Starting phenix.real_space_refine on Thu Nov 14 00:48:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cog_16776/11_2024/8cog_16776.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cog_16776/11_2024/8cog_16776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.499 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cog_16776/11_2024/8cog_16776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cog_16776/11_2024/8cog_16776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cog_16776/11_2024/8cog_16776.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cog_16776/11_2024/8cog_16776.cif" } resolution = 3.499 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= 0.005 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 1858 2.51 5 N 498 2.21 5 O 568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2949 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2921 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.66, per 1000 atoms: 0.90 Number of scatterers: 2949 At special positions: 0 Unit cell: (79.92, 62.64, 82.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 2 15.00 Mg 1 11.99 O 568 8.00 N 498 7.00 C 1858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 216 " - pdb=" SG CYS F 256 " distance=2.10 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: 0.76 Conformation dependent library (CDL) restraints added in 375.8 milliseconds 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 692 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 6 sheets defined 45.7% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'F' and resid 54 through 60 removed outlier: 4.060A pdb=" N GLN F 58 " --> pdb=" O GLY F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 91 Processing helix chain 'F' and resid 111 through 125 removed outlier: 4.157A pdb=" N ARG F 115 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 145 Processing helix chain 'F' and resid 171 through 174 Processing helix chain 'F' and resid 180 through 193 removed outlier: 3.554A pdb=" N LYS F 190 " --> pdb=" O ASP F 186 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 193 " --> pdb=" O MET F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 216 Processing helix chain 'F' and resid 221 through 232 Processing helix chain 'F' and resid 250 through 255 Processing helix chain 'F' and resid 256 through 262 removed outlier: 4.021A pdb=" N ALA F 259 " --> pdb=" O CYS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 282 Processing helix chain 'F' and resid 285 through 294 removed outlier: 4.201A pdb=" N LYS F 290 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 320 removed outlier: 3.582A pdb=" N LYS F 314 " --> pdb=" O ASP F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 335 No H-bonds generated for 'chain 'F' and resid 333 through 335' Processing helix chain 'F' and resid 336 through 348 Processing helix chain 'F' and resid 358 through 365 removed outlier: 3.802A pdb=" N GLU F 363 " --> pdb=" O GLN F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing sheet with id=AA1, first strand: chain 'F' and resid 16 through 17 removed outlier: 4.125A pdb=" N LYS F 17 " --> pdb=" O ASP F 10 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASN F 11 " --> pdb=" O THR F 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.518A pdb=" N GLY F 35 " --> pdb=" O TYR F 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'F' and resid 168 through 169 Processing sheet with id=AA5, first strand: chain 'F' and resid 168 through 169 Processing sheet with id=AA6, first strand: chain 'F' and resid 237 through 240 140 hydrogen bonds defined for protein. 366 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: 0.83 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.06: 1 1.06 - 1.25: 329 1.25 - 1.45: 949 1.45 - 1.64: 1696 1.64 - 1.84: 38 Bond restraints: 3013 Sorted by residual: bond pdb=" C PHE F 374 " pdb=" O PHE F 374 " ideal model delta sigma weight residual 1.231 0.861 0.370 2.00e-02 2.50e+03 3.43e+02 bond pdb=" C PHE F 374 " pdb=" OXT PHE F 374 " ideal model delta sigma weight residual 1.231 1.547 -0.316 2.00e-02 2.50e+03 2.50e+02 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.392 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" N ALA F 330 " pdb=" CA ALA F 330 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.10e-03 1.98e+04 1.99e+01 bond pdb=" N VAL F 162 " pdb=" CA VAL F 162 " ideal model delta sigma weight residual 1.456 1.493 -0.037 8.70e-03 1.32e+04 1.80e+01 ... (remaining 3008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 3978 4.44 - 8.88: 99 8.88 - 13.32: 9 13.32 - 17.76: 0 17.76 - 22.20: 1 Bond angle restraints: 4087 Sorted by residual: angle pdb=" CA PHE F 374 " pdb=" C PHE F 374 " pdb=" OXT PHE F 374 " ideal model delta sigma weight residual 121.00 98.80 22.20 3.00e+00 1.11e-01 5.48e+01 angle pdb=" C PRO F 242 " pdb=" N ASP F 243 " pdb=" CA ASP F 243 " ideal model delta sigma weight residual 120.28 128.35 -8.07 1.44e+00 4.82e-01 3.14e+01 angle pdb=" CA PHE F 261 " pdb=" C PHE F 261 " pdb=" O PHE F 261 " ideal model delta sigma weight residual 119.38 112.89 6.49 1.23e+00 6.61e-01 2.78e+01 angle pdb=" N HIS F 274 " pdb=" CA HIS F 274 " pdb=" C HIS F 274 " ideal model delta sigma weight residual 111.69 105.95 5.74 1.23e+00 6.61e-01 2.18e+01 angle pdb=" N LYS F 283 " pdb=" CA LYS F 283 " pdb=" C LYS F 283 " ideal model delta sigma weight residual 113.23 107.48 5.75 1.24e+00 6.50e-01 2.15e+01 ... (remaining 4082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.00: 1686 25.00 - 50.01: 98 50.01 - 75.01: 28 75.01 - 100.02: 4 100.02 - 125.02: 1 Dihedral angle restraints: 1817 sinusoidal: 737 harmonic: 1080 Sorted by residual: dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 174.97 125.02 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" CA ARG F 27 " pdb=" C ARG F 27 " pdb=" N ALA F 28 " pdb=" CA ALA F 28 " ideal model delta harmonic sigma weight residual -180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ARG F 195 " pdb=" C ARG F 195 " pdb=" N GLY F 196 " pdb=" CA GLY F 196 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 1814 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.056: 188 0.056 - 0.112: 153 0.112 - 0.168: 81 0.168 - 0.223: 24 0.223 - 0.279: 7 Chirality restraints: 453 Sorted by residual: chirality pdb=" CA VAL F 9 " pdb=" N VAL F 9 " pdb=" C VAL F 9 " pdb=" CB VAL F 9 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ILE F 249 " pdb=" N ILE F 249 " pdb=" C ILE F 249 " pdb=" CB ILE F 249 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA VAL F 8 " pdb=" N VAL F 8 " pdb=" C VAL F 8 " pdb=" CB VAL F 8 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 450 not shown) Planarity restraints: 523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP F 401 " 0.092 2.00e-02 2.50e+03 3.97e-02 4.33e+01 pdb=" C2 ADP F 401 " -0.039 2.00e-02 2.50e+03 pdb=" C4 ADP F 401 " -0.008 2.00e-02 2.50e+03 pdb=" C5 ADP F 401 " -0.004 2.00e-02 2.50e+03 pdb=" C6 ADP F 401 " 0.008 2.00e-02 2.50e+03 pdb=" C8 ADP F 401 " -0.042 2.00e-02 2.50e+03 pdb=" N1 ADP F 401 " 0.004 2.00e-02 2.50e+03 pdb=" N3 ADP F 401 " -0.007 2.00e-02 2.50e+03 pdb=" N6 ADP F 401 " 0.057 2.00e-02 2.50e+03 pdb=" N7 ADP F 401 " -0.022 2.00e-02 2.50e+03 pdb=" N9 ADP F 401 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 374 " 0.021 2.00e-02 2.50e+03 5.21e-02 2.72e+01 pdb=" C PHE F 374 " -0.088 2.00e-02 2.50e+03 pdb=" O PHE F 374 " 0.048 2.00e-02 2.50e+03 pdb=" OXT PHE F 374 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 30 " -0.041 2.00e-02 2.50e+03 2.77e-02 1.35e+01 pdb=" CG PHE F 30 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE F 30 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE F 30 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE F 30 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE F 30 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE F 30 " -0.042 2.00e-02 2.50e+03 ... (remaining 520 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 799 2.86 - 3.37: 3094 3.37 - 3.88: 4750 3.88 - 4.39: 5826 4.39 - 4.90: 9265 Nonbonded interactions: 23734 Sorted by model distance: nonbonded pdb=" O ILE F 121 " pdb=" OG1 THR F 125 " model vdw 2.346 3.040 nonbonded pdb=" OG SER F 13 " pdb=" O ASP F 156 " model vdw 2.417 3.040 nonbonded pdb=" O2B ADP F 401 " pdb="MG MG F 402 " model vdw 2.435 2.170 nonbonded pdb=" OG1 THR F 148 " pdb=" N GLU F 166 " model vdw 2.438 3.120 nonbonded pdb=" O2' ADP F 401 " pdb=" O3' ADP F 401 " model vdw 2.443 2.432 ... (remaining 23729 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=0.00 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: 0.700 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.250 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.017 0.370 3013 Z= 1.168 Angle : 2.044 22.203 4087 Z= 1.412 Chirality : 0.094 0.279 453 Planarity : 0.008 0.052 523 Dihedral : 17.629 125.023 1122 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.22 % Allowed : 11.71 % Favored : 86.08 % Cbeta Deviations : 0.29 % 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: -2.96 (0.39), residues: 369 helix: -2.12 (0.36), residues: 144 sheet: -0.10 (0.83), residues: 35 loop : -2.20 