Starting phenix.real_space_refine on Thu Nov 14 03:18:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/11_2024/8sib_40505.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/11_2024/8sib_40505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/11_2024/8sib_40505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/11_2024/8sib_40505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/11_2024/8sib_40505.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/11_2024/8sib_40505.cif" } resolution = 2.62 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= 0.017 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 18 5.16 5 C 2261 2.51 5 N 619 2.21 5 O 646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3544 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3544 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 3.08, per 1000 atoms: 0.87 Number of scatterers: 3544 At special positions: 0 Unit cell: (66.4, 94.62, 74.7, 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 18 16.00 O 646 8.00 N 619 7.00 C 2261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 44 " distance=2.04 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 36 " distance=2.04 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 44 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 412.0 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 840 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 38.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 116 through 125 removed outlier: 3.534A pdb=" N LEU A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 3.511A pdb=" N LEU A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 4.447A pdb=" N HIS A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 258 through 273 removed outlier: 4.302A pdb=" N LEU A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.755A pdb=" N GLN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 removed outlier: 3.624A pdb=" N GLN A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.832A pdb=" N THR A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 390 through 398 removed outlier: 3.538A pdb=" N ALA A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 418 Processing helix chain 'A' and resid 419 through 426 removed outlier: 3.943A pdb=" N ALA A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 449 removed outlier: 3.507A pdb=" N LEU A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.823A pdb=" N GLU A 15 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.479A pdb=" N LYS A 107 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU A 247 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A 109 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASP A 249 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU A 111 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR A 201 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE A 246 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY A 203 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 248 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA A 205 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS A 200 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 135 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU A 172 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 137 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 312 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE A 381 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 314 " --> pdb=" O PHE A 381 " (cutoff:3.500A) 117 hydrogen bonds defined for protein. 342 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: 0.89 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1156 1.34 - 1.47: 780 1.47 - 1.59: 1652 1.59 - 1.71: 0 1.71 - 1.83: 26 Bond restraints: 3614 Sorted by residual: bond pdb=" C GLU A 343 " pdb=" N PRO A 344 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.25e-02 6.40e+03 7.38e+00 bond pdb=" N SER A 101 " pdb=" CA SER A 101 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.16e+00 bond pdb=" C LEU A 30 " pdb=" N PRO A 31 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.04e+00 bond pdb=" C SER A 307 " pdb=" N PRO A 308 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.18e-02 7.18e+03 4.02e+00 bond pdb=" CB ILE A 412 " pdb=" CG2 ILE A 412 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.36e+00 ... (remaining 3609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 4661 2.66 - 5.32: 200 5.32 - 7.98: 21 7.98 - 10.64: 10 10.64 - 13.30: 4 Bond angle restraints: 4896 Sorted by residual: angle pdb=" C ARG A 46 " pdb=" N LEU A 47 " pdb=" CA LEU A 47 " ideal