Starting phenix.real_space_refine on Sun Mar 10 20:46:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4s_33606/03_2024/7y4s_33606.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4s_33606/03_2024/7y4s_33606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4s_33606/03_2024/7y4s_33606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4s_33606/03_2024/7y4s_33606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4s_33606/03_2024/7y4s_33606.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y4s_33606/03_2024/7y4s_33606.pdb" } resolution = 3.5 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= 0.097 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 12 5.16 5 C 3126 2.51 5 N 912 2.21 5 O 890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4940 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2470 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 149 Chain: "B" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2470 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 149 Time building chain proxies: 3.15, per 1000 atoms: 0.64 Number of scatterers: 4940 At special positions: 0 Unit cell: (103.455, 176.605, 83.6, 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 12 16.00 O 890 8.00 N 912 7.00 C 3126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 934.2 milliseconds 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1288 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 6 sheets defined 40.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 125 through 228 Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 235 through 254 removed outlier: 4.212A pdb=" N CYS A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 285 removed outlier: 3.749A pdb=" N PHE A 281 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG A 282 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 228 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 235 through 254 removed outlier: 4.212A pdb=" N CYS B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 285 removed outlier: 3.749A pdb=" N PHE B 281 " --> pdb=" O TRP B 277 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG B 282 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 302 through 304 removed outlier: 3.556A pdb=" N VAL A 311 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 467 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 424 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 440 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE A 426 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 386 Processing sheet with id=AA4, first strand: chain 'B' and resid 302 through 304 removed outlier: 3.556A pdb=" N VAL B 311 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 467 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 424 " --> pdb=" O ALA B 440 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 440 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE B 426 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 333 through 335 Processing sheet with id=AA6, first strand: chain 'B' and resid 385 through 386 299 hydrogen bonds defined for protein. 873 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: 1.40 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1722 1.34 - 1.46: 918 1.46 - 1.58: 2394 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 5052 Sorted by residual: bond pdb=" CB VAL A 375 " pdb=" CG1 VAL A 375 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.99e+00 bond pdb=" CB VAL B 375 " pdb=" CG1 VAL B 375 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.98e+00 bond pdb=" CB VAL A 375 " pdb=" CG2 VAL A 375 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" CB VAL B 375 " pdb=" CG2 VAL B 375 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" CA PRO B 448 " pdb=" C PRO B 448 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.03e+00 ... (remaining 5047 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.52: 160 105.52 - 112.65: 2610 112.65 - 119.78: 1591 119.78 - 126.91: 2451 126.91 - 134.04: 82 Bond angle restraints: 6894 Sorted by residual: angle pdb=" C VAL B 375 " pdb=" CA VAL B 375 " pdb=" CB VAL B 375 " ideal model delta sigma weight residual 109.33 112.78 -3.45 9.80e-01 1.04e+00 1.24e+01 angle pdb=" C ASP B 459 " pdb=" N LYS B 460 " pdb=" CA LYS B 460 " ideal model delta sigma weight residual 121.54 127.67 -6.13 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C ASP A 459 " pdb=" N LYS A 460 " pdb=" CA LYS A 460 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" CA VAL B 375 " pdb=" C VAL B 375 " pdb=" N PRO B 376 " ideal model delta sigma weight residual 116.57 119.49 -2.92 9.80e-01 1.04e+00 8.90e+00 angle pdb=" CA ARG A 404 " pdb=" CB ARG A 404 " pdb=" CG ARG A 404 " ideal model delta sigma weight residual 114.10 119.40 -5.30 2.00e+00 2.50e-01 7.02e+00 ... (remaining 6889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 2762 15.14 - 30.28: 216 30.28 - 45.41: 50 45.41 - 60.55: 8 60.55 - 75.69: 8 Dihedral angle restraints: 3044 sinusoidal: 1066 harmonic: 1978 Sorted by residual: dihedral pdb=" CA SER A 430 " pdb=" C SER A 430 " pdb=" N ASP A 431 " pdb=" CA ASP A 431 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA SER B 430 " pdb=" C SER B 430 " pdb=" N