Starting phenix.real_space_refine on Sun Mar 10 17:04:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr0_34041/03_2024/7yr0_34041.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr0_34041/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr0_34041/03_2024/7yr0_34041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr0_34041/03_2024/7yr0_34041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr0_34041/03_2024/7yr0_34041.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr0_34041/03_2024/7yr0_34041.pdb" } 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 Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 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: 2.44, per 1000 atoms: 0.72 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 - 3.50 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 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: 1.36 Conformation dependent library (CDL) restraints added in 589.2 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: 0.40 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: 0.79 Time building geometry restraints manager: 1.47 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: 100.55 - 107.25: 117 107.25 - 113.94: 1840 113.94 - 120.63: 1324 120.63 - 127.33: 1402 127.33 - 134.02: 37 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 2.440 nonbonded pdb=" O VAL B 3 " pdb=" OG SER B 26 " model vdw 2.229 2.440 nonbonded pdb=" OG SER C 35 " pdb=" OD2 ASP C 99 " model vdw 2.250 2.440 nonbonded pdb=" NH1 ARG C 87 " pdb=" OD1 ASP C 89 " model vdw 2.253 2.520 nonbonded pdb=" O ALA A 419 " pdb=" NZ LYS A 424 " model vdw 2.259 2.520 ... (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 ========== 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.030 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.880 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.390 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: 0.1663 time to fit residues: 15.1005 Evaluate side-chains 57 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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: 4.9990 chunk 31 optimal weight: 0.0270 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.0570 chunk 37 optimal weight: 4.9990 overall best weight: 1.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3472 Z= 0.317 Angle : 0.690 9.556 4720 Z= 0.342 Chirality : 0.047 0.243 515 Planarity : 0.004 0.033 605 Dihedral : 9.966 61.787 552 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.40 % Favored : 88.12 % Rotamer: Outliers : 1.97 % Allowed : 14.61 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.42), residues: 421 helix: -2.64 (1.20), residues: 18 sheet: 0.30 (0.58), residues: 97 loop : -1.90 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.004 0.002 HIS B 92 PHE 0.012 0.002 PHE A 515 TYR 0.027 0.002 TYR B 50 ARG 0.005 0.001 ARG C 38 *********************** 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 71 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.392 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 68 average time/residue: 0.1652 time to fit residues: 13.7394 Evaluate side-chains 64 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 500 THR 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: 0.8980 chunk 11 optimal weight: 7.9990 chunk 30 optimal weight: 0.0370 chunk 25 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1455 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= 0.184 Angle : 0.635 9.586 4720 Z= 0.307 Chirality : 0.046 0.250 515 Planarity : 0.003 0.033 605 Dihedral : 7.782 59.343 552 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.31 % Favored : 91.45 % Rotamer: Outliers : 2.25 % Allowed : 17.13 % Favored : 80.62 % 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 (0.42), residues: 421 helix: -1.95 (1.71), residues: 12 sheet: 0.28 (0.58), residues: 98 loop : -1.84 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.002 0.001 HIS A 339 PHE 0.008 0.001 PHE C 29 TYR 0.022 0.001 TYR B 50 ARG 0.001 0.000 ARG C 87 *********************** 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 71 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.402 Fit side-chains REVERT: C 80 TYR cc_start: 0.8047 (m-80) cc_final: 0.7738 (m-80) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.1552 time to fit residues: 12.8134 Evaluate side-chains 65 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 500 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.0970 chunk 28 optimal weight: 0.0980 chunk 19 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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: 0.7717 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3472 Z= 0.160 Angle : 0.605 9.700 4720 Z= 0.294 Chirality : 0.045 0.267 515 Planarity : 0.003 0.034 605 Dihedral : 6.775 58.667 552 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.03 % Favored : 90.74 % Rotamer: Outliers : 2.81 % Allowed : 18.26 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.41), residues: 421 helix: -2.09 (1.23), residues: 20 sheet: 0.63 (0.58), residues: 93 loop : -1.94 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS B 92 PHE 0.017 0.001 PHE C 29 TYR 0.015 0.001 TYR A 501 ARG 0.001 0.000 ARG C 87 *********************** 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 74 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.396 Fit side-chains REVERT: C 80 TYR cc_start: 0.8045 (m-80) cc_final: 0.7836 (m-80) REVERT: C 82 GLU cc_start: 0.5738 (pp20) cc_final: 0.5428 (tm-30) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 0.1656 time to fit residues: 14.0824 Evaluate side-chains 64 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE 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: 3.