model delta sigma weight residual 121.54 133.47 -11.93 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C GLU A 76 " pdb=" N GLU A 77 " pdb=" CA GLU A 77 " ideal model delta sigma weight residual 122.46 129.98 -7.52 1.41e+00 5.03e-01 2.84e+01 angle pdb=" C CYS A 36 " pdb=" N GLN A 37 " pdb=" CA GLN A 37 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C VAL A 48 " pdb=" N LYS A 49 " pdb=" CA LYS A 49 " ideal model delta sigma weight residual 121.54 130.64 -9.10 1.91e+00 2.74e-01 2.27e+01 angle pdb=" C GLY A 100 " pdb=" N SER A 101 " pdb=" CA SER A 101 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 ... (remaining 4891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 2018 15.41 - 30.83: 117 30.83 - 46.24: 29 46.24 - 61.66: 8 61.66 - 77.07: 7 Dihedral angle restraints: 2179 sinusoidal: 877 harmonic: 1302 Sorted by residual: dihedral pdb=" CA SER A 307 " pdb=" C SER A 307 " pdb=" N PRO A 308 " pdb=" CA PRO A 308 " ideal model delta harmonic sigma weight residual -180.00 -123.29 -56.71 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LEU A 30 " pdb=" C LEU A 30 " pdb=" N PRO A 31 " pdb=" CA PRO A 31 " ideal model delta harmonic sigma weight residual -180.00 -126.99 -53.01 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ILE A 383 " pdb=" C ILE A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta harmonic sigma weight residual -180.00 -131.62 -48.38 0 5.00e+00 4.00e-02 9.36e+01 ... (remaining 2176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 438 0.065 - 0.130: 103 0.130 - 0.195: 19 0.195 - 0.260: 1 0.260 - 0.325: 5 Chirality restraints: 566 Sorted by residual: chirality pdb=" CB VAL A 176 " pdb=" CA VAL A 176 " pdb=" CG1 VAL A 176 " pdb=" CG2 VAL A 176 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CG LEU A 47 " pdb=" CB LEU A 47 " pdb=" CD1 LEU A 47 " pdb=" CD2 LEU A 47 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE A 383 " pdb=" CA ILE A 383 " pdb=" CG1 ILE A 383 " pdb=" CG2 ILE A 383 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 563 not shown) Planarity restraints: 622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 95 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE A 95 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE A 95 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN A 96 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " -0.058 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO A 31 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 31 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C PRO A 31 " 0.055 2.00e-02 2.50e+03 pdb=" O PRO A 31 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY A 32 " -0.018 2.00e-02 2.50e+03 ... (remaining 619 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 836 2.79 - 3.32: 3127 3.32 - 3.85: 5541 3.85 - 4.37: 6449 4.37 - 4.90: 11243 Nonbonded interactions: 27196 Sorted by model distance: nonbonded pdb=" O PHE A 290 " pdb=" OG1 THR A 318 " model vdw 2.265 3.040 nonbonded pdb=" O ALA A 163 " pdb=" OG1 THR A 167 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR A 108 " pdb=" O LEU A 216 " model vdw 2.338 3.040 nonbonded pdb=" NH1 ARG A 41 " pdb=" O ARG A 46 " model vdw 2.348 3.120 nonbonded pdb=" N LEU A 30 " pdb=" O LEU A 30 " model vdw 2.374 2.496 ... (remaining 27191 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: 1.190 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.590 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 0.007 0.060 3614 Z= 0.439 Angle : 1.304 13.305 4896 Z= 0.754 Chirality : 0.064 0.325 566 Planarity : 0.008 0.088 622 Dihedral : 11.699 75.711 1330 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 1.33 % Allowed : 12.89 % Favored : 85.78 % Rotamer: Outliers : 0.78 % Allowed : 3.88 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 17.65 % Twisted General : 0.92 % 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: -5.28 (0.28), residues: 450 helix: -4.12 (0.18), residues: 167 sheet: -1.75 (0.55), residues: 62 loop : -3.55 (0.33), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 6 HIS 0.012 0.002 HIS A 242 PHE 0.021 0.004 PHE A 381 TYR 0.028 0.003 TYR A 108 ARG 0.007 0.001 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 102 HIS cc_start: 0.7321 (m-70) cc_final: 0.6998 (m170) REVERT: A 198 LYS cc_start: 0.8504 (mmtt) cc_final: 0.7943 (ttpp) REVERT: A 211 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7185 (mm-30) REVERT: A 352 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8615 (mttp) REVERT: A 370 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8435 (mm-30) outliers start: 3 outliers final: 1 residues processed: 