Starting phenix.real_space_refine on Mon Apr 28 11:14:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hlb_34871/04_2025/8hlb_34871.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hlb_34871/04_2025/8hlb_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/cci-nas-00/data/ceres_data/8hlb_34871/04_2025/8hlb_34871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hlb_34871/04_2025/8hlb_34871.map" model { file = "/net/cci-nas-00/data/ceres_data/8hlb_34871/04_2025/8hlb_34871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hlb_34871/04_2025/8hlb_34871.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 4.66, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 1.1 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: 0.92 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: 1.81 Time building geometry restraints manager: 2.00 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: 0.00 - 1.61: 10052 1.61 - 3.21: 285 3.21 - 4.82: 44 4.82 - 6.42: 7 6.42 - 8.03: 4 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 3.040 nonbonded pdb=" O ASP A 81 " pdb=" OH TYR D 103 " model vdw 2.214 3.040 nonbonded pdb=" O SER E 30 " pdb=" OH TYR E 71 " model vdw 2.238 3.040 nonbonded pdb=" O VAL C 29 " pdb=" ND2 ASN C 96 " model vdw 2.256 3.120 nonbonded pdb=" OG SER E 121 " pdb=" OE1 GLU E 123 " model vdw 2.277 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.410 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- 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 7652 Z= 0.147 Angle : 0.655 8.026 10424 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 Details of bonding type rmsd hydrogen bonds : bond 0.19616 ( 173) hydrogen bonds : angle 8.04598 ( 411) SS BOND : bond 0.00316 ( 16) SS BOND : angle 0.82350 ( 32) covalent geometry : bond 0.00299 ( 7636) covalent geometry : angle 0.65397 (10392) *********************** 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 to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.768 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: 0.1896 time to fit residues: 35.4505 Evaluate side-chains 119 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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: 4.9990 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 B 3 GLN B 175 GLN C 93 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** E 91 HIS E 147 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.134572 restraints weight = 10037.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133613 restraints weight = 7582.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135190 restraints weight = 7542.437| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 7652 Z= 0.334 Angle : 0.798 8.208 10424 Z= 0.425 Chirality : 0.051 0.208 1172 Planarity : 0.006 0.066 1327 Dihedral : 5.468 26.365 1048 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.00 % Favored : 87.59 % Rotamer: Outliers : 1.41 % Allowed : 12.10 % Favored : 86.49 % 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: -2.54 (0.27), residues: 967 helix: -0.29 (1.16), residues: 22 sheet: -1.16 (0.29), residues: 338 loop : -2.14 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 107 HIS 0.014 0.003 HIS E 90 PHE 0.020 0.003 PHE B 79 TYR 0.052 0.003 TYR B 102 ARG 0.004 0.001 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 173) hydrogen bonds : angle 7.22892 ( 411) SS BOND : bond 0.00526 ( 16) SS BOND : angle 1.46585 ( 32) covalent geometry : bond 0.00793 ( 7636) covalent geometry : angle 0.79542 (10392) *********************** 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 145 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: B 86 GLN cc_start: 0.7339 (mm-40) cc_final: 0.6952 (mp10) REVERT: B 101 ARG cc_start: 0.6218 (mmm160) cc_final: 0.5770 (mmm160) REVERT: C 57 ASN cc_start: 0.8237 (m-40) cc_final: 0.8003 (m-40) REVERT: C 135 SER cc_start: 0.8325 (p) cc_final: 0.8098 (p) REVERT: C 174 ASP cc_start: 0.8500 (p0) cc_final: 0.8002 (p0) REVERT: C 176 THR cc_start: 0.7581 (m) cc_final: 0.7124 (m) REVERT: E 98 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7554 (m-10) REVERT: E 147 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.7068 (tt0) REVERT: E 195 GLU cc_start: 0.7793 (pp20) cc_final: 0.7331 (pp20) outliers start: 12 outliers final: 6 residues processed: 139 average time/residue: 0.1786 time to fit residues: 34.1474 Evaluate side-chains 129 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 5 THR Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 147 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.0020 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 5 optimal weight: 0.0370 chunk 37 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 77 optimal weight: 0.0770 overall best weight: 0.