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- 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: 0.7803 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3472 Z= 0.288 Angle : 0.668 9.627 4720 Z= 0.330 Chirality : 0.045 0.229 515 Planarity : 0.004 0.032 605 Dihedral : 7.077 58.814 552 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.45 % Favored : 89.31 % Rotamer: Outliers : 4.21 % Allowed : 18.82 % 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: -1.89 (0.41), residues: 421 helix: -2.06 (1.25), residues: 20 sheet: 0.28 (0.57), residues: 97 loop : -1.86 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 47 HIS 0.003 0.001 HIS A 339 PHE 0.011 0.002 PHE A 342 TYR 0.020 0.002 TYR B 50 ARG 0.003 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 76 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.430 Fit side-chains REVERT: C 80 TYR cc_start: 0.8135 (m-80) cc_final: 0.7916 (m-80) REVERT: C 82 GLU cc_start: 0.5976 (pp20) cc_final: 0.5493 (tm-30) REVERT: B 71 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7320 (p0) outliers start: 15 outliers final: 9 residues processed: 70 average time/residue: 0.1596 time to fit residues: 13.7599 Evaluate side-chains 68 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 417 ASN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 82 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0770 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- 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: 0.7749 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3472 Z= 0.177 Angle : 0.637 9.639 4720 Z= 0.309 Chirality : 0.046 0.290 515 Planarity : 0.003 0.033 605 Dihedral : 6.768 57.324 552 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.26 % Favored : 90.50 % Rotamer: Outliers : 3.93 % Allowed : 19.94 % Favored : 76.12 % 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: -1.79 (0.41), residues: 421 helix: -2.12 (1.23), residues: 20 sheet: 0.62 (0.57), residues: 93 loop : -1.86 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.001 0.001 HIS B 92 PHE 0.008 0.001 PHE A 374 TYR 0.024 0.001 TYR B 50 ARG 0.002 0.000 ARG A 346 *********************** 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 75 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.381 Fit side-chains REVERT: A 490 PHE cc_start: 0.5918 (OUTLIER) cc_final: 0.5645 (t80) REVERT: C 82 GLU cc_start: 0.5802 (pp20) cc_final: 0.5465 (tm-30) outliers start: 14 outliers final: 11 residues processed: 68 average time/residue: 0.1621 time to fit residues: 13.5393 Evaluate side-chains 71 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 417 ASN Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 500 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.0040 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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: 0.7726 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3472 Z= 0.168 Angle : 0.627 9.577 4720 Z= 0.305 Chirality : 0.046 0.300 515 Planarity : 0.003 0.032 605 Dihedral : 6.431 57.722 552 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.55 % Favored : 91.21 % Rotamer: Outliers : 4.21 % Allowed : 20.79 % Favored : 75.00 % 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 (0.41), residues: 421 helix: -2.21 (1.19), residues: 20 sheet: 0.70 (0.58), residues: 93 loop : -1.85 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.001 0.001 HIS B 92 PHE 0.006 0.001 PHE A 377 TYR 0.011 0.001 TYR C 94 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 76 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.391 Fit side-chains REVERT: A 490 PHE cc_start: 0.6032 (OUTLIER) cc_final: 0.5658 (t80) REVERT: C 82 GLU cc_start: 0.5773 (pp20) cc_final: 0.5477 (tm-30) REVERT: B 71 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7371 (p0) outliers start: 15 outliers final: 10 residues processed: 68 average time/residue: 0.1629 time to fit residues: 13.6358 Evaluate side-chains 72 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 417 ASN Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 71 ASP 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: 5.