ASP B 431 " pdb=" CA ASP B 431 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB MET A 285 " pdb=" CG MET A 285 " pdb=" SD MET A 285 " pdb=" CE MET A 285 " ideal model delta sinusoidal sigma weight residual 60.00 119.60 -59.60 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 470 0.031 - 0.061: 203 0.061 - 0.092: 70 0.092 - 0.122: 19 0.122 - 0.153: 12 Chirality restraints: 774 Sorted by residual: chirality pdb=" CA VAL B 395 " pdb=" N VAL B 395 " pdb=" C VAL B 395 " pdb=" CB VAL B 395 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA VAL A 395 " pdb=" N VAL A 395 " pdb=" C VAL A 395 " pdb=" CB VAL A 395 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA VAL B 304 " pdb=" N VAL B 304 " pdb=" C VAL B 304 " pdb=" CB VAL B 304 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 771 not shown) Planarity restraints: 928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 399 " 0.042 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO A 400 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 400 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 400 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 399 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO B 400 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 400 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 400 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 375 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.71e+00 pdb=" N PRO A 376 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " -0.030 5.00e-02 4.00e+02 ... (remaining 925 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 1698 2.88 - 3.38: 4794 3.38 - 3.89: 7875 3.89 - 4.39: 8095 4.39 - 4.90: 14623 Nonbonded interactions: 37085 Sorted by model distance: nonbonded pdb=" OE1 GLU B 348 " pdb=" NH1 ARG B 412 " model vdw 2.373 2.520 nonbonded pdb=" OE1 GLU A 348 " pdb=" NH1 ARG A 412 " model vdw 2.373 2.520 nonbonded pdb=" O THR A 292 " pdb=" N HIS A 337 " model vdw 2.407 2.520 nonbonded pdb=" O THR B 292 " pdb=" N HIS B 337 " model vdw 2.407 2.520 nonbonded pdb=" OH TYR A 346 " pdb=" OE2 GLU A 348 " model vdw 2.513 2.440 ... (remaining 37080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 0.780 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: 0.000 Extract box with map and model: 3.830 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.490 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 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 : 0.004 0.057 5052 Z= 0.276 Angle : 0.740 8.109 6894 Z= 0.383 Chirality : 0.042 0.153 774 Planarity : 0.008 0.064 928 Dihedral : 12.744 75.690 1756 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.46 % Allowed : 2.30 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.47 (0.31), residues: 678 helix: 3.05 (0.26), residues: 276 sheet: -0.87 (0.46), residues: 120 loop : -0.26 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 277 HIS 0.001 0.000 HIS B 373 PHE 0.012 0.002 PHE A 426 TYR 0.006 0.002 TYR A 450 ARG 0.004 0.001 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.581 Fit side-chains REVERT: A 389 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8067 (mmtt) REVERT: B 389 LYS cc_start: 0.8459 (mtmt) cc_final: 0.8068 (mmtt) outliers start: 2 outliers final: 1 residues processed: 107 average time/residue: 0.2570 time to fit residues: 32.6777 Evaluate side-chains 72 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 34 optimal weight: 50.0000 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.0070 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5052 Z= 0.203 Angle : 0.551 5.713 6894 Z= 0.274 Chirality : 0.038 0.123 774 Planarity : 0.006 0.054 928 Dihedral : 4.551 57.912 741 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.23 % Allowed : 8.99 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.15 (0.33), residues: 678 helix: 4.24 (0.29), residues: 246 sheet: -0.87 (0.46), residues: 122 loop : 0.09 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 347 HIS 0.001 0.000 HIS A 458 PHE 0.013 0.002 PHE B 452 TYR 0.004 0.001 TYR B 346 ARG 0.005 0.001 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.553 Fit side-chains REVERT: A 389 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8039 (mmtt) REVERT: A 454 ASP cc_start: 0.6826 (t0) cc_final: 0.6168 (t0) REVERT: B 389 LYS cc_start: 0.8438 (mtmt) cc_final: 0.8045 (mmtt) REVERT: B 398 LYS cc_start: 0.7181 (tptp) cc_final: 0.6893 (tptt) REVERT: B 454 ASP cc_start: 0.6815 (t0) cc_final: 0.6159 (t0) outliers start: 14 outliers final: 4 residues processed: 90 average time/residue: 0.2603 time to fit residues: 27.8707 Evaluate side-chains 72 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 431 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 50.0000 chunk 19 optimal weight: 0.1980 chunk 51 optimal weight: 0.0870 chunk 42 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 46 optimal weight: 9.