Starting phenix.real_space_refine on Tue Feb 13 19:26:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlb_34871/02_2024/8hlb_34871.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlb_34871/02_2024/8hlb_34871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlb_34871/02_2024/8hlb_34871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlb_34871/02_2024/8hlb_34871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlb_34871/02_2024/8hlb_34871.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hlb_34871/02_2024/8hlb_34871.pdb" } resolution = 3.63 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= 0.034 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 38 5.16 5 C 4672 2.51 5 N 1257 2.21 5 O 1494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7461 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 868 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "B" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1622 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 203} Chain: "C" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1662 Classifications: {'peptide': 216} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 203} Chain: "D" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1675 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1634 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 201} Time building chain proxies: 4.49, per 1000 atoms: 0.60 Number of scatterers: 7461 At special positions: 0 Unit cell: (65.25, 97.875, 130.5, 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 38 16.00 O 1494 8.00 N 1257 7.00 C 4672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 31 " distance=2.03 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 45 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 115 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 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: 2.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 25 sheets defined 5.4% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 189 through 193 removed outlier: 3.684A pdb=" N SER B 192 " --> pdb=" O PRO B 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.875A pdb=" N SER D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.587A pdb=" N GLY D 139 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 191 through 196 removed outlier: 4.298A pdb=" N GLY D 196 " --> pdb=" O SER D 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.668A pdb=" N HIS E 189 " --> pdb=" O TYR E 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 43 removed outlier: 7.219A pdb=" N VAL A 52 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 58 removed outlier: 5.080A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N MET B 50 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL B 34 " --> pdb=" O MET B 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 128 removed outlier: 6.101A pdb=" N TYR B 180 " --> pdb=" O ASP B 148 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 181 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 158 removed outlier: 4.320A pdb=" N TYR B 198 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7 removed outlier: 4.056A pdb=" N CYS C 23 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE C 75 " --> pdb=" O CYS C 23 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 76 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.790A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AB3, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AB4, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.584A pdb=" N SER C 181 " --> pdb=" O CYS C 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 158 removed outlier: 3.678A pdb=" N GLN C 151 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AB7, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.580A pdb=" N LEU D 115 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.580A pdb=" N LEU D 115 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 126 through 129 removed outlier: 3.822A pdb=" N PHE D 128 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER D 186 " --> pdb=" O CYS D 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 158 through 160 Processing sheet with id=AC2, first strand: chain 'D' and resid 175 through 176 removed outlier: 3.539A pdb=" N SER D 183 " --> pdb=" O VAL D 175 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 12 through 13 Processing sheet with id=AC4, first strand: chain 'E' and resid 22 through 24 removed outlier: 3.712A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.311A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR E 102 " --> pdb=" O TYR E 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 117 Processing sheet with id=AC7, first strand: chain 'E' and resid 144 through 150 177 hydrogen bonds defined for protein. 