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.012 TRP F 78 HIS 0.010 0.004 HIS F 86 PHE 0.042 0.010 PHE F 30 TYR 0.041 0.009 TYR F 68 ARG 0.025 0.003 ARG F 311 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: F 4 ILE cc_start: 0.8449 (pt) cc_final: 0.8141 (mt) REVERT: F 11 ASN cc_start: 0.9091 (t0) cc_final: 0.8705 (p0) REVERT: F 40 GLN cc_start: 0.7500 (mt0) cc_final: 0.7162 (pm20) REVERT: F 156 ASP cc_start: 0.8848 (t0) cc_final: 0.8255 (t0) REVERT: F 240 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7353 (pp20) REVERT: F 313 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7475 (tp40) outliers start: 7 outliers final: 0 residues processed: 89 average time/residue: 0.1957 time to fit residues: 20.2778 Evaluate side-chains 52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3013 Z= 0.235 Angle : 0.715 7.578 4087 Z= 0.366 Chirality : 0.048 0.301 453 Planarity : 0.005 0.038 523 Dihedral : 8.587 113.137 420 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.48 % Allowed : 16.46 % Favored : 80.06 % 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: -1.48 (0.41), residues: 369 helix: -0.33 (0.39), residues: 155 sheet: -1.01 (0.64), residues: 65 loop : -1.53 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 85 HIS 0.005 0.001 HIS F 370 PHE 0.014 0.002 PHE F 261 TYR 0.017 0.002 TYR F 293 ARG 0.003 0.001 ARG F 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.336 Fit side-chains REVERT: F 4 ILE cc_start: 0.8234 (pt) cc_final: 0.7914 (mt) REVERT: F 40 GLN cc_start: 0.7482 (mt0) cc_final: 0.7146 (pm20) REVERT: F 71 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7987 (pp20) REVERT: F 81 MET cc_start: 0.9007 (tpt) cc_final: 0.8446 (tpt) REVERT: F 136 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8262 (mp-120) REVERT: F 240 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7241 (tm-30) REVERT: F 324 MET cc_start: 0.4053 (OUTLIER) cc_final: 0.3574 (tpp) outliers start: 11 outliers final: 5 residues processed: 68 average time/residue: 0.1130 time to fit residues: 9.8623 Evaluate side-chains 58 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 136 GLN Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 110 ASN F 120 GLN F 136 GLN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3013 Z= 0.229 Angle : 0.663 8.838 4087 Z= 0.329 Chirality : 0.046 0.147 453 Planarity : 0.004 0.042 523 Dihedral : 7.809 101.803 420 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.16 % Allowed : 19.30 % Favored : 77.53 % 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: -0.86 (0.43), residues: 369 helix: 0.14 (0.42), residues: 156 sheet: 0.12 (0.65), residues: 60 loop : -1.56 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 78 HIS 0.005 0.001 HIS F 370 PHE 0.013 0.001 PHE F 254 TYR 0.011 0.001 TYR F 293 ARG 0.003 0.000 ARG F 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.338 Fit side-chains REVERT: F 40 GLN cc_start: 0.7527 (mt0) cc_final: 0.7240 (pm20) REVERT: F 71 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8040 (pp20) REVERT: F 240 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7399 (tm-30) REVERT: F 313 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7284 (tp40) REVERT: F 324 MET cc_start: 0.3727 (OUTLIER) cc_final: 0.3296 (tpp) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.1110 time to fit residues: 8.8132 Evaluate side-chains 52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 324 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 ASN F 77 ASN F 100 HIS ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3013 Z= 0.271 Angle : 0.653 6.756 4087 Z= 0.327 Chirality : 0.047 0.156 453 Planarity : 0.005 0.044 523 Dihedral : 7.720 98.868 420 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.38 % Allowed : 18.04 % Favored : 76.58 % 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 (0.42), residues: 369 helix: 0.45 (0.42), residues: 150 sheet: 0.36 (0.64), residues: 60 loop : -1.74 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 78 HIS 0.005 0.001 HIS F 370 PHE 0.015 0.001 PHE F 254 TYR 0.013 0.001 TYR F 293 ARG 0.003 0.000 ARG F 195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.335 Fit side-chains REVERT: F 40 GLN cc_start: 0.7458 (mt0) cc_final: 0.7140 (pm20) REVERT: F 71 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8004 (pp20) REVERT: F 136 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8541 (mp10) REVERT: F 195 ARG cc_start: 0.8777 (mtp180) cc_final: 0.8511 (mtp180) REVERT: F 240 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7649 (tm-30) REVERT: F 313 