Starting phenix.real_space_refine on Sun Mar 10 18:08:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjr_22898/03_2024/7kjr_22898_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjr_22898/03_2024/7kjr_22898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjr_22898/03_2024/7kjr_22898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjr_22898/03_2024/7kjr_22898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjr_22898/03_2024/7kjr_22898_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjr_22898/03_2024/7kjr_22898_updated.pdb" } resolution = 2.08 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= 0.002 sd= 0.067 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 18 5.16 5 C 2446 2.51 5 N 580 2.21 5 O 794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "D PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3840 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1575 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1575 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 261 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "D" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 261 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Time building chain proxies: 2.82, per 1000 atoms: 0.73 Number of scatterers: 3840 At special positions: 0 Unit cell: (77.789, 67.611, 90.148, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 2 15.00 O 794 8.00 N 580 7.00 C 2446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 715.0 milliseconds 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 2 sheets defined 53.3% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 43 through 62 removed outlier: 3.535A pdb=" N GLN A 57 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 99 Processing helix chain 'A' and resid 103 through 133 removed outlier: 5.545A pdb=" N TYR A 107 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 110 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS A 133 " --> pdb=" O CYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 140 No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'B' and resid 43 through 62 removed outlier: 3.538A pdb=" N GLN B 57 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 99 Processing helix chain 'B' and resid 103 through 133 removed outlier: 4.673A pdb=" N TYR B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 140 No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 220 through 223 No H-bonds generated for 'chain 'B' and resid 220 through 223' Processing helix chain 'C' and resid 26 through 54 Proline residue: C 34 - end of helix removed outlier: 5.027A pdb=" N GLY C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 46 Proline residue: D 34 - end of helix Processing helix chain 'D' and resid 48 through 54 Processing sheet with id= A, first strand: chain 'A' and resid 155 through 160 removed outlier: 5.965A pdb=" N HIS A 150 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N CYS A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE A 232 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR A 217 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE A 230 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 155 through 160 removed outlier: 5.963A pdb=" N HIS B 150 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N CYS B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE B 232 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR B 217 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE B 230 " --> pdb=" O THR B 217 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 857 1.33 - 1.45: 906 1.45 - 1.57: 2029 1.57 - 1.69: 2 1.69 - 1.81: 24 Bond restraints: 3818 Sorted by residual: bond pdb=" O4P PEE B 301 " pdb=" P PEE B 301 " ideal model delta sigma weight residual 1.653 1.769 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O4P PEE A 301 " pdb=" P PEE A 301 " ideal model delta sigma weight residual 1.653 1.769 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C4 PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 1.409 1.365 0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C4 PEE B 301 " pdb=" O4P PEE B 301 " ideal model delta sigma weight residual 1.409 1.366 0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C ILE B 62 " pdb=" O ILE B 62 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.19e-02 