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 338 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5052 Z= 0.169 Angle : 0.538 8.821 6894 Z= 0.262 Chirality : 0.038 0.176 774 Planarity : 0.005 0.045 928 Dihedral : 3.780 13.887 738 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.84 % Allowed : 14.52 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.33 (0.33), residues: 678 helix: 4.45 (0.29), residues: 246 sheet: -0.84 (0.47), residues: 122 loop : 0.16 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 457 HIS 0.001 0.000 HIS B 373 PHE 0.014 0.002 PHE B 293 TYR 0.007 0.001 TYR B 346 ARG 0.005 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.553 Fit side-chains REVERT: A 389 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8041 (mmtt) REVERT: B 389 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8032 (mmtt) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.2504 time to fit residues: 24.0091 Evaluate side-chains 72 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 431 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 338 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5052 Z= 0.268 Angle : 0.560 5.229 6894 Z= 0.272 Chirality : 0.039 0.140 774 Planarity : 0.005 0.047 928 Dihedral : 3.881 14.133 738 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.38 % Allowed : 13.82 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.37 (0.33), residues: 678 helix: 4.48 (0.29), residues: 246 sheet: -1.38 (0.46), residues: 122 loop : 0.47 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 347 HIS 0.002 0.000 HIS A 345 PHE 0.020 0.002 PHE A 293 TYR 0.004 0.001 TYR A 427 ARG 0.005 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.513 Fit side-chains REVERT: A 285 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7700 (mtt) REVERT: A 389 LYS cc_start: 0.8428 (mtmt) cc_final: 0.8069 (mmtt) REVERT: B 285 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7798 (mtt) REVERT: B 389 LYS cc_start: 0.8372 (mtmt) cc_final: 0.8013 (mmtt) outliers start: 19 outliers final: 13 residues processed: 80 average time/residue: 0.2173 time to fit residues: 21.4174 Evaluate side-chains 77 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN B 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5052 Z= 0.253 Angle : 0.552 5.149 6894 Z= 0.268 Chirality : 0.039 0.133 774 Planarity : 0.005 0.046 928 Dihedral : 3.886 13.987 738 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.61 % Allowed : 14.75 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.49 (0.33), residues: 678 helix: 4.55 (0.29), residues: 246 sheet: -1.36 (0.49), residues: 110 loop : 0.51 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 347 HIS 0.002 0.000 HIS A 337 PHE 0.026 0.002 PHE A 293 TYR 0.004 0.001 TYR A 427 ARG 0.005 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 0.531 Fit side-chains REVERT: A 285 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7745 (mtt) REVERT: A 389 LYS cc_start: 0.8347 (mtmt) cc_final: 0.8011 (mmtt) REVERT: B 389 LYS cc_start: 0.8425 (mtmt) cc_final: 0.8082 (mmtt) outliers start: 20 outliers final: 13 residues processed: 80 average time/residue: 0.2131 time to fit residues: 20.9853 Evaluate side-chains 74 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 431 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 65 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 50.0000 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 338 GLN B 264 GLN B 338 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5052 Z= 0.207 Angle : 0.535 5.327 6894 Z= 0.261 Chirality : 0.038 0.126 774 Planarity : 0.005 0.046 928 Dihedral : 3.829 14.157 738 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.84 % Allowed : 13.82 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.53 (0.33), residues: 678 helix: 4.59 (0.29), residues: 246 sheet: -1.40 (0.49), residues: 110 loop : 0.54 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 347 HIS 0.001 0.000 HIS B 337 PHE 0.019 0.002 PHE A 293 TYR 0.003 0.001 TYR A 450 ARG 0.005 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 63 time to evaluate : 0.496 Fit side-chains REVERT: A 285 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7651 (mtt) REVERT: A 389 LYS cc_start: 0.8341 (mtmt) cc_final: 0.8041 (mmtt) REVERT: B 285 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7797 (mtt) REVERT: B 389 LYS cc_start: 0.8368 (mtmt) cc_final: 0.8049 (mmtt) outliers start: 21 outliers final: 16 residues processed: 79 average time/residue: 0.2136 time to fit residues: 20.8786 Evaluate side-chains 77 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 65 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.0060 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 338 GLN B 264 GLN B 338 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5052 Z= 0.179 Angle : 0.527 5.757 6894 Z= 0.258 Chirality : 0.038 0.124 774 Planarity : 0.005 0.047 928 Dihedral : 3.720 14.223 738 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.38 % Allowed : 14.75 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.58 (0.34), residues: 678 helix: 4.63 (0.28), residues: 246 sheet: -1.26 (0.48), residues: 116 loop : 0.57 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 347 HIS 0.001 0.000 HIS B 156 PHE 0.015 0.002 PHE A 293 TYR 0.002 0.001 TYR A 346 ARG 0.006 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 0.626 Fit side-chains REVERT: A 285 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7569 (mtt) REVERT: A 389 LYS cc_start: 0.8357 (mtmt) cc_final: 0.8053 (mmtt) REVERT: B 285 