411 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: 1.82 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2354 1.34 - 1.46: 1570 1.46 - 1.58: 3668 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 7636 Sorted by residual: bond pdb=" N GLN A 82 " pdb=" CA GLN A 82 " ideal model delta sigma weight residual 1.461 1.489 -0.028 1.19e-02 7.06e+03 5.65e+00 bond pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.52e-02 4.33e+03 4.36e+00 bond pdb=" C TYR E 36 " pdb=" N GLN E 37 " ideal model delta sigma weight residual 1.330 1.303 0.027 1.39e-02 5.18e+03 3.74e+00 bond pdb=" N TYR E 36 " pdb=" CA TYR E 36 " ideal model delta sigma weight residual 1.455 1.476 -0.021 1.23e-02 6.61e+03 2.89e+00 bond pdb=" C GLU D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.12e-02 7.97e+03 2.44e+00 ... (remaining 7631 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.10: 261 107.10 - 113.88: 4303 113.88 - 120.66: 2757 120.66 - 127.45: 2986 127.45 - 134.23: 85 Bond angle restraints: 10392 Sorted by residual: angle pdb=" C SER A 79 " pdb=" CA SER A 79 " pdb=" CB SER A 79 " ideal model delta sigma weight residual 116.63 110.25 6.38 1.16e+00 7.43e-01 3.03e+01 angle pdb=" CA SER A 79 " pdb=" C SER A 79 " pdb=" N SER A 80 " ideal model delta sigma weight residual 119.63 116.78 2.85 8.10e-01 1.52e+00 1.24e+01 angle pdb=" CA GLN E 89 " pdb=" C GLN E 89 " pdb=" O GLN E 89 " ideal model delta sigma weight residual 121.06 117.19 3.87 1.16e+00 7.43e-01 1.11e+01 angle pdb=" C GLN E 89 " pdb=" CA GLN E 89 " pdb=" CB GLN E 89 " ideal model delta sigma weight residual 109.56 102.50 7.06 2.22e+00 2.03e-01 1.01e+01 angle pdb=" O TYR D 103 " pdb=" C TYR D 103 " pdb=" N VAL D 104 " ideal model delta sigma weight residual 122.25 125.97 -3.72 1.18e+00 7.18e-01 9.93e+00 ... (remaining 10387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 4110 16.01 - 32.02: 353 32.02 - 48.04: 113 48.04 - 64.05: 17 64.05 - 80.06: 10 Dihedral angle restraints: 4603 sinusoidal: 1769 harmonic: 2834 Sorted by residual: dihedral pdb=" CB CYS A 98 " pdb=" SG CYS A 98 " pdb=" SG CYS A 115 " pdb=" CB CYS A 115 " ideal model delta sinusoidal sigma weight residual 93.00 162.36 -69.36 1 1.00e+01 1.00e-02 6.22e+01 dihedral pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " pdb=" SG CYS A 112 " pdb=" CB CYS A 112 " ideal model delta sinusoidal sigma weight residual 93.00 161.10 -68.10 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CB CYS A 18 " pdb=" SG CYS A 18 " pdb=" SG CYS A 31 " pdb=" CB CYS A 31 " ideal model delta sinusoidal sigma weight residual 93.00 160.13 -67.13 1 1.00e+01 1.00e-02 5.87e+01 ... (remaining 4600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 894 0.043 - 0.087: 187 0.087 - 0.130: 83 0.130 - 0.173: 6 0.173 - 0.216: 2 Chirality restraints: 1172 Sorted by residual: chirality pdb=" CA GLN E 89 " pdb=" N GLN E 89 " pdb=" C GLN E 89 " pdb=" CB GLN E 89 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA ILE D 48 " pdb=" N ILE D 48 " pdb=" C ILE D 48 " pdb=" CB ILE D 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 1169 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 43 " 0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO E 44 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO E 44 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO E 44 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 80 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO C 81 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 81 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 81 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 38 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C GLN E 38 " -0.032 2.00e-02 2.50e+03 pdb=" O GLN E 38 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS E 39 " 0.010 2.00e-02 2.50e+03 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 666 2.74 - 3.28: 7361 3.28 - 3.82: 11738 3.82 - 4.36: 13697 4.36 - 4.90: 23984 Nonbonded interactions: 57446 Sorted by model distance: nonbonded pdb=" O ILE C 110 " pdb=" OH TYR C 144 " model vdw 2.204 2.440 nonbonded pdb=" O ASP A 81 " pdb=" OH TYR D 103 " model vdw 2.214 2.440 nonbonded pdb=" O SER E 30 " pdb=" OH TYR E 71 " model vdw 2.238 2.440 nonbonded pdb=" O VAL C 29 " pdb=" ND2 ASN C 96 " model vdw 2.256 2.520 nonbonded pdb=" OG SER E 121 " pdb=" OE1 GLU E 123 " model vdw 2.277 2.440 ... (remaining 57441 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 3.970 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 23.710 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7636 Z= 0.199 Angle : 0.654 8.026 10392 Z= 0.353 Chirality : 0.044 0.216 1172 Planarity : 0.005 0.100 1327 Dihedral : 13.637 80.061 2739 