7.06e+03 2.25e+00 ... (remaining 3813 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.79: 72 106.79 - 113.61: 2087 113.61 - 120.43: 1478 120.43 - 127.24: 1499 127.24 - 134.06: 50 Bond angle restraints: 5186 Sorted by residual: angle pdb=" CB GLN C 37 " pdb=" CG GLN C 37 " pdb=" CD GLN C 37 " ideal model delta sigma weight residual 112.60 118.61 -6.01 1.70e+00 3.46e-01 1.25e+01 angle pdb=" CB GLU B 226 " pdb=" CG GLU B 226 " pdb=" CD GLU B 226 " ideal model delta sigma weight residual 112.60 118.44 -5.84 1.70e+00 3.46e-01 1.18e+01 angle pdb=" O1P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 109.92 99.97 9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" O1P PEE B 301 " pdb=" P PEE B 301 " pdb=" O4P PEE B 301 " ideal model delta sigma weight residual 109.92 99.99 9.93 3.00e+00 1.11e-01 1.09e+01 angle pdb=" O1P PEE A 301 " pdb=" P PEE A 301 " pdb=" O2P PEE A 301 " ideal model delta sigma weight residual 119.43 129.00 -9.57 3.00e+00 1.11e-01 1.02e+01 ... (remaining 5181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.46: 2076 30.46 - 60.92: 93 60.92 - 91.39: 14 91.39 - 121.85: 1 121.85 - 152.31: 6 Dihedral angle restraints: 2190 sinusoidal: 868 harmonic: 1322 Sorted by residual: dihedral pdb=" C4 PEE A 301 " pdb=" O4P PEE A 301 " pdb=" P PEE A 301 " pdb=" O2P PEE A 301 " ideal model delta sinusoidal sigma weight residual 284.22 131.91 152.31 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C4 PEE B 301 " pdb=" O4P PEE B 301 " pdb=" P PEE B 301 " pdb=" O2P PEE B 301 " ideal model delta sinusoidal sigma weight residual 284.22 132.36 151.86 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C3 PEE B 301 " pdb=" C1 PEE B 301 " pdb=" C2 PEE B 301 " pdb=" O3P PEE B 301 " ideal model delta sinusoidal sigma weight residual 62.73 -63.97 126.70 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 2187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 352 0.036 - 0.071: 156 0.071 - 0.107: 47 0.107 - 0.142: 15 0.142 - 0.178: 6 Chirality restraints: 576 Sorted by residual: chirality pdb=" CG LEU A 147 " pdb=" CB LEU A 147 " pdb=" CD1 LEU A 147 " pdb=" CD2 LEU A 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CG LEU B 147 " pdb=" CB LEU B 147 " pdb=" CD1 LEU B 147 " pdb=" CD2 LEU B 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CG LEU A 101 " pdb=" CB LEU A 101 " pdb=" CD1 LEU A 101 " pdb=" CD2 LEU A 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 573 not shown) Planarity restraints: 626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 113 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C TYR B 113 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR B 113 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE B 114 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 37 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" CD GLN D 37 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN D 37 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN D 37 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 114 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C PHE B 114 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE B 114 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 115 " 0.011 2.00e-02 2.50e+03 ... (remaining 623 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 920 2.78 - 3.31: 3603 3.31 - 3.84: 7359 3.84 - 4.37: 8455 4.37 - 4.90: 13685 Nonbonded interactions: 34022 Sorted by model distance: nonbonded pdb=" O HOH A 424 " pdb=" O HOH A 451 " model vdw 2.254 2.440 nonbonded pdb=" O HOH B 401 " pdb=" O HOH B 433 " model vdw 2.274 2.440 nonbonded pdb=" OG SER A 216 " pdb=" OE1 GLN A 218 " model vdw 2.274 2.440 nonbonded pdb=" OG SER B 216 " pdb=" OE1 GLN B 218 " model vdw 2.276 2.440 nonbonded pdb=" O HOH A 401 " pdb=" O HOH A 437 " model vdw 2.294 2.440 ... (remaining 34017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.590 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: 5.460 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 15.750 Find NCS groups from input model: 0.210 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:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 : 0.006 0.116 3818 Z= 0.390 Angle : 0.843 9.946 5186 Z= 0.426 Chirality : 0.047 0.178 576 Planarity : 0.005 0.036 626 Dihedral : 19.500 152.312 1342 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.25 % Allowed : 13.05 % Favored : 86.70 % 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: 1.13 (0.37), residues: 436 helix: 1.81 (0.31), residues: 234 sheet: 0.02 (0.48), residues: 90 loop : -0.81 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 149 HIS 0.003 0.001 HIS B 204 PHE 0.015 0.003 PHE B 146 TYR 0.011 0.002 TYR B 109 ARG 0.011 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.494 Fit side-chains REVERT: A 43 PHE cc_start: 0.7754 (m-10) cc_final: 0.6681 (t80) REVERT: A 136 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7714 (mmtm) REVERT: B 136 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7686 (mmtm) REVERT: B 192 LYS cc_start: 0.8741 (tttm) cc_final: 0.8044 (tptt) outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 1.3261 time to fit residues: 94.4110 Evaluate side-chains 69 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN C 42 ASN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3818 Z= 0.224 Angle : 0.546 7.571 5186 Z= 0.298 Chirality : 0.040 0.133 576 Planarity : 0.005 0.029 626 Dihedral : 18.025 166.897 525 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.97 % Allowed : 12.32 % Favored : 85.71 % 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: 1.38 (0.37), residues: 436 helix: 2.05 (0.31), residues: 234 sheet: 0.27 (0.47), residues: 86 loop : -0.90 (0.51), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 149 HIS 0.003 0.001 HIS A 204 PHE 0.013 0.002 PHE B 87 TYR 0.010 0.001 TYR B 109 ARG 0.006 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.434 Fit side-chains REVERT: A 43 PHE cc_start: 0.7661 (m-10) cc_final: 0.6527 (t80) REVERT: A 136 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7677 (mmtm) REVERT: B 136 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7658 (mmtm) REVERT: B 192 LYS cc_start: 0.8748 (tttm) cc_final: 0.8033 (tptt) outliers start: 8 outliers final: 4 residues processed: 71 average time/residue: 1.3016 time to fit residues: 95.4263 Evaluate side-chains 71 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3818 Z= 0.182 Angle : 0.483 6.679 5186 Z= 0.267 Chirality : 0.039 0.133 576 Planarity : 0.005 0.027 626 Dihedral : 16.699 174.632 522 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.23 % Allowed : 13.05 % Favored : 85.71 % 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: 1.37 (0.37), residues: 436 helix: 2.01 (0.32), residues: 234 sheet: 0.23 (0.46), residues: 86 loop : -0.80 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 149 HIS 0.002 0.001 HIS A 204 PHE 0.011 0.001 PHE A 87 TYR 0.007 0.001 TYR B 109 ARG 0.005 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.481 Fit side-chains REVERT: A 43 PHE cc_start: 0.7662 (m-10) cc_final: 0.6555 (t80) REVERT: A 136 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7662 (mmtm) REVERT: A 152 ASN cc_start: 0.7808 (m-40) cc_final: 0.7068 (p0) REVERT: B 136 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7648 (mmtm) REVERT: B 152 ASN cc_start: 0.7804 (m-40) cc_final: 0.7107 (p0) REVERT: B 192 LYS cc_start: 0.8696 (tttm) cc_final: 0.8031 (tptt) outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 1.3216 time to fit residues: 92.7200 Evaluate side-chains 70 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3818 Z= 0.161 Angle : 0.463 6.112 5186 Z= 0.255 Chirality : 0.039 0.133 576 Planarity : 0.004 0.027 626 Dihedral : 15.637 160.409 522 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.48 % Allowed : 13.30 % Favored : 85.22 % 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: 1.40 (0.38), residues: 436 helix: 2.04 (0.32), residues: 234 sheet: 0.25 (0.47), residues: 86 loop : -0.78 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 149 HIS 0.002 0.001 HIS A 204 PHE 0.009 0.001 PHE B 87 TYR 0.006 0.001 TYR A 109 ARG 0.005 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.490 Fit side-chains REVERT: A 43 PHE cc_start: 0.7672 (m-10) cc_final: 0.6582 (t80) REVERT: A 136 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7651 (mmtm) REVERT: B 136 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7643 (mmpt) REVERT: B 152 ASN cc_start: 0.7796 (m-40) cc_final: 0.7115 (p0) REVERT: B 192 LYS cc_start: 0.8665 (tttm) cc_final: 0.8007 (tptt) outliers start: 6 outliers final: 4 residues processed: 67 average time/residue: 1.3238 time to fit