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 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 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.171994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141789 restraints weight = 9931.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140772 restraints weight = 7383.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142362 restraints weight = 8002.720| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7652 Z= 0.121 Angle : 0.619 6.491 10424 Z= 0.321 Chirality : 0.043 0.171 1172 Planarity : 0.005 0.051 1327 Dihedral : 4.916 22.049 1048 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.34 % Favored : 92.24 % Rotamer: Outliers : 1.88 % Allowed : 13.16 % Favored : 84.96 % 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: -2.28 (0.27), residues: 967 helix: -0.20 (1.14), residues: 22 sheet: -1.05 (0.28), residues: 343 loop : -1.91 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 67 HIS 0.004 0.001 HIS D 35 PHE 0.017 0.002 PHE B 79 TYR 0.021 0.002 TYR B 102 ARG 0.003 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 173) hydrogen bonds : angle 6.76372 ( 411) SS BOND : bond 0.00350 ( 16) SS BOND : angle 1.07920 ( 32) covalent geometry : bond 0.00270 ( 7636) covalent geometry : angle 0.61714 (10392) *********************** 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 146 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.6885 (ttm) cc_final: 0.6427 (ttp) REVERT: A 39 GLN cc_start: 0.6911 (tt0) cc_final: 0.6609 (tt0) REVERT: B 101 ARG cc_start: 0.6131 (mmm160) cc_final: 0.5701 (mmm160) REVERT: C 52 ILE cc_start: 0.9318 (mm) cc_final: 0.9080 (mm) REVERT: C 57 ASN cc_start: 0.7993 (m-40) cc_final: 0.7705 (m110) REVERT: C 174 ASP cc_start: 0.8485 (p0) cc_final: 0.8100 (p0) REVERT: E 92 TYR cc_start: 0.7103 (m-80) cc_final: 0.6691 (m-80) REVERT: E 195 GLU cc_start: 0.7706 (pp20) cc_final: 0.7254 (pp20) outliers start: 16 outliers final: 9 residues processed: 140 average time/residue: 0.1803 time to fit residues: 34.7513 Evaluate side-chains 132 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain D residue 58 ILE 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 152 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.1980 chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 151 GLN C 162 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.167793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137478 restraints weight = 9984.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135868 restraints weight = 8018.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137583 restraints weight = 8992.439| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7652 Z= 0.223 Angle : 0.701 9.964 10424 Z= 0.364 Chirality : 0.046 0.173 1172 Planarity : 0.005 0.049 1327 Dihedral : 5.098 24.112 1048 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.13 % Favored : 89.45 % Rotamer: Outliers : 2.70 % Allowed : 15.39 % Favored : 81.90 % 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: -2.38 (0.27), residues: 967 helix: -0.22 (1.11), residues: 22 sheet: -1.12 (0.28), residues: 344 loop : -1.99 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 67 HIS 0.009 0.002 HIS E 91 PHE 0.026 0.002 PHE B 79 TYR 0.039 0.002 TYR B 102 ARG 0.006 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 173) hydrogen bonds : angle 6.84072 ( 411) SS BOND : bond 0.00433 ( 16) SS BOND : angle 1.19225 ( 32) covalent geometry : bond 0.00531 ( 7636) covalent geometry : angle 0.69945 (10392) *********************** 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 to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.910 Fit side-chains REVERT: A 30 MET cc_start: 0.6925 (ttm) cc_final: 0.6198 (ttm) REVERT: B 3 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: B 101 ARG cc_start: 0.6183 (mmm160) cc_final: 0.4959 (mmm160) REVERT: C 52 ILE cc_start: 0.9393 (mm) cc_final: 0.9136 (mm) REVERT: C 151 GLN cc_start: 0.7283 (mt0) cc_final: 0.6898 (mt0) REVERT: C 162 ASN cc_start: 0.8017 (t160) cc_final: 0.7787 (t0) REVERT: C 174 ASP cc_start: 0.8455 (p0) cc_final: 0.8012 (p0) REVERT: E 98 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7003 (m-10) REVERT: E 118 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7496 (p90) REVERT: E 195 GLU cc_start: 0.7799 (pp20) cc_final: 0.7333 (pp20) outliers start: 23 outliers final: 16 residues processed: 143 average time/residue: 0.1747 time to fit residues: 34.7035 Evaluate side-chains 140 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 60 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 58 ILE 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 67 SER Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 152 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 74 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 86 GLN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.171051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.140402 restraints weight = 9818.