Starting phenix.real_space_refine on Fri Dec 27 05:45:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yl3_33902/12_2024/7yl3_33902.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yl3_33902/12_2024/7yl3_33902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yl3_33902/12_2024/7yl3_33902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yl3_33902/12_2024/7yl3_33902.map" model { file = "/net/cci-nas-00/data/ceres_data/7yl3_33902/12_2024/7yl3_33902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yl3_33902/12_2024/7yl3_33902.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1800 2.51 5 N 552 2.21 5 O 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 2958 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "K" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "F" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "H" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "G" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "L" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "D" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Time building chain proxies: 2.25, per 1000 atoms: 0.76 Number of scatterers: 2958 At special positions: 0 Unit cell: (132.08, 88.4, 42.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 594 8.00 N 552 7.00 C 1800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 2 " - pdb=" SG CYS C 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 2 " - pdb=" SG CYS B 7 " distance=2.85 Simple disulfide: pdb=" SG CYS I 2 " - pdb=" SG CYS I 7 " distance=2.03 Simple disulfide: pdb=" SG CYS A 2 " - pdb=" SG CYS A 7 " distance=2.03 Simple disulfide: pdb=" SG CYS J 2 " - pdb=" SG CYS J 7 " distance=2.03 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS L 2 " - pdb=" SG CYS L 7 " 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 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 311.7 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 11 removed outlier: 3.530A pdb=" N THR C 9 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA C 8 " --> pdb=" O THR B 9 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ARG B 11 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN C 10 " --> pdb=" O ARG B 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.400A pdb=" N VAL C 17 " --> pdb=" O HIS A 18 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N SER A 20 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER C 19 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.615A pdb=" N ILE C 26 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.644A pdb=" N THR C 30 " --> pdb=" O ASN B 31 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 10 through 22 removed outlier: 7.041A pdb=" N GLN E 10 " --> pdb=" O ARG G 11 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA G 13 " --> pdb=" O GLN E 10 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU E 12 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N PHE G 15 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN E 14 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL G 17 " --> pdb=" O ASN E 14 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU E 16 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N SER G 19 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N HIS E 18 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ASN G 21 " --> pdb=" O HIS E 18 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER E 20 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 26 through 32 removed outlier: 6.795A pdb=" N ILE E 26 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER G 29 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER E 28 " --> pdb=" O SER G 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 7 through 11 removed outlier: 6.816A pdb=" N ALA I 8 " --> pdb=" O THR L 9 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ARG L 11 " --> pdb=" O ALA I 8 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN I 10 " --> pdb=" O ARG L 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 17 through 20 removed outlier: 6.404A pdb=" N VAL I 17 " --> pdb=" O HIS J 18 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER J 20 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER I 19 " --> pdb=" O SER J 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 25 through 27 removed outlier: 6.637A pdb=" N ILE I 26 " --> pdb=" O LEU L 27 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 30 through 32 removed outlier: 6.691A pdb=" N THR I 30 " --> pdb=" O ASN L 31 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 10 through 22 removed outlier: 3.587A pdb=" N ALA K 13 " --> pdb=" O LEU H 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 26 through 32 74 hydrogen bonds defined for protein. 