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 0.0040 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 0.0570 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.2116 ------------------------------------------------------------------------------- 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: 0.7811 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3472 Z= 0.261 Angle : 0.665 9.706 4720 Z= 0.327 Chirality : 0.046 0.233 515 Planarity : 0.003 0.032 605 Dihedral : 6.881 58.988 552 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.93 % Favored : 88.84 % Rotamer: Outliers : 3.93 % Allowed : 20.22 % Favored : 75.84 % 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: -2.33 (1.13), residues: 20 sheet: 0.51 (0.57), residues: 93 loop : -1.88 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.002 0.001 HIS A 339 PHE 0.010 0.001 PHE A 377 TYR 0.020 0.001 TYR A 501 ARG 0.004 0.000 ARG C 38 *********************** 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 72 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.395 Fit side-chains REVERT: C 82 GLU cc_start: 0.5711 (pp20) cc_final: 0.5413 (tm-30) REVERT: B 71 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7374 (p0) outliers start: 14 outliers final: 8 residues processed: 65 average time/residue: 0.1676 time to fit residues: 13.2746 Evaluate side-chains 67 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 417 ASN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 82 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 36 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7767 moved from start: 0.2149 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= 0.184 Angle : 0.647 9.716 4720 Z= 0.315 Chirality : 0.045 0.245 515 Planarity : 0.003 0.032 605 Dihedral : 6.496 58.747 552 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.55 % Favored : 91.21 % Rotamer: Outliers : 4.21 % Allowed : 20.22 % Favored : 75.56 % 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: -1.80 (0.41), residues: 421 helix: -2.38 (1.12), residues: 20 sheet: 0.59 (0.57), residues: 93 loop : -1.84 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.002 0.001 HIS A 339 PHE 0.007 0.001 PHE A 377 TYR 0.015 0.001 TYR A 501 ARG 0.002 0.000 ARG C 87 *********************** 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 75 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.404 Fit side-chains REVERT: A 490 PHE cc_start: 0.6014 (OUTLIER) cc_final: 0.5695 (t80) REVERT: C 82 GLU cc_start: 0.5870 (pp20) cc_final: 0.5585 (tm-30) REVERT: B 71 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7386 (p0) outliers start: 15 outliers final: 10 residues processed: 68 average time/residue: 0.1634 time to fit residues: 13.6265 Evaluate side-chains 68 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 417 ASN Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 71 ASP 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: 4.9990 chunk 3 optimal weight: 0.0670 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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: 0.7748 moved from start: 0.2245 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= 0.174 Angle : 0.641 9.730 4720 Z= 0.313 Chirality : 0.045 0.245 515 Planarity : 0.003 0.032 605 Dihedral : 6.331 58.899 552 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.03 % Favored : 90.74 % Rotamer: Outliers : 3.37 % Allowed : 21.35 % Favored : 75.28 % 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 (0.41), residues: 421 helix: -2.43 (1.11), residues: 20 sheet: 0.65 (0.58), residues: 93 loop : -1.82 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS B 92 PHE 0.007 0.001 PHE A 377 TYR 0.014 0.001 TYR A 501 ARG 0.001 0.000 ARG A 457 ********************** 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 68 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.392 Fit side-chains REVERT: A 490 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5770 (t80) REVERT: C 82 GLU cc_start: 0.5842 (pp20) cc_final: 0.5525 (tm-30) REVERT: B 71 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7387 (p0) outliers start: 12 outliers final: 9 residues processed: 62 average time/residue: 0.1559 time to fit residues: 11.9792 Evaluate side-chains 66 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 417 ASN Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 71 ASP 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: 0.6980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.0020 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.130317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.106553 restraints weight = 8091.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.109144 restraints weight = 5411.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.110957 restraints weight = 4143.212| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2261 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= 0.172 Angle : 0.633 9.756 4720 Z= 0.308 Chirality : 0.044 0.243 515 Planarity : 0.003 0.031 605 Dihedral : 6.212 58.872 552 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.03 % Favored : 90.74 % Rotamer: Outliers : 3.93 % Allowed : 20.79 % Favored : 75.28 % 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: -1.73 (0.41), residues: 421 helix: -2.39 (1.12), residues: 20 sheet: 0.71 (0.58), residues: 93 loop : -1.81 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS B 92 PHE 0.020 0.001 PHE A 429 TYR 0.013 0.001 TYR A 501 ARG 0.001 0.000 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1318.81 seconds wall clock time: 24 minutes 18.87 seconds (1458.87 seconds total)