Starting phenix.real_space_refine on Wed Mar 12 00:58:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uby_42109/03_2025/8uby_42109_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uby_42109/03_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_42109/03_2025/8uby_42109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uby_42109/03_2025/8uby_42109.map" model { file = "/net/cci-nas-00/data/ceres_data/8uby_42109/03_2025/8uby_42109_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uby_42109/03_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-5624/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: 4.66, per 1000 atoms: 0.69 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 659.4 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: 0.49 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: 2.26 Time building geometry restraints manager: 2.38 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: 3.100 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: 0.120 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.700 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:12.770 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.210 ------------------------------------------------------------------------------- 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= 0.139 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 *********************** 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 : 0.620 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: 2.1446 time to fit residues: 126.6467 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 : 0.563 ------------------------------------------------------------------------------- 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 = 0.102101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.083169 restraints weight = 15235.700| |-----------------------------------------------------------------------------| 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: 3.78 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1608 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= 0.228 Angle : 0.520 5.589 4731 Z= 0.279 Chirality : 0.034 0.115 569 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 *********************** 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 : 0.493 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: 2.2915 time to fit residues: 85.5715 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 : 0.496 ------------------------------------------------------------------------------- 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: 0.6980 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 0.0570 chunk 10 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.106207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.087933 restraints weight = 15505.061| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.96 r_work: 0.3042 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3456 Z= 0.166 Angle : 0.465 5.140 4731 Z= 0.249 Chirality : 0.033 0.112 569 Planarity : 0.004 0.052 558 Dihedral : 5.574 55.251 666 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.13 % Allowed : 14.97 % 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: 3.89 (0.41), residues: 417 helix: 3.10 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.89 (0.73), residues: 63 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 0.010 0.001 PHE A 496 TYR 0.018 0.001 TYR A 117 ARG 0.003 0.001 ARG A 423 *********************** 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 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8525 (mptm) REVERT: A 452 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7594 (tp30) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 2.1090 time to fit residues: 85.5740 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 : 0.509 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 452 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.099671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.080707 restraints weight = 15583.464| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.00 r_work: 0.2869 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2145 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= 0.207 Angle : 0.486 5.168 4731 Z= 0.261 Chirality : 0.034 0.117 569 Planarity : 0.004 0.050 558 Dihedral : 5.523 55.167 664 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.26 % Allowed : 14.41 % Favored : 83.33 % 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: 3.12 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.79 (0.72), 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 174 *********************** 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 42 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8545 (mptm) REVERT: A 452 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7614 (tp30) outliers start: 8 outliers final: 3 residues processed: 39 average time/residue: 2.1580 time to fit residues: 87.4155 Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.086147 restraints weight = 15504.488| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.95 r_work: 0.3001 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2243 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= 0.178 Angle : 0.468 5.190 4731 Z= 0.251 Chirality : 0.033 0.113 569 Planarity : 0.004 0.049 558 Dihedral : 5.459 54.637 664 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.69 % Allowed : 14.12 % 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: 3.87 (0.41), residues: 417 helix: 3.11 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.83 (0.72), 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 0.019 0.001 TYR A 117 ARG 0.002 0.000 ARG A 516 *********************** 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 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8582 (mptm) REVERT: A 452 GLU cc_start: 0.7939 (tp30) cc_final: 0.7677 (tp30) outliers start: 6 outliers final: 3 residues processed: 35 average time/residue: 2.0500 time to fit residues: 74.8591 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 : 0.539 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.097938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.079098 restraints weight = 15453.255| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.97 r_work: 0.2844 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3456 Z= 0.223 Angle : 0.486 5.234 4731 Z= 0.261 Chirality : 0.034 0.123 569 Planarity : 0.004 0.048 558 Dihedral : 5.608 54.703 664 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.26 % Allowed : 13.84 % 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: 3.08 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.81 (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 0.020 0.001 TYR A 117 ARG 0.001 0.000 ARG A 516 *********************** 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 41 