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.38 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.27), residues: 967 helix: -0.35 (1.20), residues: 22 sheet: -0.98 (0.28), residues: 362 loop : -1.78 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 52 HIS 0.003 0.001 HIS E 90 PHE 0.021 0.002 PHE E 139 TYR 0.021 0.002 TYR E 140 ARG 0.004 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.860 Fit side-chains REVERT: B 86 GLN cc_start: 0.7289 (mm-40) cc_final: 0.7055 (mp10) REVERT: C 2 ILE cc_start: 0.8155 (mm) cc_final: 0.7927 (mm) REVERT: C 52 ILE cc_start: 0.9261 (mm) cc_final: 0.9059 (mm) REVERT: C 135 SER cc_start: 0.7864 (p) cc_final: 0.7603 (p) REVERT: C 149 LYS cc_start: 0.8001 (tttm) cc_final: 0.7631 (tttm) REVERT: C 174 ASP cc_start: 0.8622 (p0) cc_final: 0.8245 (p0) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1959 time to fit residues: 36.6003 Evaluate side-chains 119 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.0000 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 82 GLN C 162 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7636 Z= 0.239 Angle : 0.610 6.967 10392 Z= 0.317 Chirality : 0.044 0.174 1172 Planarity : 0.005 0.068 1327 Dihedral : 4.666 21.351 1048 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.89 % Favored : 90.69 % Rotamer: Outliers : 1.29 % Allowed : 8.34 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.27), residues: 967 helix: -0.03 (1.25), residues: 22 sheet: -0.96 (0.28), residues: 360 loop : -1.81 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 67 HIS 0.005 0.001 HIS E 90 PHE 0.020 0.002 PHE B 79 TYR 0.025 0.002 TYR B 102 ARG 0.001 0.000 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: B 86 GLN cc_start: 0.7359 (mm-40) cc_final: 0.7049 (mp10) REVERT: C 2 ILE cc_start: 0.8179 (mm) cc_final: 0.7930 (mm) REVERT: C 52 ILE cc_start: 0.9351 (mm) cc_final: 0.9114 (mm) REVERT: C 135 SER cc_start: 0.8034 (p) cc_final: 0.7782 (p) REVERT: C 149 LYS cc_start: 0.7813 (tttm) cc_final: 0.7437 (tttm) REVERT: C 174 ASP cc_start: 0.8640 (p0) cc_final: 0.8220 (p0) REVERT: E 195 GLU cc_start: 0.7606 (pp20) cc_final: 0.7198 (pp20) outliers start: 11 outliers final: 9 residues processed: 133 average time/residue: 0.1935 time to fit residues: 35.0434 Evaluate side-chains 128 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 0.0570 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 208 ASN C 151 GLN C 162 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7636 Z= 0.262 Angle : 0.616 7.052 10392 Z= 0.320 Chirality : 0.044 0.145 1172 Planarity : 0.005 0.053 1327 Dihedral : 4.758 22.045 1048 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.31 % Favored : 90.28 % Rotamer: Outliers : 2.59 % Allowed : 11.99 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.27), residues: 967 helix: -0.19 (1.19), residues: 22 sheet: -1.03 (0.27), residues: 366 loop : -1.84 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 67 HIS 0.007 0.001 HIS E 90 PHE 0.019 0.002 PHE B 79 TYR 0.031 0.002 TYR B 102 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 GLN cc_start: 0.7339 (mm-40) cc_final: 0.7052 (mp10) REVERT: C 52 ILE cc_start: 0.9391 (mm) cc_final: 0.9151 (mm) REVERT: C 57 ASN cc_start: 0.8054 (m-40) cc_final: 0.7834 (m-40) REVERT: C 174 ASP cc_start: 0.8511 (p0) cc_final: 0.8152 (p0) REVERT: E 98 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7034 (m-10) REVERT: E 195 GLU cc_start: 0.7715 (pp20) cc_final: 0.7296 (pp20) outliers start: 22 outliers final: 14 residues processed: 137 average time/residue: 0.1753 time to fit residues: 33.3219 Evaluate side-chains 131 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 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 175 GLN B 208 ASN C 162 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7636 Z= 0.223 Angle : 0.610 9.403 10392 Z= 0.314 Chirality : 0.043 0.138 1172 Planarity : 0.005 0.046 1327 Dihedral : 4.721 21.757 1048 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.89 % Favored : 90.69 % Rotamer: Outliers : 2.70 % Allowed : 13.16 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.27), residues: 967 helix: -0.17 (1.18), residues: 22 sheet: -1.03 (0.28), residues: 360 loop : -1.80 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 67 HIS 0.005 0.001 HIS E 90 PHE 0.027 0.002 PHE B 79 TYR 0.027 0.002 TYR B 102 ARG 0.004 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 39 GLN cc_start: 0.6902 (tt0) cc_final: 0.6620 (tt0) REVERT: B 86 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7098 (mp10) REVERT: C 52 ILE cc_start: 0.9400 (mm) cc_final: 0.9136 (mm) REVERT: C 174 ASP cc_start: 0.8616 (p0) cc_final: 0.8218 (p0) REVERT: E 98 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.6913 (m-10) REVERT: E 195 