Starting phenix.real_space_refine on Thu Dec 7 17:19:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/12_2023/8dwi_27755.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/12_2023/8dwi_27755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/12_2023/8dwi_27755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/12_2023/8dwi_27755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/12_2023/8dwi_27755.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/12_2023/8dwi_27755.pdb" } resolution = 3.4 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= 0.002 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2138 2.51 5 N 504 2.21 5 O 536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3192 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3192 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 71 Time building chain proxies: 2.35, per 1000 atoms: 0.74 Number of scatterers: 3192 At special positions: 0 Unit cell: (71.38, 70.55, 72.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 536 8.00 N 504 7.00 C 2138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 1.40 Conformation dependent library (CDL) restraints added in 645.0 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 38 through 67 removed outlier: 4.163A pdb=" N PHE A 47 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 48 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR A 54 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN A 59 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 60 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 61 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 64 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 133 removed outlier: 4.773A pdb=" N PHE A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Proline residue: A 125 - end of helix removed outlier: 4.502A pdb=" N TYR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 151 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 176 through 189 Proline residue: A 180 - end of helix removed outlier: 3.910A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 223 removed outlier: 3.849A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 247 removed outlier: 5.193A pdb=" N PHE A 233 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP A 244 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE A 245 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.981A pdb=" N SER A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 3.871A pdb=" N GLN A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 382 removed outlier: 4.217A pdb=" N GLY A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 389 through 408 removed outlier: 3.960A pdb=" N PHE A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N CYS A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 removed outlier: 4.321A pdb=" N LEU A 415 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 417 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 435 through 445 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 453 through 477 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' 197 hydrogen bonds defined for protein. 480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 938 1.34 - 1.46: 817 1.46 - 1.58: 1515 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 3292 Sorted by residual: bond pdb=" N TYR A 117 " pdb=" CA TYR A 117 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.89e+00 bond pdb=" N PHE A 115 " pdb=" CA PHE A 115 " ideal model delta sigma weight residual 1.458 1.481 -0.024 1.30e-02 5.92e+03 3.31e+00 bond pdb=" C VAL A 58 " pdb=" O VAL A 58 " ideal model delta sigma weight residual 1.242 1.230 0.012 1.13e-02 7.83e+03 1.22e+00 bond pdb=" C LEU A 214 " pdb=" N PRO A 215 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.18e+00 bond pdb=" C PHE A 115 " pdb=" N PHE A 116 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.43e-02 4.89e+03 9.67e-01 ... (remaining 3287 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.22: 108 107.22 - 113.91: 1864 113.91 - 120.60: 1388 120.60 - 127.28: 1096 127.28 - 133.97: 51 Bond angle restraints: 4507 Sorted by residual: angle pdb=" N ILE A 435 " pdb=" CA ILE A 435 " pdb=" C ILE A 435 " ideal model delta sigma weight residual 112.61 107.45 5.16 1.45e+00 4.76e-01 1.27e+01 angle pdb=" N PHE A 115 " pdb=" CA PHE A 115 " pdb=" C PHE A 115 " ideal model delta sigma weight residual 112.38 108.50 3.88 1.22e+00 6.72e-01 1.01e+01 angle pdb=" C LYS A 256 " pdb=" N ARG A 257 " pdb=" CA ARG A 257 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.71e+00 angle pdb=" N PHE A 116 " pdb=" CA PHE A 116 " pdb=" C PHE A 116 " ideal model delta sigma weight residual 111.69 107.87 3.82 1.23e+00 6.61e-01 9.63e+00 angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 113.07 109.28 3.79 1.36e+00 5.41e-01 7.75e+00 ... (remaining 4502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 1648 15.49 - 30.97: 142 30.97 - 46.46: 43 46.46 - 61.95: 3 61.95 - 77.44: 2 Dihedral angle restraints: 1838 sinusoidal: 627 harmonic: 1211 Sorted by residual: dihedral pdb=" CA LEU A 170 " pdb=" C LEU A 170 " pdb=" N GLU A 171 " pdb=" CA GLU A 171 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LYS A 445 " pdb=" C LYS A 445 " pdb=" N SER A 446 " pdb=" CA SER A 446 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ALA A 382 " pdb=" C ALA A 382 " pdb=" N GLY A 383 " pdb=" CA GLY A 383 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 278 0.027 - 0.054: 148 0.054 - 0.082: 58 0.082 - 0.109: 32 0.109 - 0.136: 5 Chirality restraints: 521 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA PHE A 115 " pdb=" N PHE A 115 " pdb=" C PHE A 115 " pdb=" CB PHE A 115 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA TRP A 186 " pdb=" N TRP A 186 " pdb=" C TRP A 186 " pdb=" CB TRP A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 518 not shown) Planarity restraints: 547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 