222 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: 0.69 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 521 1.33 - 1.45: 871 1.45 - 1.57: 1590 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 2994 Sorted by residual: bond pdb=" C THR E 36 " pdb=" N TYC E 37 " ideal model delta sigma weight residual 1.329 1.204 0.125 1.40e-02 5.10e+03 7.95e+01 bond pdb=" C THR F 36 " pdb=" N TYC F 37 " ideal model delta sigma weight residual 1.329 1.205 0.124 1.40e-02 5.10e+03 7.91e+01 bond pdb=" C THR G 36 " pdb=" N TYC G 37 " ideal model delta sigma weight residual 1.329 1.205 0.124 1.40e-02 5.10e+03 7.91e+01 bond pdb=" C THR K 36 " pdb=" N TYC K 37 " ideal model delta sigma weight residual 1.329 1.207 0.122 1.40e-02 5.10e+03 7.63e+01 bond pdb=" C THR H 36 " pdb=" N TYC H 37 " ideal model delta sigma weight residual 1.329 1.207 0.122 1.40e-02 5.10e+03 7.55e+01 ... (remaining 2989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.93: 4021 5.93 - 11.86: 11 11.86 - 17.79: 12 17.79 - 23.72: 18 23.72 - 29.65: 6 Bond angle restraints: 4068 Sorted by residual: angle pdb=" C THR E 36 " pdb=" N TYC E 37 " pdb=" CA TYC E 37 " ideal model delta sigma weight residual 121.70 151.35 -29.65 1.80e+00 3.09e-01 2.71e+02 angle pdb=" C THR G 36 " pdb=" N TYC G 37 " pdb=" CA TYC G 37 " ideal model delta sigma weight residual 121.70 151.34 -29.64 1.80e+00 3.09e-01 2.71e+02 angle pdb=" C THR F 36 " pdb=" N TYC F 37 " pdb=" CA TYC F 37 " ideal model delta sigma weight residual 121.70 151.34 -29.64 1.80e+00 3.09e-01 2.71e+02 angle pdb=" C THR D 36 " pdb=" N TYC D 37 " pdb=" CA TYC D 37 " ideal model delta sigma weight residual 121.70 150.02 -28.32 1.80e+00 3.09e-01 2.48e+02 angle pdb=" C THR K 36 " pdb=" N TYC K 37 " pdb=" CA TYC K 37 " ideal model delta sigma weight residual 121.70 150.00 -28.30 1.80e+00 3.09e-01 2.47e+02 ... (remaining 4063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.18: 1560 10.18 - 20.37: 154 20.37 - 30.55: 47 30.55 - 40.74: 24 40.74 - 50.92: 12 Dihedral angle restraints: 1797 sinusoidal: 669 harmonic: 1128 Sorted by residual: dihedral pdb=" CB CYS C 2 " pdb=" SG CYS C 2 " pdb=" SG CYS B 7 " pdb=" CB CYS B 7 " ideal model delta sinusoidal sigma weight residual 93.00 64.33 28.67 1 1.00e+01 1.00e-02 1.18e+01 dihedral pdb=" CA CYS I 2 " pdb=" CB CYS I 2 " pdb=" SG CYS I 2 " pdb=" SG CYS I 7 " ideal model delta sinusoidal sigma weight residual -73.00 -123.92 50.92 1 2.00e+01 2.50e-03 8.87e+00 dihedral pdb=" CA CYS B 2 " pdb=" CB CYS B 2 " pdb=" SG CYS B 2 " pdb=" SG CYS B 7 " ideal model delta sinusoidal sigma weight residual -73.00 -123.91 50.91 1 2.00e+01 2.50e-03 8.87e+00 ... (remaining 1794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 408 0.058 - 0.117: 64 0.117 - 0.175: 8 0.175 - 0.233: 6 0.233 - 0.292: 6 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ASN A 14 " pdb=" N ASN A 14 " pdb=" C ASN A 14 " pdb=" CB ASN A 14 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ASN C 14 " pdb=" N ASN C 14 " pdb=" C ASN C 14 " pdb=" CB ASN C 14 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA ASN I 14 " pdb=" N ASN I 14 " pdb=" C ASN I 14 " pdb=" CB ASN I 14 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 489 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR J 36 " 0.018 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C THR J 36 " -0.055 2.00e-02 2.50e+03 pdb=" O THR J 36 " 0.018 2.00e-02 2.50e+03 pdb=" N TYC J 37 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 36 " 0.018 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C THR I 36 " -0.055 2.00e-02 2.50e+03 pdb=" O THR I 36 " 0.018 2.00e-02 2.50e+03 pdb=" N TYC I 37 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR L 36 " 0.018 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C THR L 36 " -0.055 2.00e-02 2.50e+03 pdb=" O THR L 36 " 0.017 2.00e-02 2.50e+03 pdb=" N TYC L 37 " 0.019 2.00e-02 2.50e+03 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 8 2.30 - 2.95: 1508 2.95 - 3.60: 3838 3.60 - 4.25: 6365 4.25 - 4.90: 11193 Nonbonded