GLU cc_start: 0.7716 (pp20) cc_final: 0.7305 (pp20) outliers start: 23 outliers final: 15 residues processed: 141 average time/residue: 0.1759 time to fit residues: 34.1896 Evaluate side-chains 135 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 208 ASN C 162 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7636 Z= 0.273 Angle : 0.651 9.245 10392 Z= 0.334 Chirality : 0.045 0.175 1172 Planarity : 0.005 0.041 1327 Dihedral : 4.867 22.528 1048 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.03 % Favored : 89.56 % Rotamer: Outliers : 2.59 % Allowed : 15.39 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.27), residues: 967 helix: -0.23 (1.17), residues: 22 sheet: -1.08 (0.28), residues: 345 loop : -1.90 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 67 HIS 0.007 0.002 HIS E 91 PHE 0.014 0.002 PHE C 75 TYR 0.031 0.002 TYR B 102 ARG 0.003 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6980 (ttm) cc_final: 0.6646 (ttp) REVERT: B 86 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7161 (mp10) REVERT: C 52 ILE cc_start: 0.9415 (mm) cc_final: 0.9154 (mm) REVERT: C 174 ASP cc_start: 0.8518 (p0) cc_final: 0.8006 (p0) REVERT: E 98 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7099 (m-10) REVERT: E 195 GLU cc_start: 0.7723 (pp20) cc_final: 0.7306 (pp20) outliers start: 22 outliers final: 18 residues processed: 135 average time/residue: 0.1727 time to fit residues: 32.2079 Evaluate side-chains 137 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 162 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7636 Z= 0.276 Angle : 0.653 8.962 10392 Z= 0.335 Chirality : 0.045 0.185 1172 Planarity : 0.005 0.042 1327 Dihedral : 4.913 23.451 1048 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.51 % Favored : 90.07 % Rotamer: Outliers : 3.06 % Allowed : 16.22 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.27), residues: 967 helix: -0.23 (1.17), residues: 22 sheet: -1.14 (0.28), residues: 345 loop : -1.92 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 67 HIS 0.007 0.001 HIS E 91 PHE 0.015 0.002 PHE C 75 TYR 0.032 0.002 TYR B 102 ARG 0.004 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.7004 (ttm) cc_final: 0.6355 (ttm) REVERT: B 86 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7188 (mp10) REVERT: C 52 ILE cc_start: 0.9434 (mm) cc_final: 0.9176 (mm) REVERT: D 144 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8192 (pp) REVERT: E 92 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7122 (m-80) REVERT: E 98 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7120 (m-10) REVERT: E 118 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7304 (p90) REVERT: E 195 GLU cc_start: 0.7733 (pp20) cc_final: 0.7314 (pp20) outliers start: 26 outliers final: 18 residues processed: 138 average time/residue: 0.1730 time to fit residues: 33.0191 Evaluate side-chains 136 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 chunk 67 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7636 Z= 0.187 Angle : 0.611 8.866 10392 Z= 0.309 Chirality : 0.043 0.166 1172 Planarity : 0.004 0.039 1327 Dihedral : 4.717 22.200 1048 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.48 % Favored : 91.11 % Rotamer: Outliers : 2.94 % Allowed : 17.27 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.27), residues: 967 helix: -0.02 (1.20), residues: 22 sheet: -1.07 (0.28), residues: 349 loop : -1.78 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 52 HIS 0.004 0.001 HIS E 90 PHE 0.012 0.002 PHE C 122 TYR 0.022 0.002 TYR B 102 ARG 0.002 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.7022 (ttm) cc_final: 0.6660 (ttp) REVERT: B 86 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7175 (mp10) REVERT: C 52 ILE cc_start: 0.9413 (mm) cc_final: 0.9155 (mm) REVERT: D 144 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8194 (pp) REVERT: E 92 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.6903 (m-80) REVERT: E 118 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7165 (p90) REVERT: E 195 GLU cc_start: 0.7709 (pp20) cc_final: 0.7301 (pp20) outliers start: 25 outliers final: 18 residues processed: 145 average time/residue: 0.1894 time to fit residues: 37.8463 Evaluate side-chains 139 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN C 162 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7636 Z= 0.203 Angle : 0.616 9.118 10392 Z= 0.312 Chirality : 0.043 0.143 1172 Planarity : 0.005 0.039 1327 Dihedral : 4.694 21.870 1048 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.38 % Favored : 91.21 % Rotamer: Outliers : 2.94 % Allowed : 17.27 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.27), residues: 967 helix: -0.00 (1.21), residues: 22 sheet: -1.08 (0.28), residues: 349 loop : -1.76 