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140236 restraints weight = 8119.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142256 restraints weight = 7982.876| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7652 Z= 0.128 Angle : 0.640 9.150 10424 Z= 0.329 Chirality : 0.044 0.144 1172 Planarity : 0.005 0.043 1327 Dihedral : 4.914 22.709 1048 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.86 % Favored : 91.83 % Rotamer: Outliers : 2.70 % Allowed : 16.69 % Favored : 80.61 % 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: -2.22 (0.27), residues: 967 helix: -0.22 (1.07), residues: 22 sheet: -0.93 (0.29), residues: 326 loop : -1.91 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 67 HIS 0.005 0.001 HIS C 38 PHE 0.023 0.002 PHE B 79 TYR 0.026 0.002 TYR B 102 ARG 0.003 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.02838 ( 173) hydrogen bonds : angle 6.59501 ( 411) SS BOND : bond 0.00302 ( 16) SS BOND : angle 0.82010 ( 32) covalent geometry : bond 0.00296 ( 7636) covalent geometry : angle 0.63946 (10392) *********************** 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 149 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6865 (ttm) cc_final: 0.6430 (ttp) REVERT: C 52 ILE cc_start: 0.9328 (mm) cc_final: 0.9071 (mm) REVERT: C 151 GLN cc_start: 0.7274 (mt0) cc_final: 0.6827 (mt0) REVERT: C 162 ASN cc_start: 0.8056 (t160) cc_final: 0.7684 (t0) REVERT: C 174 ASP cc_start: 0.8413 (p0) cc_final: 0.7986 (p0) REVERT: E 38 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: E 118 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7285 (p90) REVERT: E 195 GLU cc_start: 0.7764 (pp20) cc_final: 0.7301 (pp20) outliers start: 23 outliers final: 16 residues processed: 140 average time/residue: 0.1708 time to fit residues: 33.3323 Evaluate side-chains 135 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 58 ILE 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 38 GLN Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 152 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 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 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.166895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.136562 restraints weight = 10018.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135043 restraints weight = 7839.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.136715 restraints weight = 8999.933| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 7652 Z= 0.238 Angle : 0.711 9.100 10424 Z= 0.370 Chirality : 0.046 0.173 1172 Planarity : 0.005 0.047 1327 Dihedral : 5.191 24.974 1048 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.44 % Favored : 89.25 % Rotamer: Outliers : 4.00 % Allowed : 15.75 % Favored : 80.26 % 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: -2.36 (0.27), residues: 967 helix: -0.12 (1.10), residues: 22 sheet: -1.10 (0.29), residues: 345 loop : -1.99 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 67 HIS 0.009 0.002 HIS C 38 PHE 0.024 0.002 PHE B 79 TYR 0.043 0.002 TYR B 102 ARG 0.006 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 173) hydrogen bonds : angle 6.73402 ( 411) SS BOND : bond 0.00468 ( 16) SS BOND : angle 1.06571 ( 32) covalent geometry : bond 0.00566 ( 7636) covalent geometry : angle 0.71002 (10392) *********************** 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 163 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.884 Fit side-chains REVERT: A 30 MET cc_start: 0.6988 (ttm) cc_final: 0.6443 (ttp) REVERT: A 102 TRP cc_start: 0.6981 (m-10) cc_final: 0.5897 (m100) REVERT: B 101 ARG cc_start: 0.6202 (mmm160) cc_final: 0.4880 (mmm160) REVERT: C 52 ILE cc_start: 0.9393 (mm) cc_final: 0.9138 (mm) REVERT: C 121 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.8025 (mm) REVERT: C 162 ASN cc_start: 0.8225 (t0) cc_final: 0.7800 (t0) REVERT: D 144 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8129 (pp) REVERT: E 98 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.6999 (m-10) REVERT: E 179 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7384 (tp) REVERT: E 195 GLU cc_start: 0.7778 (pp20) cc_final: 0.7329 (pp20) outliers start: 34 outliers final: 22 residues processed: 151 average time/residue: 0.1693 time to fit residues: 35.8627 Evaluate side-chains 144 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 58 ILE 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 67 SER Chi-restraints excluded: chain E residue 98 PHE 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 179 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 208 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.170011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.140192 restraints weight = 9741.