80 average time/residue: 1.3821 time to fit residues: 113.5365 Evaluate side-chains 43 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 22 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 86 GLN A 144 GLN A 154 GLN A 276 HIS A 404 ASN A 432 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3614 Z= 0.250 Angle : 0.833 11.468 4896 Z= 0.424 Chirality : 0.047 0.247 566 Planarity : 0.006 0.075 622 Dihedral : 7.546 41.602 483 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.89 % Allowed : 13.11 % Favored : 86.00 % Rotamer: Outliers : 3.36 % Allowed : 11.63 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.69 % 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: -3.55 (0.33), residues: 450 helix: -1.49 (0.34), residues: 178 sheet: -2.09 (0.60), residues: 51 loop : -3.23 (0.35), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 78 HIS 0.006 0.001 HIS A 51 PHE 0.010 0.001 PHE A 146 TYR 0.009 0.001 TYR A 327 ARG 0.007 0.001 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 37 GLN cc_start: 0.6648 (OUTLIER) cc_final: 0.6399 (mm-40) REVERT: A 198 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8282 (tttt) REVERT: A 265 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: A 327 TYR cc_start: 0.8834 (t80) cc_final: 0.8606 (t80) REVERT: A 349 THR cc_start: 0.8662 (m) cc_final: 0.8300 (t) REVERT: A 352 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8715 (mppt) REVERT: A 443 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7982 (ttp) REVERT: A 460 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8055 (tm-30) outliers start: 13 outliers final: 1 residues processed: 61 average time/residue: 1.2889 time to fit residues: 81.1913 Evaluate side-chains 44 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 443 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.0000 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3614 Z= 0.264 Angle : 0.853 15.155 4896 Z= 0.420 Chirality : 0.047 0.181 566 Planarity : 0.004 0.041 622 Dihedral : 7.122 44.156 481 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.67 % Allowed : 12.89 % Favored : 86.44 % Rotamer: Outliers : 2.84 % Allowed : 13.70 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.46 % 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: -2.65 (0.37), residues: 450 helix: -0.23 (0.38), residues: 178 sheet: -2.00 (0.59), residues: 51 loop : -3.11 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.006 0.001 HIS A 51 PHE 0.008 0.001 PHE A 356 TYR 0.006 0.001 TYR A 18 ARG 0.006 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8535 (mmtt) cc_final: 0.8284 (tttt) REVERT: A 265 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: A 291 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6774 (tt0) REVERT: A 460 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8057 (tm-30) outliers start: 11 outliers final: 3 residues processed: 48 average time/residue: 1.3791 time to fit residues: 68.3801 Evaluate side-chains 39 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 303 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 21 optimal weight: 0.0370 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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: 0.8138 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3614 Z= 0.263 Angle : 0.820 16.086 4896 Z= 0.408 Chirality : 0.048 0.239 566 Planarity : 0.004 0.042 622 Dihedral : 6.889 40.044 481 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.67 % Allowed : 12.89 % Favored : 86.44 % Rotamer: Outliers : 4.13 % Allowed : 14.21 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.46 % 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: -2.24 (0.38), residues: 450 helix: 0.28 (0.40), residues: 178 sheet: -1.93 (0.60), residues: 51 loop : -2.99 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 207 HIS 0.006 0.001 HIS A 51 PHE 0.020 0.002 PHE A 356 TYR 0.009 0.001 TYR A 327 ARG 0.004 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.397 Fit side-chains REVERT: A 92 TYR cc_start: 0.8565 (p90) cc_final: 0.7496 (p90) REVERT: A 198 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8278 (tttt) REVERT: A 352 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8499 (mtmt) REVERT: A 460 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8080 (tm-30) outliers start: 16 outliers final: 5 residues processed: 55 average time/residue: 1.2220 time to fit residues: 69.6442 Evaluate side-chains 42 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 303 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.0770 chunk 39 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3614 