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 52 HIS 0.004 0.001 HIS E 91 PHE 0.024 0.002 PHE E 139 TYR 0.023 0.002 TYR B 102 ARG 0.009 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6960 (ttm) cc_final: 0.6594 (ttp) REVERT: B 6 GLU cc_start: 0.7756 (pp20) cc_final: 0.7499 (pm20) REVERT: B 86 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7194 (mp10) REVERT: C 52 ILE cc_start: 0.9414 (mm) cc_final: 0.9147 (mm) REVERT: D 144 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8200 (pp) REVERT: E 92 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: E 118 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7116 (p90) REVERT: E 195 GLU cc_start: 0.7717 (pp20) cc_final: 0.7308 (pp20) outliers start: 25 outliers final: 21 residues processed: 138 average time/residue: 0.1743 time to fit residues: 33.3901 Evaluate side-chains 144 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7636 Z= 0.212 Angle : 0.620 8.660 10392 Z= 0.314 Chirality : 0.043 0.146 1172 Planarity : 0.005 0.039 1327 Dihedral : 4.715 21.895 1048 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.89 % Favored : 90.69 % Rotamer: Outliers : 3.29 % Allowed : 17.04 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.27), residues: 967 helix: 0.08 (1.22), residues: 22 sheet: -1.01 (0.28), residues: 343 loop : -1.77 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 52 HIS 0.005 0.001 HIS E 91 PHE 0.026 0.002 PHE E 139 TYR 0.025 0.002 TYR B 102 ARG 0.007 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6969 (ttm) cc_final: 0.6350 (ttm) REVERT: B 6 GLU cc_start: 0.7846 (pp20) cc_final: 0.7612 (pm20) REVERT: B 86 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7217 (mp10) REVERT: C 52 ILE cc_start: 0.9412 (mm) cc_final: 0.9154 (mm) REVERT: D 144 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8198 (pp) REVERT: E 92 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.6930 (m-80) REVERT: E 118 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7073 (p90) REVERT: E 195 GLU cc_start: 0.7710 (pp20) cc_final: 0.7312 (pp20) outliers start: 28 outliers final: 22 residues processed: 139 average time/residue: 0.1741 time to fit residues: 33.8145 Evaluate side-chains 147 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7636 Z= 0.195 Angle : 0.618 8.360 10392 Z= 0.312 Chirality : 0.043 0.172 1172 Planarity : 0.005 0.039 1327 Dihedral : 4.657 21.216 1048 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.38 % Favored : 91.21 % Rotamer: Outliers : 3.29 % Allowed : 17.16 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.27), residues: 967 helix: 0.16 (1.24), residues: 22 sheet: -1.02 (0.28), residues: 350 loop : -1.70 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 52 HIS 0.004 0.001 HIS E 91 PHE 0.025 0.002 PHE E 139 TYR 0.023 0.002 TYR B 102 ARG 0.007 0.000 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6958 (ttm) cc_final: 0.6322 (ttm) REVERT: B 86 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7244 (mp10) REVERT: C 52 ILE cc_start: 0.9402 (mm) cc_final: 0.9147 (mm) REVERT: C 120 PHE cc_start: 0.8134 (m-10) cc_final: 0.7859 (m-10) REVERT: D 144 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8194 (pp) REVERT: E 92 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.6904 (m-80) REVERT: E 118 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.6980 (p90) REVERT: E 195 GLU cc_start: 0.7704 (pp20) cc_final: 0.7305 (pp20) outliers start: 28 outliers final: 22 residues processed: 138 average time/residue: 0.1734 time to fit residues: 33.0816 Evaluate side-chains 145 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 0.0170 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 0.0970 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.172594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.141774 restraints weight = 9914.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.141577 restraints weight = 8480.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.143586 restraints weight = 8381.518| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7636 Z= 0.170 Angle : 0.603 8.195 10392 Z= 0.304 Chirality : 0.043 0.141 1172 Planarity : 0.004 0.039 1327 Dihedral : 4.587 20.674 1048 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.86 % Favored : 91.73 % Rotamer: Outliers : 3.06 % Allowed : 17.39 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.27), residues: 967 helix: 0.23 (1.24), residues: 22 sheet: -0.98 (0.28), residues: 350 loop : -1.66 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 52 HIS 0.003 0.001 HIS E 91 PHE 0.024 0.002 PHE E 139 TYR 0.021 0.001 TYR B 102 ARG 0.007 0.000 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1719.32 seconds wall clock time: 32 minutes 7.91 seconds (1927.91 seconds total)