435 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO A 436 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 163 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 375 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.032 5.00e-02 4.00e+02 ... (remaining 544 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 816 2.79 - 3.32: 3337 3.32 - 3.84: 5401 3.84 - 4.37: 6043 4.37 - 4.90: 10257 Nonbonded interactions: 25854 Sorted by model distance: nonbonded pdb=" OG1 THR A 304 " pdb=" OD1 ASN A 467 " model vdw 2.258 2.440 nonbonded pdb=" N ASP A 104 " pdb=" OD1 ASP A 104 " model vdw 2.447 2.520 nonbonded pdb=" O ALA A 46 " pdb=" N PHE A 50 " model vdw 2.517 2.520 nonbonded pdb=" O PHE A 116 " pdb=" N GLY A 118 " model vdw 2.524 2.520 nonbonded pdb=" O ASN A 323 " pdb=" N ASN A 327 " model vdw 2.545 2.520 ... (remaining 25849 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.680 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.740 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3203 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 : 0.003 0.032 3292 Z= 0.208 Angle : 0.629 6.398 4507 Z= 0.365 Chirality : 0.042 0.136 521 Planarity : 0.006 0.075 547 Dihedral : 13.015 77.435 1066 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.29 (0.43), residues: 420 helix: 0.78 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -1.77 (0.61), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 246 HIS 0.007 0.001 HIS A 414 PHE 0.016 0.001 PHE A 299 TYR 0.010 0.001 TYR A 335 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.351 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1697 time to fit residues: 11.5479 Evaluate side-chains 33 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.330 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 207 GLN A 430 ASN A 488 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4705 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 3292 Z= 0.377 Angle : 0.915 18.741 4507 Z= 0.454 Chirality : 0.052 0.244 521 Planarity : 0.008 0.069 547 Dihedral : 5.699 19.255 448 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.14 % Allowed : 13.06 % Favored : 82.80 % 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: -1.56 (0.38), residues: 420 helix: -0.60 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -2.02 (0.56), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 244 HIS 0.007 0.003 HIS A 183 PHE 0.033 0.003 PHE A 116 TYR 0.015 0.002 TYR A 421 ARG 0.007 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.364 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 56 average time/residue: 0.1323 time to fit residues: 9.4310 Evaluate side-chains 38 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0373 time to fit residues: 0.9173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.0570 chunk 25 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.0050 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 overall best weight: 0.3030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4759 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3292 Z= 0.184 Angle : 0.634 9.758 4507 Z= 0.314 Chirality : 0.040 0.113 521 Planarity : 0.006 0.063 547 Dihedral : 4.957 22.898 448 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.23 % Allowed : 20.06 % Favored : 77.71 % 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: -0.73 (0.40), residues: 420 helix: 0.11 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.19 (0.55), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 240 HIS 0.007 0.002 HIS A 414 PHE 0.022 0.002 PHE A 322 TYR 0.007 0.001 TYR A 306 ARG 0.006 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.339 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 42 average time/residue: 0.1410 time to fit residues: 7.5905 Evaluate side-chains 38 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0369 time to fit residues: 0.7224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5246 moved from start: 0.8146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3292 Z= 0.222 Angle : 0.610 7.471 4507 Z= 0.315 Chirality : 0.042 0.152 521 Planarity : 0.006 0.064 547 Dihedral : 4.725 20.865 448 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.59 % Allowed : 21.66 % Favored : 76.75 % 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: -0.63 (0.41), residues: 420 helix: 0.14 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.12 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 110 HIS 0.011 0.002 HIS A 183 PHE 0.020 0.002 PHE A 322 TYR 0.015 0.001 TYR A 117 ARG 0.015 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.358 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 0.1259 time to fit residues: 7.7818 Evaluate side-chains 35 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0447 time to fit residues: 0.5603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 1.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 3292 Z= 0.342 Angle : 0.760 9.670 4507 Z= 0.399 Chirality : 0.047 0.282 521 Planarity : 0.007 0.052 547 Dihedral : 5.176 19.056 448 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.50 % Allowed : 23.57 % Favored : 72.93 % 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: -1.17 (0.39), residues: 420 helix: -0.22 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -2.16 (0.51), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 246 HIS 0.006 0.002 HIS A 414 PHE 0.020 0.002 PHE A 378 TYR 0.014 0.002 TYR A 119 ARG 0.005 0.001 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.333 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 63 average time/residue: 0.1182 time to fit residues: 9.7111 Evaluate side-chains 42 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0449 time to fit residues: 0.6764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 1.