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.138727 restraints weight = 7298.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140538 restraints weight = 8227.194| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7652 Z= 0.139 Angle : 0.647 8.850 10424 Z= 0.333 Chirality : 0.044 0.204 1172 Planarity : 0.005 0.042 1327 Dihedral : 5.007 23.228 1048 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.34 % Favored : 92.35 % Rotamer: Outliers : 3.41 % Allowed : 18.10 % Favored : 78.50 % 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: -2.23 (0.27), residues: 967 helix: -0.06 (1.08), residues: 22 sheet: -0.93 (0.29), residues: 336 loop : -1.94 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 67 HIS 0.005 0.001 HIS C 38 PHE 0.022 0.002 PHE B 79 TYR 0.027 0.002 TYR B 102 ARG 0.002 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 173) hydrogen bonds : angle 6.53685 ( 411) SS BOND : bond 0.00307 ( 16) SS BOND : angle 0.84924 ( 32) covalent geometry : bond 0.00325 ( 7636) covalent geometry : angle 0.64590 (10392) *********************** 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 162 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.887 Fit side-chains REVERT: A 30 MET cc_start: 0.6925 (ttm) cc_final: 0.6124 (ttm) REVERT: A 77 ARG cc_start: 0.6742 (tpp-160) cc_final: 0.5922 (mmm160) REVERT: A 102 TRP cc_start: 0.6772 (m-10) cc_final: 0.6049 (m100) REVERT: B 101 ARG cc_start: 0.6157 (mmm160) cc_final: 0.4746 (mmm160) REVERT: C 52 ILE cc_start: 0.9408 (mm) cc_final: 0.9142 (mm) REVERT: C 120 PHE cc_start: 0.8243 (m-10) cc_final: 0.8025 (m-80) REVERT: C 121 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.8019 (mm) REVERT: C 162 ASN cc_start: 0.8215 (t0) cc_final: 0.7820 (t0) REVERT: D 144 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8044 (pp) REVERT: E 38 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: E 195 GLU cc_start: 0.7664 (pp20) cc_final: 0.7268 (pp20) outliers start: 29 outliers final: 20 residues processed: 150 average time/residue: 0.2046 time to fit residues: 41.9976 Evaluate side-chains 144 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 58 ILE 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 38 GLN Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 151 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.0870 chunk 52 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 80 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 208 ASN C 94 GLN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.173358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144566 restraints weight = 9817.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142974 restraints weight = 8146.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145152 restraints weight = 8708.075| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7652 Z= 0.119 Angle : 0.642 8.541 10424 Z= 0.328 Chirality : 0.044 0.182 1172 Planarity : 0.005 0.041 1327 Dihedral : 4.922 22.171 1048 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.65 % Favored : 92.04 % Rotamer: Outliers : 3.53 % Allowed : 18.33 % Favored : 78.14 % 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: -2.11 (0.27), residues: 967 helix: 0.05 (1.09), residues: 22 sheet: -0.88 (0.29), residues: 335 loop : -1.84 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 67 HIS 0.004 0.001 HIS D 35 PHE 0.022 0.002 PHE B 79 TYR 0.022 0.001 TYR B 102 ARG 0.004 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.02742 ( 173) hydrogen bonds : angle 6.36120 ( 411) SS BOND : bond 0.00294 ( 16) SS BOND : angle 1.16486 ( 32) covalent geometry : bond 0.00276 ( 7636) covalent geometry : angle 0.63956 (10392) *********************** 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 153 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.889 Fit side-chains REVERT: A 30 MET cc_start: 0.6980 (ttm) cc_final: 0.6161 (ttm) REVERT: A 102 TRP cc_start: 0.6475 (m-10) cc_final: 0.5872 (m100) REVERT: B 101 