interactions: 22912 Sorted by model distance: nonbonded pdb=" OG1 THR C 6 " pdb=" N THR B 6 " model vdw 1.654 3.120 nonbonded pdb=" N THR I 6 " pdb=" OG1 THR J 6 " model vdw 1.802 3.120 nonbonded pdb=" CG2 THR B 6 " pdb=" NH1 ARG D 11 " model vdw 1.997 3.540 nonbonded pdb=" CB THR C 4 " pdb=" O THR B 4 " model vdw 2.009 3.470 nonbonded pdb=" O THR I 4 " pdb=" CB THR J 4 " model vdw 2.203 3.470 ... (remaining 22907 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'I' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.560 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.008 0.125 2994 Z= 0.541 Angle : 2.133 29.653 4068 Z= 1.207 Chirality : 0.061 0.292 492 Planarity : 0.005 0.032 534 Dihedral : 10.324 42.455 1032 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -4.03 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 18 PHE 0.011 0.002 PHE E 15 ARG 0.001 0.000 ARG K 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.339 Fit side-chains REVERT: J 11 ARG cc_start: 0.7375 (mtt180) cc_final: 0.6689 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1218 time to fit residues: 7.2366 Evaluate side-chains 29 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 8.9990 chunk 22 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2994 Z= 0.284 Angle : 0.548 7.278 4068 Z= 0.287 Chirality : 0.044 0.146 492 Planarity : 0.003 0.025 534 Dihedral : 9.064 33.437 480 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.16 % Allowed : 9.57 % Favored : 88.27 % 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: -4.18 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS J 18 PHE 0.014 0.002 PHE F 15 ARG 0.002 0.001 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.330 Fit side-chains REVERT: J 35 ASN cc_start: 0.7883 (m-40) cc_final: 0.7651 (m110) REVERT: H 35 ASN cc_start: 0.7956 (m110) cc_final: 0.7480 (m110) REVERT: D 11 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7171 (pmt-80) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.1289 time to fit residues: 9.2294 Evaluate side-chains 44 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain D residue 34 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.0570 chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 GLN ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2994 Z= 0.153 Angle : 0.548 8.228 4068 Z= 0.253 Chirality : 0.042 0.131 492 Planarity : 0.002 0.011 534 Dihedral : 6.437 22.826 480 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.40 % Allowed : 14.20 % Favored : 82.41 % 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: -4.25 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 18 PHE 0.007 0.001 PHE H 15 ARG 0.001 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.352 Fit side-chains REVERT: B 11 ARG cc_start: 0.4746 (mmp-170) cc_final: 0.4531 (mmp-170) outliers start: 11 outliers final: 10 residues processed: 50 average time/residue: 0.1131 time to fit residues: 7.3847 Evaluate side-chains 44 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 34 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.0020 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.1910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2994 Z= 0.188 Angle : 0.545 7.836 4068 Z= 0.254 Chirality : 0.041 0.134 492 Planarity : 0.002 0.010 534 Dihedral : 7.073 28.099 480 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.40 % Allowed : 15.12 % Favored : 81.48 % 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: -4.29 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 18 PHE 0.008 0.001 PHE F 15 ARG 0.002 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.336 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 48 average time/residue: 0.1131 time to fit residues: 7.0523 Evaluate side-chains 46 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 34 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2994 Z= 0.298 Angle : 0.605 8.030 4068 Z= 0.288 Chirality : 0.042 0.139 492 Planarity : 0.003 0.024 534 Dihedral : 10.632 40.936 480 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.63 % Allowed : 16.05 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS A 18 PHE 0.012 0.002 PHE D 15 ARG 0.002 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 51 average time/residue: 0.1114 time to fit residues: 7.3645 Evaluate side-chains 48 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 34 