residues: 91.5587 Evaluate side-chains 69 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.0370 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3818 Z= 0.164 Angle : 0.468 6.266 5186 Z= 0.256 Chirality : 0.039 0.134 576 Planarity : 0.004 0.027 626 Dihedral : 14.295 135.182 522 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.23 % Allowed : 13.55 % Favored : 85.22 % 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: 1.43 (0.38), residues: 436 helix: 2.07 (0.32), residues: 234 sheet: 0.23 (0.47), residues: 86 loop : -0.80 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.002 0.001 HIS A 204 PHE 0.010 0.001 PHE B 87 TYR 0.008 0.001 TYR B 109 ARG 0.004 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.459 Fit side-chains REVERT: A 43 PHE cc_start: 0.7669 (m-10) cc_final: 0.6573 (t80) REVERT: A 68 ARG cc_start: 0.7916 (ttt-90) cc_final: 0.7519 (ttt90) REVERT: A 136 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7646 (mmpt) REVERT: B 136 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7642 (mmpt) REVERT: B 152 ASN cc_start: 0.7806 (m-40) cc_final: 0.7120 (p0) REVERT: B 192 LYS cc_start: 0.8644 (tttm) cc_final: 0.7995 (tptt) outliers start: 5 outliers final: 4 residues processed: 66 average time/residue: 1.3263 time to fit residues: 90.2751 Evaluate side-chains 69 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3818 Z= 0.172 Angle : 0.477 6.440 5186 Z= 0.260 Chirality : 0.039 0.135 576 Planarity : 0.004 0.026 626 Dihedral : 13.712 120.280 522 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.23 % Allowed : 13.05 % Favored : 85.71 % 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: 1.44 (0.38), residues: 436 helix: 2.08 (0.33), residues: 234 sheet: 0.25 (0.47), residues: 86 loop : -0.78 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 128 HIS 0.002 0.001 HIS A 204 PHE 0.010 0.001 PHE B 87 TYR 0.008 0.001 TYR B 109 ARG 0.004 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.445 Fit side-chains REVERT: A 43 PHE cc_start: 0.7689 (m-10) cc_final: 0.6585 (t80) REVERT: A 68 ARG cc_start: 0.7905 (ttt-90) cc_final: 0.7506 (ttt90) REVERT: A 136 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7646 (mmpt) REVERT: B 136 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7650 (mmpt) REVERT: B 152 ASN cc_start: 0.7794 (m-40) cc_final: 0.7103 (p0) REVERT: B 192 LYS cc_start: 0.8650 (tttm) cc_final: 0.8000 (tptt) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 1.2965 time to fit residues: 92.3121 Evaluate side-chains 72 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3818 Z= 0.187 Angle : 0.493 6.779 5186 Z= 0.267 Chirality : 0.040 0.133 576 Planarity : 0.004 0.026 626 Dihedral : 13.062 131.258 522 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.99 % Allowed : 13.55 % Favored : 85.47 % 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: 1.42 (0.38), residues: 436 helix: 2.05 (0.33), residues: 234 sheet: 0.27 (0.47), residues: 86 loop : -0.80 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 128 HIS 0.002 0.001 HIS B 204 PHE 0.011 0.001 PHE B 87 TYR 0.008 0.001 TYR B 109 ARG 0.004 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.477 Fit side-chains REVERT: A 43 PHE cc_start: 0.7675 (m-10) cc_final: 0.6549 (t80) REVERT: A 68 ARG cc_start: 0.7910 (ttt-90) cc_final: 0.7517 (ttt90) REVERT: A 136 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7665 (mmpt) REVERT: A 152 ASN cc_start: 0.7798 (m-40) cc_final: 0.7058 (p0) REVERT: B 64 THR cc_start: 0.8509 (m) cc_final: 0.8234 (p) REVERT: B 152 ASN cc_start: 0.7798 (m-40) cc_final: 0.7100 (p0) REVERT: B 192 LYS cc_start: 0.8655 (tttm) cc_final: 0.7999 (tptt) outliers start: 4 outliers final: 4 residues processed: 68 average time/residue: 1.2994 time to fit residues: 91.1667 Evaluate side-chains 71 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3818 Z= 0.197 Angle : 0.501 6.979 5186 Z= 0.271 Chirality : 0.040 0.133 576 Planarity : 0.004 0.026 626 Dihedral : 12.832 133.784 522 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.23 % Allowed : 13.30 % Favored : 85.47 % 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: 1.39 (0.38), residues: 436 helix: 2.04 (0.33), residues: 234 sheet: 0.27 (0.47), residues: 86 loop : -0.85 (0.52), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 128 HIS 0.002 0.001 HIS B 204 PHE 0.011 