Starting phenix.real_space_refine on Sat Apr 6 03:44:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uby_42109/04_2024/8uby_42109_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uby_42109/04_2024/8uby_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uby_42109/04_2024/8uby_42109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uby_42109/04_2024/8uby_42109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uby_42109/04_2024/8uby_42109_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uby_42109/04_2024/8uby_42109_trim.pdb" } 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 Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 3.81, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 5.95 Conformation dependent library (CDL) restraints added in 810.2 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: 0.48 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: 2.55 Time building geometry restraints manager: 5.90 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: 99.96 - 106.77: 110 106.77 - 113.58: 8008 113.58 - 120.39: 2371 120.39 - 127.20: 1760 127.20 - 134.01: 33 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 1.850 nonbonded pdb=" O MET A 382 " pdb=" HG SER A 385 " model vdw 1.786 1.850 nonbonded pdb=" O SER A 104 " pdb=" HE ARG A 107 " model vdw 1.799 1.850 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 1.850 ... (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: 2.930 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: 11.760 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 26.990 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.090 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.595 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: 2.1661 time to fit residues: 128.3481 Evaluate side-chains 37 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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: 0.7980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1524 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= 0.225 Angle : 0.516 5.281 4731 Z= 0.276 Chirality : 0.034 0.114 569 Planarity : 0.005 0.059 558 Dihedral : 5.873 58.303 666 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.85 % Allowed : 17.23 % Favored : 81.92 % 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: 3.97 (0.41), residues: 417 helix: 3.13 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.69 (0.75), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.005 0.002 HIS A 145 PHE 0.014 0.001 PHE A 114 TYR 0.020 0.001 TYR A 117 ARG 0.004 0.001 ARG A 223 *********************** 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 fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 452 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7476 (tp30) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 2.3107 time to fit residues: 86.4171 Evaluate side-chains 37 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1858 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= 0.190 Angle : 0.474 5.144 4731 Z= 0.253 Chirality : 0.033 0.117 569 Planarity : 0.004 0.053 558 Dihedral : 5.671 59.268 666 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.64 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: 3.87 (0.41), residues: 417 helix: 3.09 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.87 (0.73), residues: 63 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 0.004 0.001 ARG A 223 *********************** 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 fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8621 (mptm) outliers start: 5 outliers final: 2 residues processed: 38 average time/residue: 2.3249 time to fit residues: 91.6688 Evaluate side-chains 36 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2155 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= 0.216 Angle : 0.485 5.203 4731 Z= 0.261 Chirality : 0.034 0.120 569 Planarity : 0.004 0.050 558 Dihedral : 5.622 58.946 664 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.69 % Allowed : 14.69 % 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: 3.88 (0.41), residues: 417 helix: 3.11 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.73 (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 0.011 0.001 PHE A 496 TYR 0.021 0.001 TYR A 117 ARG 0.003 0.001 ARG A 223 *********************** 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 fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8643 (mptm) REVERT: A 452 GLU cc_start: 0.7844 (tp30) cc_final: 0.7643 (tp30) outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 2.4391 time to fit residues: 90.9592 Evaluate side-chains 32 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2345 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= 0.211 Angle : 0.479 5.247 4731 Z= 0.258 Chirality : 0.034 0.118 569 Planarity : 0.004 0.049 558 Dihedral : 5.661 57.287 664 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: 3.77 (0.41), residues: 417 helix: 3.04 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.82 (0.71), 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 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 39 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8163 (mmm160) REVERT: A 330 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8650 (mptm) outliers start: 8 outliers final: 2 residues processed: 36 average time/residue: 2.3494 time to fit residues: 87.6988 Evaluate side-chains 35 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 223 ARG 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 23 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3456 Z= 0.193 Angle : 0.474 5.162 4731 Z= 0.255 Chirality : 0.034 0.121 569 Planarity : 0.004 0.048 558 Dihedral : 5.674 55.669 664 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.85 % Allowed : 14.97 % 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: 3.75 (0.41), residues: 417 helix: 3.02 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.78 (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 0.011 0.001 PHE A 114 TYR 0.019 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 *********************** 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 36 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8647 (mptm) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 2.4141 time to fit residues: 90.1413 Evaluate side-chains 35 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 23 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2556 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= 0.181 Angle : 0.468 5.211 4731 Z= 0.251 Chirality : 0.033 0.120 569 Planarity : 0.004 0.048 558 Dihedral : 5.661 52.874 664 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 3.77 (0.41), residues: 417 helix: 3.03 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.75 (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 0.018 0.001 TYR A 117 ARG 0.002 0.000 ARG A 174 *********************** 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 fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 259 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8844 (mp) REVERT: A 330 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8657 (mptm) outliers start: 5 outliers final: 1 residues processed: 37 average time/residue: 2.3766 time to fit residues: 91.1002 Evaluate side-chains 35 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU 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 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3456 Z= 0.229 Angle : 0.483 5.243 4731 Z= 0.259 Chirality : 0.034 0.122 569 Planarity : 0.004 0.048 558 Dihedral : 5.476 50.183 663 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 3.74 (0.41), residues: 417 helix: 3.00 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.71 (0.74), residues: 66 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 0.012 0.001 PHE A 114 TYR 0.019 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 *********************** 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 fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 259 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8857 (mp) REVERT: A 330 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8669 (mptm) outliers start: 4 outliers final: 1 residues processed: 38 average time/residue: 2.4388 time to fit residues: 95.9036 Evaluate side-chains 36 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU 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 11 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 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 308 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2748 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= 0.218 Angle : 0.484 5.313 4731 Z= 0.260 Chirality : 0.034 0.121 569 Planarity : 0.004 0.048 558 Dihedral : 5.597 50.898 663 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.85 % Allowed : 14.69 % 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: 3.72 (0.41), residues: 417 helix: 2.98 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.70 (0.75), 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 0.012 0.001 PHE A 114 TYR 0.019 0.001 TYR A 117 ARG 0.001 0.000 ARG A 174 *********************** 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 37 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 259 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8858 (mp) REVERT: A 330 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8673 (mptm) outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 2.3607 time to fit residues: 90.6046 Evaluate side-chains 36 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU 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 32 optimal weight: 0.0980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 9 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.0470 overall best weight: 0.2478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3456 Z= 0.136 Angle : 0.449 5.007 4731 Z= 0.238 Chirality : 0.033 0.110 569 Planarity : 0.004 0.047 558 Dihedral : 5.295 50.176 663 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 3.96 (0.41), residues: 417 helix: 3.14 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.60 (0.76), residues: 65 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 0.008 0.001 PHE A 429 TYR 0.017 0.001 TYR A 117 ARG 0.001 0.000 ARG A 423 ********************** 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 39 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 117 TYR cc_start: 0.9212 (OUTLIER) cc_final: 0.8784 (p90) REVERT: A 330 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8696 (mptm) REVERT: A 396 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8154 (mmpt) outliers start: 3 outliers final: 1 residues processed: 39 average time/residue: 2.3958 time to fit residues: 96.8622 Evaluate side-chains 36 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TYR 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 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.098904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.080410 restraints weight = 15449.055| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.00 r_work: 0.2870 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2778 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= 0.184 Angle : 0.466 5.109 4731 Z= 0.249 Chirality : 0.033 0.118 569 Planarity : 0.004 0.048 558 Dihedral : 5.315 51.533 663 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.85 % Allowed : 15.25 % 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: 3.92 (0.41), residues: 417 helix: 3.10 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -0.59 (0.76), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 201 HIS 0.001 0.001 HIS A 145 PHE 0.011 0.001 PHE A 496 TYR 0.018 0.001 TYR A 117 ARG 0.005 0.001 ARG A 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3413.36 seconds wall clock time: 61 minutes 1.20 seconds (3661.20 seconds total)