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7385 (tt0) REVERT: F 324 MET cc_start: 0.3812 (OUTLIER) cc_final: 0.3351 (tpp) outliers start: 17 outliers final: 8 residues processed: 64 average time/residue: 0.1125 time to fit residues: 9.3922 Evaluate side-chains 57 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 136 GLN Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 369 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3013 Z= 0.205 Angle : 0.602 6.803 4087 Z= 0.301 Chirality : 0.044 0.145 453 Planarity : 0.004 0.043 523 Dihedral : 7.571 97.140 420 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.38 % Allowed : 18.67 % Favored : 75.95 % 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: -0.28 (0.43), residues: 369 helix: 0.80 (0.44), residues: 143 sheet: 0.51 (0.66), residues: 60 loop : -1.34 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 78 HIS 0.003 0.001 HIS F 370 PHE 0.013 0.001 PHE F 254 TYR 0.012 0.001 TYR F 293 ARG 0.002 0.000 ARG F 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.331 Fit side-chains REVERT: F 40 GLN cc_start: 0.7438 (mt0) cc_final: 0.7111 (pm20) REVERT: F 71 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7996 (pp20) REVERT: F 240 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7596 (tm-30) REVERT: F 313 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7433 (tt0) REVERT: F 324 MET cc_start: 0.3501 (OUTLIER) cc_final: 0.3046 (tpp) outliers start: 17 outliers final: 9 residues processed: 63 average time/residue: 0.1200 time to fit residues: 9.8587 Evaluate side-chains 58 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 324 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3013 Z= 0.218 Angle : 0.606 6.779 4087 Z= 0.302 Chirality : 0.046 0.301 453 Planarity : 0.004 0.041 523 Dihedral : 7.525 97.107 420 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.75 % Allowed : 18.67 % Favored : 76.58 % 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 (0.43), residues: 369 helix: 0.83 (0.44), residues: 143 sheet: 0.56 (0.66), residues: 60 loop : -1.20 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 78 HIS 0.003 0.001 HIS F 100 PHE 0.014 0.001 PHE F 254 TYR 0.011 0.001 TYR F 293 ARG 0.002 0.000 ARG F 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.356 Fit side-chains REVERT: F 7 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8373 (mt) REVERT: F 40 GLN cc_start: 0.7401 (mt0) cc_final: 0.7061 (pm20) REVERT: F 71 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8006 (pp20) REVERT: F 240 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7678 (tm-30) REVERT: F 313 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7434 (tt0) REVERT: F 324 MET cc_start: 0.3455 (OUTLIER) cc_final: 0.3038 (tpp) outliers start: 15 outliers final: 10 residues processed: 64 average time/residue: 0.1190 time to fit residues: 9.8561 Evaluate side-chains 64 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 324 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.0060 chunk 6 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3013 Z= 0.188 Angle : 0.585 6.807 4087 Z= 0.290 Chirality : 0.044 0.140 453 Planarity : 0.004 0.035 523 Dihedral : 7.427 95.893 420 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.80 % Allowed : 20.25 % Favored : 75.95 % 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: -0.05 (0.43), residues: 369 helix: 0.94 (0.44), residues: 143 sheet: 0.62 (0.66), residues: 60 loop : -1.14 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 78 HIS 0.002 0.001 HIS F 100 PHE 0.013 0.001 PHE F 254 TYR 0.011 0.001 TYR F 293 ARG 0.002 0.000 ARG F 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.382 Fit side-chains REVERT: F 7 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8377 (mt) REVERT: F 40 GLN cc_start: 0.7360 (mt0) cc_final: 0.7030 (pm20) REVERT: F 71 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8036 (pp20) REVERT: F 240 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7580 (tm-30) REVERT: F 282 MET cc_start: 0.8399 (mmm) cc_final: 0.8077 (mmm) REVERT: F 313 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7510 (tt0) outliers start: 12 outliers final: 8 residues processed: 60 average time/residue: 0.1126 time to fit residues: 8.7672 Evaluate side-chains 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 256 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.0050 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3013 Z= 0.185 Angle : 0.590 6.841 4087 Z= 0.287 Chirality : 0.044 0.150 453 Planarity : 0.004 0.031 523 Dihedral : 7.328 94.455 420 