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.079203 restraints weight = 15580.837| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.98 r_work: 0.2849 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3456 Z= 0.134 Angle : 0.472 5.174 4731 Z= 0.254 Chirality : 0.034 0.114 569 Planarity : 0.004 0.047 558 Dihedral : 5.816 54.615 664 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.98 % Allowed : 14.12 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.41), residues: 417 helix: 3.06 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.70 (0.74), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.002 0.001 HIS A 145 PHE 0.010 0.001 PHE A 114 TYR 0.016 0.001 TYR A 117 ARG 0.002 0.000 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.04857 ( 272) hydrogen bonds : angle 3.91996 ( 816) covalent geometry : bond 0.00287 ( 3456) covalent geometry : angle 0.47223 ( 4731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8831 (mm) cc_final: 0.8626 (mt) REVERT: A 330 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8593 (mptm) REVERT: A 452 GLU cc_start: 0.7927 (tp30) cc_final: 0.7656 (tp30) outliers start: 7 outliers final: 3 residues processed: 37 average time/residue: 2.2960 time to fit residues: 88.2174 Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 350 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.097416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.078809 restraints weight = 15656.295| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.97 r_work: 0.2844 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3456 Z= 0.144 Angle : 0.480 5.306 4731 Z= 0.258 Chirality : 0.034 0.119 569 Planarity : 0.004 0.047 558 Dihedral : 5.883 54.766 664 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.41 % Allowed : 14.12 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.41), residues: 417 helix: 3.04 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.76 (0.74), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.002 0.001 HIS A 145 PHE 0.011 0.001 PHE A 114 TYR 0.020 0.001 TYR A 117 ARG 0.002 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.04941 ( 272) hydrogen bonds : angle 3.92303 ( 816) covalent geometry : bond 0.00316 ( 3456) covalent geometry : angle 0.47968 ( 4731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8838 (mm) cc_final: 0.8634 (mt) REVERT: A 330 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8599 (mptm) REVERT: A 452 GLU cc_start: 0.7926 (tp30) cc_final: 0.7661 (tp30) outliers start: 5 outliers final: 3 residues processed: 34 average time/residue: 2.2074 time to fit residues: 78.1227 Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 350 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 6 optimal weight: 0.0370 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.084634 restraints weight = 16250.215| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.93 r_work: 0.2986 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3456 Z= 0.121 Angle : 0.461 5.132 4731 Z= 0.247 Chirality : 0.033 0.112 569 Planarity : 0.004 0.046 558 Dihedral : 5.807 54.672 664 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.85 % Allowed : 14.41 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.90 (0.41), residues: 417 helix: 3.12 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.70 (0.75), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.001 0.001 HIS A 145 PHE 0.009 0.001 PHE A 496 TYR 0.016 0.001 TYR A 117 ARG 0.002 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 272) hydrogen bonds : angle 3.84352 ( 816) covalent geometry : bond 0.00252 ( 3456) covalent geometry : angle 0.46146 ( 4731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 203 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.9021 (t) REVERT: A 294 ILE cc_start: 0.8921 (mm) cc_final: 0.8708 (mt) REVERT: A 330 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8667 (mptm) REVERT: A 452 GLU cc_start: 0.7941 (tp30) cc_final: 0.7691 (tp30) outliers start: 3 outliers final: 1 residues processed: 36 average time/residue: 2.1238 time to fit residues: 79.5646 Evaluate side-chains 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 350 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.083265 restraints weight = 16257.536| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.93 r_work: 0.2956 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3456 Z= 0.159 Angle : 0.487 5.239 4731 Z= 0.261 Chirality : 0.034 0.120 569 Planarity : 0.004 0.047 558 Dihedral : 5.996 56.339 664 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.41 % Allowed : 14.41 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.41), residues: 417 helix: 3.03 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.75 (0.74), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 201 HIS 0.002 0.001 HIS A 145 PHE 0.013 0.001 PHE A 114 TYR 0.019 0.001 TYR A 117 ARG 0.002 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.05035 ( 272) hydrogen bonds : angle 3.94124 ( 816) covalent geometry : bond 0.00359 ( 3456) covalent geometry : angle 0.48669 ( 4731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4857.14 seconds wall clock time: 84 minutes 20.86 seconds (5060.86 seconds total)