Z= 0.232 Angle : 0.811 16.796 4896 Z= 0.396 Chirality : 0.047 0.223 566 Planarity : 0.005 0.080 622 Dihedral : 6.674 39.530 481 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.78 % Favored : 85.78 % Rotamer: Outliers : 3.88 % Allowed : 16.80 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.46 % 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: -1.93 (0.40), residues: 450 helix: 0.54 (0.41), residues: 178 sheet: -1.78 (0.62), residues: 51 loop : -2.81 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.004 0.001 HIS A 191 PHE 0.019 0.002 PHE A 356 TYR 0.005 0.001 TYR A 108 ARG 0.004 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8563 (p90) cc_final: 0.7420 (p90) REVERT: A 198 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8279 (tttt) REVERT: A 302 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7185 (pp20) REVERT: A 358 GLN cc_start: 0.8537 (mm110) cc_final: 0.8316 (mm110) REVERT: A 460 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8110 (tm-30) outliers start: 15 outliers final: 6 residues processed: 51 average time/residue: 1.0931 time to fit residues: 57.9077 Evaluate side-chains 42 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 371 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 31 optimal weight: 0.0000 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 50 GLN A 154 GLN A 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3614 Z= 0.212 Angle : 0.789 17.576 4896 Z= 0.387 Chirality : 0.047 0.198 566 Planarity : 0.005 0.068 622 Dihedral : 6.456 37.474 481 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.67 % Allowed : 12.89 % Favored : 86.44 % Rotamer: Outliers : 3.88 % Allowed : 19.12 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.46 % 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: -1.66 (0.40), residues: 450 helix: 0.82 (0.41), residues: 178 sheet: -1.38 (0.65), residues: 49 loop : -2.78 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.006 0.001 HIS A 51 PHE 0.018 0.001 PHE A 356 TYR 0.010 0.001 TYR A 327 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.401 Fit side-chains REVERT: A 92 TYR cc_start: 0.8534 (p90) cc_final: 0.7424 (p90) REVERT: A 114 ASP cc_start: 0.8304 (t70) cc_final: 0.8036 (t0) REVERT: A 198 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8268 (tttt) REVERT: A 265 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: A 291 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: A 302 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7317 (pp20) REVERT: A 358 GLN cc_start: 0.8576 (mm110) cc_final: 0.8339 (mm110) outliers start: 15 outliers final: 7 residues processed: 54 average time/residue: 1.1431 time to fit residues: 63.9887 Evaluate side-chains 50 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 392 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3614 Z= 0.258 Angle : 0.821 17.487 4896 Z= 0.404 Chirality : 0.047 0.206 566 Planarity : 0.004 0.056 622 Dihedral : 6.399 37.706 481 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.00 % Favored : 85.56 % Rotamer: Outliers : 4.13 % Allowed : 20.41 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -1.66 (0.40), residues: 450 helix: 0.79 (0.41), residues: 179 sheet: -1.37 (0.65), residues: 49 loop : -2.78 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 207 HIS 0.006 0.001 HIS A 51 PHE 0.016 0.001 PHE A 356 TYR 0.005 0.001 TYR A 108 ARG 0.002 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.450 Fit side-chains REVERT: A 92 TYR cc_start: 0.8551 (p90) cc_final: 0.7381 (p90) REVERT: A 114 ASP cc_start: 0.8367 (t70) cc_final: 0.8095 (t0) REVERT: A 198 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8266 (tttt) REVERT: A 302 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7239 (pp20) REVERT: A 358 GLN cc_start: 0.8646 (mm110) cc_final: 0.8423 (mm110) REVERT: A 435 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8485 (pp) outliers start: 16 outliers final: 8 residues processed: 54 average time/residue: 1.0976 time to fit residues: 61.5895 Evaluate side-chains 50 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 435 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 0.0050 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3614 Z= 0.223 Angle : 0.800 17.350 4896 Z= 0.393 Chirality : 0.047 0.188 566 Planarity : 0.004 0.052 622 Dihedral : 6.324 37.287 481 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.56 % Favored : 86.00 % Rotamer: Outliers : 3.62 % Allowed : 21.19 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.69 % 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: -1.60 (0.40), residues: 450 helix: 0.84 (0.41), residues: 179 sheet: -1.27 (0.66), residues: 49 loop : -2.76 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.006 0.001 HIS A 51 PHE 0.015 0.001 PHE A 356 TYR 0.006 0.001 TYR A 108 ARG 0.005 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.470 Fit side-chains REVERT: A 92 TYR cc_start: 0.8528 (p90) cc_final: 0.7359 (p90) REVERT: A 114 ASP cc_start: 0.8322 (t70) cc_final: 0.8077 (t0) REVERT: A 198 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8263 (tttt) REVERT: A 302 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7263 (pp20) REVERT: A 358 GLN cc_start: 0.8646 (mm110) cc_final: 0.8423 (mm110) REVERT: A 435 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8488 (pp) outliers start: 14 outliers final: 6 residues processed: 51 average time/residue: 0.9867 time to fit residues: 52.5210 Evaluate side-chains 47 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 435 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3614 Z= 0.229 Angle : 0.820 17.714 4896 Z= 0.404 Chirality : 0.047 0.191 566 Planarity : 0.004 0.042 622 Dihedral : 6.143 33.328 481 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.11 % Favored : 86.22 % Rotamer: Outliers : 2.84 % Allowed : 22.22 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -1.52 (0.40), residues: 450 helix: 0.95 (0.41), residues: 179 sheet: -1.19 (0.67), residues: 49 loop : -2.77 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.006 0.001 HIS A 149 PHE 0.015 0.001 PHE A 356 TYR 0.005 0.001 TYR A 108 ARG 0.002 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.409 Fit side-chains REVERT: A 92 TYR cc_start: 0.8533 (p90) cc_final: 0.7372 (p90) REVERT: A 114 ASP cc_start: 0.8309 (t70) cc_final: 0.8071 (t0) REVERT: A 198 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8257 (tttt) REVERT: A 302 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7271 (pp20) REVERT: A 358 GLN cc_start: 0.8635 (mm110) cc_final: 0.8343 (mm110) REVERT: A 435 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8434 (pp) outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 1.0335 time to fit residues: 54.9222 Evaluate side-chains 48 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 435 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3614 Z= 0.224 Angle : 0.815 17.993 4896 Z= 0.400 Chirality : 0.047 0.171 566 Planarity : 0.004 0.041 622 Dihedral : 6.075 33.841 481 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.56 % Favored : 86.00 % Rotamer: Outliers : 2.84 % Allowed : 23.26 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.51 (0.40), residues: 450 helix: 0.94 (0.41), residues: 179 sheet: -1.18 (0.67), residues: 49 loop : -2.74 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.006 0.001 HIS A 51 PHE 0.015 0.001 PHE A 356 TYR 0.010 0.001 TYR A 327 ARG 0.002 0.000 ARG A 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.425 Fit side-chains REVERT: A 92 TYR cc_start: 0.8557 (p90) cc_final: 0.7352 (p90) REVERT: A 114 ASP cc_start: 0.8312 (t70) cc_final: 0.8080 (t0) REVERT: A 198 LYS cc_start: 0.8518 (mmtt) cc_final: 0.8251 (tttt) REVERT: A 302 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7255 (pp20) REVERT: A 358 GLN cc_start: 0.8646 (mm110) cc_final: 0.8356 (mm110) REVERT: A 435 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8407 (pp) outliers start: 11 outliers final: 7 residues processed: 49 average time/residue: 1.0382 time to fit residues: 53.0473 Evaluate side-chains 49 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 435 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.0670 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 27 optimal weight: 0.0770 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.132217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.104305 restraints weight = 6565.440| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.66 r_work: 0.3418 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3614 Z= 0.212 Angle : 0.823 18.299 4896 Z= 0.400 Chirality : 0.047 0.186 566 Planarity : 0.004 0.041 622 Dihedral : 6.031 34.994 481 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.11 % Favored : 86.22 % Rotamer: Outliers : 2.33 % Allowed : 24.03 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.44 (0.40), residues: 450 helix: 1.01 (0.42), residues: 179 sheet: -1.18 (0.67), residues: 49 loop : -2.71 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 207 HIS 0.006 0.001 HIS A 329 PHE 0.014 0.001 PHE A 356 TYR 0.006 0.001 TYR A 327 ARG 0.003 0.000 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1829.34 seconds wall clock time: 33 minutes 35.10 seconds (2015.10 seconds total)