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.43 % Allowed : 20.25 % Favored : 75.32 % 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: 0.09 (0.43), residues: 369 helix: 1.08 (0.44), residues: 143 sheet: 0.63 (0.66), residues: 60 loop : -1.06 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 78 HIS 0.002 0.001 HIS F 100 PHE 0.013 0.001 PHE F 254 TYR 0.010 0.001 TYR F 293 ARG 0.001 0.000 ARG F 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.350 Fit side-chains REVERT: F 7 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8356 (mt) REVERT: F 40 GLN cc_start: 0.7264 (mt0) cc_final: 0.6948 (pm20) REVERT: F 71 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8027 (pp20) REVERT: F 240 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7620 (tm-30) REVERT: F 282 MET cc_start: 0.8368 (mmm) cc_final: 0.8063 (mmm) REVERT: F 313 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7504 (tt0) REVERT: F 324 MET cc_start: 0.3330 (OUTLIER) cc_final: 0.3071 (tpp) outliers start: 14 outliers final: 8 residues processed: 59 average time/residue: 0.1183 time to fit residues: 9.2080 Evaluate side-chains 59 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 324 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3013 Z= 0.224 Angle : 0.617 7.556 4087 Z= 0.301 Chirality : 0.045 0.150 453 Planarity : 0.004 0.031 523 Dihedral : 7.377 95.366 420 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.48 % Allowed : 20.89 % Favored : 75.63 % 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: 0.05 (0.43), residues: 369 helix: 1.06 (0.44), residues: 143 sheet: 0.68 (0.66), residues: 60 loop : -1.13 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 78 HIS 0.003 0.001 HIS F 100 PHE 0.017 0.002 PHE F 351 TYR 0.018 0.001 TYR F 52 ARG 0.002 0.000 ARG F 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.352 Fit side-chains REVERT: F 40 GLN cc_start: 0.7254 (mt0) cc_final: 0.6927 (pm20) REVERT: F 71 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7881 (pp20) REVERT: F 240 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7734 (tm-30) REVERT: F 282 MET cc_start: 0.8346 (mmm) cc_final: 0.8042 (mmm) REVERT: F 324 MET cc_start: 0.3358 (OUTLIER) cc_final: 0.3095 (tpp) REVERT: F 354 MET cc_start: 0.7860 (mmm) cc_final: 0.7430 (mpp) outliers start: 11 outliers final: 9 residues processed: 54 average time/residue: 0.1090 time to fit residues: 7.6853 Evaluate side-chains 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 324 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3013 Z= 0.212 Angle : 0.618 7.585 4087 Z= 0.301 Chirality : 0.044 0.142 453 Planarity : 0.004 0.030 523 Dihedral : 7.374 95.694 420 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.48 % Allowed : 21.20 % Favored : 75.32 % 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: 0.08 (0.43), residues: 369 helix: 1.10 (0.44), residues: 143 sheet: 0.74 (0.66), residues: 60 loop : -1.15 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 78 HIS 0.004 0.001 HIS F 100 PHE 0.013 0.001 PHE F 254 TYR 0.017 0.001 TYR F 52 ARG 0.002 0.000 ARG F 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.364 Fit side-chains REVERT: F 40 GLN cc_start: 0.7203 (mt0) cc_final: 0.6858 (pm20) REVERT: F 240 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7730 (tm-30) REVERT: F 282 MET cc_start: 0.8377 (mmm) cc_final: 0.8061 (mmm) REVERT: F 324 MET cc_start: 0.3348 (OUTLIER) cc_final: 0.3092 (tpp) REVERT: F 354 MET cc_start: 0.7900 (mmm) cc_final: 0.7483 (mpp) outliers start: 11 outliers final: 9 residues processed: 53 average time/residue: 0.1132 time to fit residues: 7.8905 Evaluate side-chains 57 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 324 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112609 restraints weight = 4241.263| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.79 r_work: 0.3184 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3013 Z= 0.189 Angle : 0.609 8.652 4087 Z= 0.295 Chirality : 0.044 0.137 453 Planarity : 0.004 0.030 523 Dihedral : 7.331 95.065 420 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.16 % Allowed : 21.20 % Favored : 75.63 % 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: 0.15 (0.44), residues: 369 helix: 1.15 (0.44), residues: 143 sheet: 0.78 (0.66), residues: 60 loop : -1.10 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 78 HIS 0.003 0.001 HIS F 100 PHE 0.013 0.001 PHE F 254 TYR 0.015 0.001 TYR F 52 ARG 0.001 0.000 ARG F 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1101.32 seconds wall clock time: 20 minutes 43.09 seconds (1243.09 seconds total)