Starting phenix.real_space_refine on Fri Dec 27 08:30:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yr0_34041/12_2024/7yr0_34041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yr0_34041/12_2024/7yr0_34041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yr0_34041/12_2024/7yr0_34041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yr0_34041/12_2024/7yr0_34041.map" model { file = "/net/cci-nas-00/data/ceres_data/7yr0_34041/12_2024/7yr0_34041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yr0_34041/12_2024/7yr0_34041.cif" } resolution = 3.98 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= -0.001 sd= 0.044 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 15 5.16 5 C 2149 2.51 5 N 571 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3383 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1560 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "B" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.18, per 1000 atoms: 0.94 Number of scatterers: 3383 At special positions: 0 Unit cell: (73.83, 85.6, 81.32, 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 15 16.00 O 648 8.00 N 571 7.00 C 2149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG D 1 " - " ASN A 343 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 436.9 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 6.3% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.995A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.799A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'C' and resid 61 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.310A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.597A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.890A pdb=" N GLY C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN C 116 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.890A pdb=" N GLY C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.697A pdb=" N LEU B 11 " --> pdb=" O LYS B 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 22 removed outlier: 3.763A pdb=" N ASP B 71 " --> pdb=" O SER B 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 47 removed outlier: 4.117A pdb=" N THR B 97 " --> pdb=" O GLN B 91 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 189 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: 0.77 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1073 1.35 - 1.46: 942 1.46 - 1.58: 1439 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3472 Sorted by residual: bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.547 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C2 NAG D 2 " pdb=" N2 NAG D 2 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" CA GLY A 381 " pdb=" C GLY A 381 " ideal model delta sigma weight residual 1.512 1.523 -0.011 8.70e-03 1.32e+04 1.56e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.38e+00 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.36e+00 ... (remaining 3467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 4462 1.26 - 2.51: 185 2.51 - 3.77: 51 3.77 - 5.02: 17 5.02 - 6.28: 5 Bond angle restraints: 4720 Sorted by residual: angle pdb=" N ILE A 402 " pdb=" CA ILE A 402 " pdb=" C ILE A 402 " ideal model delta sigma weight residual 108.53 111.81 -3.28 1.22e+00 6.72e-01 7.23e+00 angle pdb=" C GLU C 82 " pdb=" CA GLU C 82 " pdb=" CB GLU C 82 " ideal model delta sigma weight residual 110.42 115.40 -4.98 1.99e+00 2.53e-01 6.25e+00 angle pdb=" C GLU B 80 " pdb=" CA GLU B 80 " pdb=" CB GLU B 80 " ideal model delta sigma weight residual 109.26 112.83 -3.57 1.47e+00 4.63e-01 5.91e+00 angle pdb=" C MET C 48 " pdb=" N GLY C 49 " pdb=" CA GLY C 49 " ideal model delta sigma weight residual 121.46 119.21 2.25 9.50e-01 1.11e+00 5.63e+00 angle pdb=" N GLY C 49 " pdb=" CA GLY C 49 " pdb=" C GLY C 49 " ideal model delta sigma weight residual 110.90 114.36 -3.46 1.53e+00 4.27e-01 5.12e+00 ... (remaining 4715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.07: 1915 22.07 - 44.14: 136 44.14 - 66.21: 11 66.21 - 88.28: 9 88.28 - 110.35: 5 Dihedral angle restraints: 2076 sinusoidal: 851 harmonic: 1225 Sorted by residual: dihedral pdb=" CA SER B 7 " pdb=" C SER B 7 " pdb=" N PRO B 8 " pdb=" CA PRO B 8 " ideal model delta harmonic sigma weight residual 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 54.67 38.33 1 1.00e+01 1.00e-02 2.07e+01 dihedral pdb=" CA TYR C 80 " pdb=" C TYR C 80 " pdb=" N MET C 81 " pdb=" CA MET C 81 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 2073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 448 0.066 - 0.133: 61 0.133 - 0.199: 4 0.199 - 0.265: 0 0.265 - 0.331: 2 Chirality restraints: 515 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" N2 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 512 not shown) Planarity restraints: 606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 7 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO B 8 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 47 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C TRP C 47 " -0.020 2.00e-02 2.50e+03 pdb=" O TRP C 47 " 0.008 2.00e-02 2.50e+03 pdb=" N MET C 48 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 47 " 0.009 2.00e-02 2.50e+03 7.14e-03 1.27e+00 pdb=" CG TRP C 47 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP C 47 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP C 47 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 47 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 47 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 47 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 47 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 