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3292 Z= 0.251 Angle : 0.656 9.192 4507 Z= 0.329 Chirality : 0.043 0.130 521 Planarity : 0.006 0.058 547 Dihedral : 5.015 20.656 448 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.82 % Allowed : 25.80 % Favored : 70.38 % 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: -0.75 (0.40), residues: 420 helix: 0.08 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -2.07 (0.55), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.007 0.001 HIS A 414 PHE 0.012 0.002 PHE A 47 TYR 0.006 0.001 TYR A 203 ARG 0.015 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.339 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 62 average time/residue: 0.1271 time to fit residues: 10.0750 Evaluate side-chains 49 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0385 time to fit residues: 0.8488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.0570 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 1.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3292 Z= 0.212 Angle : 0.646 8.811 4507 Z= 0.323 Chirality : 0.042 0.211 521 Planarity : 0.006 0.059 547 Dihedral : 4.912 18.777 448 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.59 % Allowed : 28.98 % Favored : 69.43 % 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: -0.56 (0.40), residues: 420 helix: 0.26 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -2.06 (0.54), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.008 0.001 HIS A 414 PHE 0.027 0.002 PHE A 115 TYR 0.007 0.001 TYR A 128 ARG 0.007 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.342 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 52 average time/residue: 0.1329 time to fit residues: 8.8048 Evaluate side-chains 45 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.300 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0382 time to fit residues: 0.5447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.6474 moved from start: 1.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3292 Z= 0.237 Angle : 0.682 9.963 4507 Z= 0.335 Chirality : 0.043 0.164 521 Planarity : 0.006 0.060 547 Dihedral : 4.869 19.219 448 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.59 % Allowed : 31.21 % Favored : 67.20 % 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: -0.39 (0.41), residues: 420 helix: 0.38 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.11 (0.57), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 240 HIS 0.006 0.001 HIS A 414 PHE 0.012 0.001 PHE A 299 TYR 0.006 0.001 TYR A 128 ARG 0.008 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.344 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 0.1524 time to fit residues: 9.6744 Evaluate side-chains 48 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0352 time to fit residues: 0.6788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0370 chunk 37 optimal weight: 0.0030 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.2668 ------------------------------------------------------------------------------- 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: 0.6444 moved from start: 1.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3292 Z= 0.176 Angle : 0.643 11.395 4507 Z= 0.314 Chirality : 0.041 0.167 521 Planarity : 0.006 0.060 547 Dihedral : 4.801 19.720 448 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.64 % Allowed : 33.12 % Favored : 66.24 % 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: -0.17 (0.41), residues: 420 helix: 0.55 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -2.03 (0.56), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.008 0.001 HIS A 414 PHE 0.014 0.001 PHE A 299 TYR 0.008 0.001 TYR A 54 ARG 0.008 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.348 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.1469 time to fit residues: 9.2379 Evaluate side-chains 50 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.339 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0359 time to fit residues: 0.5931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.6579 moved from start: 1.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3292 Z= 0.255 Angle : 0.712 11.328 4507 Z= 0.350 Chirality : 0.044 0.171 521 Planarity : 0.006 0.060 547 Dihedral : 4.888 20.601 448 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.64 % Allowed : 33.44 % Favored : 65.92 % 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: -0.33 (0.41), residues: 420 helix: 0.48 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.32 (0.55), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 244 HIS 0.017 0.003 HIS A 414 PHE 0.015 0.001 PHE A 299 TYR 0.006 0.001 TYR A 335 ARG 0.008 0.001 ARG A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.345 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 55 average time/residue: 0.1433 time to fit residues: 9.8802 Evaluate side-chains 50 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.0060 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.0170 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.195076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.160141 restraints weight = 4555.549| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 3.04 r_work: 0.3961 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 1.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3292 Z= 0.217 Angle : 0.664 9.395 4507 Z= 0.326 Chirality : 0.042 0.138 521 Planarity : 0.006 0.060 547 Dihedral : 4.812 21.025 448 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.64 % Allowed : 34.08 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.31 (0.41), residues: 420 helix: 0.48 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.42 (0.56), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 244 HIS 0.018 0.003 HIS A 414 PHE 0.014 0.001 PHE A 299 TYR 0.008 0.001 TYR A 54 ARG 0.008 0.001 ARG A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1178.96 seconds wall clock time: 21 minutes 54.31 seconds (1314.31 seconds total)