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN A 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2994 Z= 0.238 Angle : 0.609 9.528 4068 Z= 0.276 Chirality : 0.042 0.137 492 Planarity : 0.002 0.016 534 Dihedral : 9.366 36.975 480 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.63 % Allowed : 17.90 % Favored : 77.47 % 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: -4.49 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 18 PHE 0.011 0.001 PHE F 15 ARG 0.001 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 50 average time/residue: 0.1062 time to fit residues: 7.0084 Evaluate side-chains 49 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 34 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2994 Z= 0.150 Angle : 0.567 8.819 4068 Z= 0.251 Chirality : 0.042 0.130 492 Planarity : 0.002 0.009 534 Dihedral : 6.313 23.423 480 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.32 % Allowed : 19.14 % Favored : 76.54 % 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: -4.44 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 18 PHE 0.008 0.001 PHE D 15 ARG 0.001 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ARG cc_start: 0.4412 (mmp-170) cc_final: 0.4138 (mmp-170) outliers start: 14 outliers final: 13 residues processed: 55 average time/residue: 0.1033 time to fit residues: 7.4638 Evaluate side-chains 47 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 34 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2994 Z= 0.326 Angle : 0.653 8.719 4068 Z= 0.303 Chirality : 0.042 0.138 492 Planarity : 0.003 0.018 534 Dihedral : 10.517 39.160 480 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 4.63 % Allowed : 18.52 % Favored : 76.85 % 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: -4.58 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS A 18 PHE 0.013 0.002 PHE D 15 ARG 0.003 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7365 (mtt180) cc_final: 0.6728 (pmt-80) outliers start: 15 outliers final: 14 residues processed: 49 average time/residue: 0.1016 time to fit residues: 6.5380 Evaluate side-chains 49 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 34 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.0870 chunk 25 optimal weight: 6.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2994 Z= 0.210 Angle : 0.607 8.453 4068 Z= 0.273 Chirality : 0.042 0.132 492 Planarity : 0.002 0.009 534 Dihedral : 8.475 33.509 480 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.32 % Allowed : 19.75 % Favored : 75.93 % 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: -4.57 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 18 PHE 0.009 0.001 PHE D 15 ARG 0.002 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 48 average time/residue: 0.0893 time to fit residues: 5.9200 Evaluate side-chains 47 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2994 Z= 0.304 Angle : 0.656 8.620 4068 Z= 0.304 Chirality : 0.042 0.137 492 Planarity : 0.002 0.013 534 Dihedral : 10.437 41.864 480 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 4.32 % Allowed : 19.14 % Favored : 76.54 % 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: -4.63 (0.32), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS A 18 PHE 0.012 0.002 PHE D 15 ARG 0.002 0.000 ARG L 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7365 (mtt180) cc_final: 0.6660 (pmt-80) outliers start: 14 outliers final: 14 residues processed: 48 average time/residue: 0.1062 time to fit residues: 6.7201 Evaluate side-chains 48 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0770 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.098788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.079201 restraints weight = 6314.950| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 3.09 r_work: 0.3875 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2994 Z= 0.220 Angle : 0.624 8.589 4068 Z= 0.282 Chirality : 0.042 0.133 492 Planarity : 0.002 0.009 534 Dihedral : 8.952 36.989 480 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.01 % Allowed : 20.06 % Favored : 75.93 % 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: -4.59 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 18 PHE 0.010 0.001 PHE F 15 ARG 0.001 0.000 ARG L 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1137.17 seconds wall clock time: 21 minutes 22.61 seconds (1282.61 seconds total)