47 " 0.001 2.00e-02 2.50e+03 ... (remaining 603 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 130 2.71 - 3.26: 3238 3.26 - 3.81: 5061 3.81 - 4.35: 6100 4.35 - 4.90: 10380 Nonbonded interactions: 24909 Sorted by model distance: nonbonded pdb=" OG1 THR C 69 " pdb=" OE2 GLU C 82 " model vdw 2.164 3.040 nonbonded pdb=" O VAL B 3 " pdb=" OG SER B 26 " model vdw 2.229 3.040 nonbonded pdb=" OG SER C 35 " pdb=" OD2 ASP C 99 " model vdw 2.250 3.040 nonbonded pdb=" NH1 ARG C 87 " pdb=" OD1 ASP C 89 " model vdw 2.253 3.120 nonbonded pdb=" O ALA A 419 " pdb=" NZ LYS A 424 " model vdw 2.259 3.120 ... (remaining 24904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.040 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.430 Find NCS groups from input model: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3472 Z= 0.204 Angle : 0.681 6.280 4720 Z= 0.347 Chirality : 0.049 0.331 515 Planarity : 0.004 0.034 605 Dihedral : 15.968 110.350 1287 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.31 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -1.76 (0.43), residues: 421 helix: -0.21 (3.10), residues: 6 sheet: 0.50 (0.59), residues: 92 loop : -1.86 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 47 HIS 0.002 0.001 HIS B 92 PHE 0.017 0.001 PHE C 29 TYR 0.012 0.001 TYR B 50 ARG 0.003 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.382 Fit side-chains REVERT: C 80 TYR cc_start: 0.8049 (m-80) cc_final: 0.7822 (m-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1739 time to fit residues: 15.7252 Evaluate side-chains 57 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3472 Z= 0.312 Angle : 0.702 9.632 4720 Z= 0.348 Chirality : 0.048 0.235 515 Planarity : 0.004 0.037 605 Dihedral : 10.015 63.953 552 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.98 % Favored : 89.55 % Rotamer: Outliers : 1.40 % Allowed : 13.76 % Favored : 84.83 % 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: -1.95 (0.42), residues: 421 helix: -2.60 (1.22), residues: 18 sheet: 0.24 (0.58), residues: 98 loop : -1.89 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.004 0.002 HIS B 92 PHE 0.012 0.002 PHE C 29 TYR 0.026 0.002 TYR B 50 ARG 0.010 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.382 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 66 average time/residue: 0.1769 time to fit residues: 14.0740 Evaluate side-chains 62 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 82 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 30 optimal weight: 0.0010 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.0670 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3472 Z= 0.175 Angle : 0.650 9.610 4720 Z= 0.312 Chirality : 0.047 0.265 515 Planarity : 0.004 0.035 605 Dihedral : 7.635 58.968 552 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.36 % Favored : 92.40 % Rotamer: Outliers : 1.97 % Allowed : 15.17 % Favored : 82.87 % 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: -1.76 (0.42), residues: 421 helix: -1.99 (1.70), residues: 12 sheet: 0.57 (0.59), residues: 92 loop : -1.83 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS B 92 PHE 0.017 0.001 PHE C 29 TYR 0.022 0.001 TYR B 50 ARG 0.002 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: C 80 TYR cc_start: 0.8043 (m-80) cc_final: 0.7732 (m-80) REVERT: C 82 GLU cc_start: 0.5749 (pp20) cc_final: 0.5367 (tm-30) outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.1902 time to fit residues: 16.0965 Evaluate side-chains 61 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3472 Z= 0.241 Angle : 0.655 9.534 4720 Z= 0.320 Chirality : 0.046 0.245 515 Planarity : 0.004 0.036 605 Dihedral : 7.209 59.291 552 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.50 % Favored : 90.02 % Rotamer: Outliers : 1.97 % Allowed : 18.54 % Favored : 79.49 % 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: -1.91 (0.41), residues: 421 helix: -2.01 (1.29), residues: 20 sheet: 0.34 (0.58), residues: 97 loop : -1.92 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS A 339 PHE 0.015 0.001 PHE C 29 TYR 0.018 0.001 TYR A 501 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: C 80 TYR cc_start: 0.8085 (m-80) cc_final: 0.7809 (m-80) REVERT: C 82 GLU cc_start: 0.5758 (pp20) cc_final: 0.5401 (tm-30) outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 0.1800 time to fit residues: 14.3410 Evaluate side-chains 62 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 82 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3472 Z= 0.226 Angle : 0.659 9.589 4720 Z= 0.321 Chirality : 0.047 0.258 515 Planarity : 0.003 0.033 605 Dihedral : 7.072 58.414 552 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.08 % Favored : 91.69 % Rotamer: Outliers : 3.09 % Allowed : 19.66 % Favored : 77.25 % 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: -1.86 (0.41), residues: 421 helix: -2.05 (1.27), residues: 20 sheet: 0.68 (0.59), residues: 90 loop : -1.94 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.014 0.003 HIS A 505 PHE 0.008 0.001 PHE A 374 TYR 0.015 0.001 TYR A 501 ARG 0.002 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: C 80 TYR cc_start: 0.8093 (m-80) cc_final: 0.7891 (m-80) REVERT: C 82 GLU cc_start: 0.5953 (pp20) cc_final: 0.5538 (tm-30) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.1740 time to fit residues: 14.1174 Evaluate side-chains 64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 0.0370 chunk 38 optimal weight: 0.0270 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3472 Z= 0.191 Angle : 0.647 9.561 4720 Z= 0.319 Chirality : 0.047 0.269 515 Planarity : 0.003 0.035 605 