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7759 (mtt) REVERT: B 389 LYS cc_start: 0.8341 (mtmt) cc_final: 0.8031 (mmtt) outliers start: 19 outliers final: 10 residues processed: 79 average time/residue: 0.2222 time to fit residues: 21.7285 Evaluate side-chains 75 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 431 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 0.0770 chunk 36 optimal weight: 10.0000 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN B 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5052 Z= 0.202 Angle : 0.534 6.075 6894 Z= 0.261 Chirality : 0.038 0.126 774 Planarity : 0.005 0.046 928 Dihedral : 3.693 14.321 738 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.46 % Allowed : 15.90 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.58 (0.34), residues: 678 helix: 4.66 (0.28), residues: 246 sheet: -1.53 (0.46), residues: 122 loop : 0.72 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 347 HIS 0.001 0.000 HIS B 156 PHE 0.015 0.002 PHE B 293 TYR 0.003 0.001 TYR A 427 ARG 0.006 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.540 Fit side-chains REVERT: A 285 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7649 (mtt) REVERT: A 389 LYS cc_start: 0.8360 (mtmt) cc_final: 0.8067 (mmtt) REVERT: B 285 MET cc_start: 0.8052 (mtt) cc_final: 0.7807 (mtt) REVERT: B 389 LYS cc_start: 0.8364 (mtmt) cc_final: 0.8050 (mmtt) outliers start: 15 outliers final: 13 residues processed: 76 average time/residue: 0.2307 time to fit residues: 21.4152 Evaluate side-chains 76 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 0.0070 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.0970 chunk 44 optimal weight: 6.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 338 GLN B 264 GLN B 338 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5052 Z= 0.161 Angle : 0.523 6.487 6894 Z= 0.256 Chirality : 0.038 0.126 774 Planarity : 0.005 0.047 928 Dihedral : 3.611 14.336 738 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.15 % Allowed : 15.44 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.61 (0.34), residues: 678 helix: 4.66 (0.28), residues: 246 sheet: -1.32 (0.46), residues: 128 loop : 0.72 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 347 HIS 0.001 0.000 HIS A 458 PHE 0.015 0.001 PHE B 293 TYR 0.002 0.000 TYR B 450 ARG 0.007 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 0.563 Fit side-chains REVERT: A 285 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7574 (mtt) REVERT: A 389 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8084 (mmtt) REVERT: B 285 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7677 (mtt) REVERT: B 389 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8086 (mmtt) outliers start: 18 outliers final: 12 residues processed: 79 average time/residue: 0.2261 time to fit residues: 21.7486 Evaluate side-chains 77 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.2980 chunk 62 optimal weight: 0.4980 chunk 53 optimal weight: 0.0170 chunk 5 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5052 Z= 0.177 Angle : 0.531 6.636 6894 Z= 0.259 Chirality : 0.038 0.126 774 Planarity : 0.005 0.047 928 Dihedral : 3.580 14.292 738 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.69 % Allowed : 16.13 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.64 (0.34), residues: 678 helix: 4.67 (0.28), residues: 246 sheet: -1.34 (0.46), residues: 128 loop : 0.76 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 347 HIS 0.001 0.000 HIS B 337 PHE 0.015 0.001 PHE B 293 TYR 0.003 0.001 TYR A 427 ARG 0.006 0.000 ARG B 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.516 Fit side-chains REVERT: A 285 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7609 (mtt) REVERT: A 389 LYS cc_start: 0.8365 (mtmt) cc_final: 0.7980 (mmtt) REVERT: B 285 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7709 (mtt) REVERT: B 389 LYS cc_start: 0.8390 (mtmt) cc_final: 0.8050 (mmtt) outliers start: 16 outliers final: 11 residues processed: 74 average time/residue: 0.2205 time to fit residues: 20.0460 Evaluate side-chains 77 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 47 optimal weight: 0.0040 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN B 264 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.180988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147533 restraints weight = 5719.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146260 restraints weight = 7289.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147265 restraints weight = 6425.876| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5052 Z= 0.234 Angle : 0.553 6.480 6894 Z= 0.268 Chirality : 0.038 0.125 774 Planarity : 0.005 0.046 928 Dihedral : 3.676 14.816 738 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.69 % Allowed : 16.13 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.63 (0.34), residues: 678 helix: 4.66 (0.28), residues: 246 sheet: -1.55 (0.46), residues: 122 loop : 0.82 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 347 HIS 0.001 0.000 HIS B 337 PHE 0.016 0.002 PHE B 293 TYR 0.004 0.001 TYR A 427 ARG 0.006 0.000 ARG B 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1450.88 seconds wall clock time: 26 minutes 42.47 seconds (1602.47 seconds total)