0.002 PHE B 87 TYR 0.009 0.001 TYR B 109 ARG 0.004 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.487 Fit side-chains REVERT: A 43 PHE cc_start: 0.7686 (m-10) cc_final: 0.6545 (t80) REVERT: A 64 THR cc_start: 0.8509 (m) cc_final: 0.8279 (p) REVERT: A 68 ARG cc_start: 0.7917 (ttt-90) cc_final: 0.7525 (ttt90) REVERT: A 136 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7666 (mmpt) REVERT: A 152 ASN cc_start: 0.7814 (m-40) cc_final: 0.7058 (p0) REVERT: B 64 THR cc_start: 0.8508 (m) cc_final: 0.8220 (p) REVERT: B 152 ASN cc_start: 0.7792 (m-40) cc_final: 0.7096 (p0) REVERT: B 192 LYS cc_start: 0.8663 (tttm) cc_final: 0.8004 (tptt) outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 1.2737 time to fit residues: 89.4106 Evaluate side-chains 71 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.0010 chunk 41 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 43 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3818 Z= 0.161 Angle : 0.486 6.104 5186 Z= 0.263 Chirality : 0.039 0.134 576 Planarity : 0.004 0.026 626 Dihedral : 12.685 135.333 522 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.99 % Allowed : 13.30 % Favored : 85.71 % 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: 1.39 (0.38), residues: 436 helix: 2.06 (0.33), residues: 234 sheet: 0.21 (0.47), residues: 86 loop : -0.87 (0.52), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 128 HIS 0.002 0.001 HIS B 204 PHE 0.009 0.001 PHE A 87 TYR 0.007 0.001 TYR B 109 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.464 Fit side-chains REVERT: A 43 PHE cc_start: 0.7667 (m-10) cc_final: 0.6542 (t80) REVERT: A 64 THR cc_start: 0.8454 (m) cc_final: 0.8231 (p) REVERT: A 68 ARG cc_start: 0.7901 (ttt-90) cc_final: 0.7514 (ttt90) REVERT: A 136 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7640 (mmpt) REVERT: B 64 THR cc_start: 0.8464 (m) cc_final: 0.8195 (p) REVERT: B 136 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7636 (mmpt) REVERT: B 152 ASN cc_start: 0.7802 (m-40) cc_final: 0.7108 (p0) REVERT: B 192 LYS cc_start: 0.8617 (tttm) cc_final: 0.7996 (tptt) outliers start: 4 outliers final: 4 residues processed: 67 average time/residue: 1.3403 time to fit residues: 92.6703 Evaluate side-chains 70 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3818 Z= 0.233 Angle : 0.545 7.526 5186 Z= 0.292 Chirality : 0.041 0.132 576 Planarity : 0.005 0.026 626 Dihedral : 12.779 137.438 522 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.99 % Allowed : 14.04 % Favored : 84.98 % 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: 1.35 (0.38), residues: 436 helix: 1.98 (0.33), residues: 234 sheet: 0.29 (0.47), residues: 86 loop : -0.85 (0.52), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 128 HIS 0.003 0.001 HIS B 204 PHE 0.013 0.002 PHE B 87 TYR 0.010 0.001 TYR B 109 ARG 0.004 0.001 ARG D 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.435 Fit side-chains REVERT: A 43 PHE cc_start: 0.7698 (m-10) cc_final: 0.6537 (t80) REVERT: A 64 THR cc_start: 0.8496 (m) cc_final: 0.8237 (p) REVERT: A 68 ARG cc_start: 0.7938 (ttt-90) cc_final: 0.7554 (ttt90) REVERT: A 152 ASN cc_start: 0.7825 (m-40) cc_final: 0.7049 (p0) REVERT: B 152 ASN cc_start: 0.7806 (m-40) cc_final: 0.7135 (p0) outliers start: 4 outliers final: 4 residues processed: 68 average time/residue: 1.3228 time to fit residues: 92.9221 Evaluate side-chains 71 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.135561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099459 restraints weight = 3550.049| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.58 r_work: 0.3061 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3818 Z= 0.170 Angle : 0.510 6.284 5186 Z= 0.276 Chirality : 0.040 0.135 576 Planarity : 0.004 0.027 626 Dihedral : 12.667 138.067 522 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.99 % Allowed : 13.79 % Favored : 85.22 % 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: 1.32 (0.38), residues: 436 helix: 1.98 (0.33), residues: 234 sheet: 0.25 (0.47), residues: 86 loop : -0.89 (0.52), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 128 HIS 0.003 0.001 HIS B 204 PHE 0.009 0.001 PHE B 87 TYR 0.007 0.001 TYR B 109 ARG 0.004 0.001 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.88 seconds wall clock time: 40 minutes 7.98 seconds (2407.98 seconds total)