Dihedral : 6.802 58.077 552 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.55 % Favored : 91.21 % Rotamer: Outliers : 3.37 % Allowed : 19.38 % Favored : 77.25 % 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: -1.70 (0.42), residues: 421 helix: -1.98 (1.76), residues: 12 sheet: 0.61 (0.59), residues: 92 loop : -1.79 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.001 0.001 HIS A 339 PHE 0.008 0.001 PHE A 374 TYR 0.014 0.001 TYR A 501 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: C 82 GLU cc_start: 0.5875 (pp20) cc_final: 0.5524 (tm-30) outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 0.1780 time to fit residues: 14.6090 Evaluate side-chains 63 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 0.0030 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3472 Z= 0.248 Angle : 0.675 9.477 4720 Z= 0.336 Chirality : 0.048 0.269 515 Planarity : 0.004 0.033 605 Dihedral : 6.801 58.191 552 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.03 % Favored : 90.74 % Rotamer: Outliers : 3.37 % Allowed : 18.82 % Favored : 77.81 % 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: -1.85 (0.41), residues: 421 helix: -2.16 (1.23), residues: 20 sheet: 0.66 (0.59), residues: 90 loop : -1.92 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.019 0.004 HIS A 505 PHE 0.008 0.001 PHE A 400 TYR 0.014 0.001 TYR A 501 ARG 0.003 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: C 82 GLU cc_start: 0.5898 (pp20) cc_final: 0.5529 (tm-30) outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 0.1865 time to fit residues: 15.5182 Evaluate side-chains 63 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 0.0870 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.005 0.054 3472 Z= 0.352 Angle : 0.744 9.578 4720 Z= 0.374 Chirality : 0.048 0.258 515 Planarity : 0.004 0.045 605 Dihedral : 7.338 59.747 552 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.64 % Favored : 87.89 % Rotamer: Outliers : 3.65 % Allowed : 19.10 % Favored : 77.25 % 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: -2.16 (0.40), residues: 421 helix: -2.28 (1.18), residues: 20 sheet: -0.04 (0.56), residues: 97 loop : -2.00 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.004 0.001 HIS A 339 PHE 0.012 0.002 PHE A 377 TYR 0.014 0.002 TYR A 501 ARG 0.005 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: C 82 GLU cc_start: 0.5860 (pp20) cc_final: 0.5456 (tm-30) outliers start: 13 outliers final: 9 residues processed: 70 average time/residue: 0.1766 time to fit residues: 14.8694 Evaluate side-chains 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3472 Z= 0.190 Angle : 0.692 9.514 4720 Z= 0.342 Chirality : 0.049 0.329 515 Planarity : 0.003 0.033 605 Dihedral : 6.537 57.212 552 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.60 % Favored : 92.16 % Rotamer: Outliers : 3.09 % Allowed : 20.51 % Favored : 76.40 % 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: -1.85 (0.42), residues: 421 helix: -2.18 (1.67), residues: 12 sheet: 0.31 (0.58), residues: 92 loop : -1.82 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.003 0.001 HIS A 339 PHE 0.009 0.001 PHE A 342 TYR 0.015 0.001 TYR A 501 ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: C 82 GLU cc_start: 0.5878 (OUTLIER) cc_final: 0.5522 (tm-30) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.1650 time to fit residues: 13.5368 Evaluate side-chains 67 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3472 Z= 0.226 Angle : 0.693 9.588 4720 Z= 0.342 Chirality : 0.046 0.236 515 Planarity : 0.003 0.035 605 Dihedral : 6.684 57.556 552 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.03 % Favored : 90.74 % Rotamer: Outliers : 3.37 % Allowed : 19.66 % Favored : 76.97 % 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: -1.83 (0.41), residues: 421 helix: -2.06 (1.74), residues: 12 sheet: 0.35 (0.58), residues: 90 loop : -1.81 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.003 0.001 HIS A 339 PHE 0.009 0.001 PHE A 377 TYR 0.016 0.001 TYR C 54 ARG 0.002 0.000 ARG C 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 490 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.5855 (t80) REVERT: C 82 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5655 (tm-30) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.1640 time to fit residues: 13.0653 Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 37 optimal weight: 0.3980 chunk 21 optimal weight: 0.0010 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 0.0770 overall best weight: 0.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.125864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101870 restraints weight = 7808.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.104257 restraints weight = 5333.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.105939 restraints weight = 4143.288| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3472 Z= 0.172 Angle : 0.656 9.636 4720 Z= 0.322 Chirality : 0.046 0.245 515 Planarity : 0.004 0.033 605 Dihedral : 6.278 56.980 552 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.60 % Favored : 92.16 % Rotamer: Outliers : 3.93 % Allowed : 19.38 % Favored : 76.69 % 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: -1.81 (0.42), residues: 421 helix: -2.16 (1.69), residues: 12 sheet: 0.30 (0.58), residues: 95 loop : -1.80 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.002 0.001 HIS A 339 PHE 0.009 0.001 PHE A 342 TYR 0.016 0.001 TYR A 501 ARG 0.002 0.000 ARG C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1285.67 seconds wall clock time: 23 minutes 53.47 seconds (1433.47 seconds total)