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8839 (mm) cc_final: 0.8638 (mt) REVERT: A 330 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8551 (mptm) REVERT: A 452 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7642 (tp30) outliers start: 8 outliers final: 3 residues processed: 38 average time/residue: 2.1450 time to fit residues: 84.6464 Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.098769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.080022 restraints weight = 15495.255| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.97 r_work: 0.2859 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2480 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= 0.171 Angle : 0.469 5.173 4731 Z= 0.251 Chirality : 0.033 0.117 569 Planarity : 0.004 0.047 558 Dihedral : 5.592 54.532 664 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.41 % Allowed : 14.69 % 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: 3.86 (0.41), residues: 417 helix: 3.10 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.82 (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 0.010 0.001 PHE A 114 TYR 0.018 0.001 TYR A 117 ARG 0.002 0.000 ARG A 516 *********************** 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 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8824 (mm) cc_final: 0.8623 (mt) REVERT: A 330 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8563 (mptm) REVERT: A 452 GLU cc_start: 0.7930 (tp30) cc_final: 0.7590 (tp30) outliers start: 5 outliers final: 3 residues processed: 34 average time/residue: 2.0271 time to fit residues: 71.9210 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 : 0.534 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.0470 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.098904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.080202 restraints weight = 15509.245| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.97 r_work: 0.2866 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2560 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= 0.170 Angle : 0.465 5.142 4731 Z= 0.249 Chirality : 0.033 0.118 569 Planarity : 0.004 0.047 558 Dihedral : 5.579 54.160 664 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.41 % Allowed : 14.69 % 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: 3.95 (0.41), residues: 417 helix: 3.15 (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 0.002 0.001 HIS A 145 PHE 0.009 0.001 PHE A 114 TYR 0.019 0.001 TYR A 117 ARG 0.001 0.000 ARG A 516 *********************** 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 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8815 (mm) cc_final: 0.8611 (mt) REVERT: A 330 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8571 (mptm) REVERT: A 452 GLU cc_start: 0.7927 (tp30) cc_final: 0.7592 (tp30) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 2.2648 time to fit residues: 84.5982 Evaluate side-chains 33 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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: 0.8980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.098478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.079875 restraints weight = 15587.714| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.97 r_work: 0.2862 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2613 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= 0.181 Angle : 0.469 5.262 4731 Z= 0.252 Chirality : 0.033 0.116 569 Planarity : 0.004 0.047 558 Dihedral : 5.660 53.956 664 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.13 % Allowed : 14.69 % 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: 3.93 (0.41), residues: 417 helix: 3.14 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.75 (0.75), 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 0.018 0.001 TYR A 117 ARG 0.002 0.000 ARG A 223 *********************** 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 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 203 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.9031 (t) REVERT: A 294 ILE cc_start: 0.8825 (mm) cc_final: 0.8617 (mt) REVERT: A 330 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8572 (mptm) REVERT: A 452 GLU cc_start: 0.7901 (tp30) cc_final: 0.7577 (tp30) outliers start: 4 outliers final: 2 residues processed: 34 average time/residue: 2.1293 time to fit residues: 75.3388 Evaluate side-chains 33 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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: 0.9980 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 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 = 0.3340 r_free = 0.3340 target = 0.101703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.084063 restraints weight = 16305.216| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.94 r_work: 0.2971 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2710 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= 0.187 Angle : 0.475 5.218 4731 Z= 0.255 Chirality : 0.034 0.118 569 Planarity : 0.004 0.047 558 Dihedral : 5.764 53.956 664 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.13 % Allowed : 14.97 % 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: 3.91 (0.41), residues: 417 helix: 3.11 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.67 (0.77), residues: 65 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 0.011 0.001 PHE A 114 TYR 0.019 0.001 TYR A 117 ARG 0.002 0.000 ARG A 223 ********************** 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 33 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 203 THR cc_start: 0.9312 (OUTLIER) cc_final: 0.9047 (t) REVERT: A 294 ILE cc_start: 0.8912 (mm) cc_final: 0.8704 (mt) REVERT: A 330 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8639 (mptm) REVERT: A 452 GLU cc_start: 0.7936 (tp30) cc_final: 0.7607 (tp30) outliers start: 4 outliers final: 2 residues processed: 33 average time/residue: 2.0937 time to fit residues: 72.0405 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.102376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.084745 restraints weight = 16162.556| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.93 r_work: 0.2972 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2742 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= 0.179 Angle : 0.470 5.165 4731 Z= 0.252 Chirality : 0.033 0.116 569 Planarity : 0.004 0.047 558 Dihedral : 5.792 53.924 664 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.69 % Allowed : 14.41 % 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: 3.91 (0.41), residues: 417 helix: 3.11 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.69 (0.76), residues: 65 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 0.010 0.001 PHE A 114 TYR 0.018 0.001 TYR A 117 ARG 0.002 0.000 ARG A 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5099.77 seconds wall clock time: 87 minutes 7.89 seconds (5227.89 seconds total)