ARG cc_start: 0.6151 (mmm160) cc_final: 0.4836 (mmm160) REVERT: C 52 ILE cc_start: 0.9380 (mm) cc_final: 0.9142 (mm) REVERT: C 120 PHE cc_start: 0.8258 (m-10) cc_final: 0.8029 (m-80) REVERT: C 162 ASN cc_start: 0.8089 (t0) cc_final: 0.7756 (t0) REVERT: D 144 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8190 (pp) REVERT: E 118 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7058 (p90) REVERT: E 195 GLU cc_start: 0.7561 (pp20) cc_final: 0.7247 (pp20) outliers start: 30 outliers final: 20 residues processed: 143 average time/residue: 0.1780 time to fit residues: 35.5128 Evaluate side-chains 141 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 205 LEU 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 67 SER Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 151 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 95 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 0.0770 chunk 76 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN C 94 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.171211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140713 restraints weight = 10006.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139340 restraints weight = 7642.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.141131 restraints weight = 8344.930| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7652 Z= 0.134 Angle : 0.664 12.219 10424 Z= 0.336 Chirality : 0.044 0.181 1172 Planarity : 0.005 0.040 1327 Dihedral : 4.907 21.988 1048 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.55 % Favored : 92.14 % Rotamer: Outliers : 3.53 % Allowed : 18.80 % Favored : 77.67 % 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: -2.06 (0.27), residues: 967 helix: -0.04 (1.08), residues: 22 sheet: -0.90 (0.28), residues: 345 loop : -1.77 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 52 HIS 0.005 0.001 HIS C 38 PHE 0.023 0.002 PHE B 79 TYR 0.024 0.002 TYR B 102 ARG 0.003 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.02783 ( 173) hydrogen bonds : angle 6.32837 ( 411) SS BOND : bond 0.00303 ( 16) SS BOND : angle 0.95962 ( 32) covalent geometry : bond 0.00313 ( 7636) covalent geometry : angle 0.66251 (10392) *********************** 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 155 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.6933 (ttm) cc_final: 0.6121 (ttm) REVERT: A 102 TRP cc_start: 0.6562 (m-10) cc_final: 0.5960 (m100) REVERT: B 101 ARG cc_start: 0.6150 (mmm160) cc_final: 0.4807 (mmm160) REVERT: C 52 ILE cc_start: 0.9405 (mm) cc_final: 0.9159 (mm) REVERT: C 94 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8164 (pp30) REVERT: C 162 ASN cc_start: 0.8295 (t0) cc_final: 0.7937 (t0) REVERT: D 144 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8078 (pp) REVERT: E 118 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.6940 (p90) REVERT: E 195 GLU cc_start: 0.7694 (pp20) cc_final: 0.7255 (pp20) outliers start: 30 outliers final: 23 residues processed: 145 average time/residue: 0.1708 time to fit residues: 34.5069 Evaluate side-chains 145 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 34 ILE 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 38 GLN Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 151 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN C 94 GLN ** C 128 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.171583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142485 restraints weight = 9993.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.141055 restraints weight = 8353.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142990 restraints weight = 9249.455| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7652 Z= 0.173 Angle : 0.702 10.755 10424 Z= 0.357 Chirality : 0.046 0.165 1172 Planarity : 0.005 0.049 1327 Dihedral : 5.006 22.680 1048 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.38 % Favored : 91.31 % Rotamer: Outliers : 3.17 % Allowed : 18.45 % Favored : 78.38 % 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 (1.14), residues: 22 sheet: -0.80 (0.29), residues: 333 loop : -1.84 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 52 HIS 0.006 0.001 HIS E 91 PHE 0.027 0.002 PHE C 122 TYR 0.028 0.002 TYR B 102 ARG 0.010 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 173) hydrogen bonds : angle 6.35557 ( 411) SS BOND : bond 0.00354 ( 16) SS BOND : angle 1.07334 ( 32) covalent geometry : bond 0.00413 ( 7636) covalent geometry : angle 0.70092 (10392) ********************** 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 147 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.7019 (ttm) cc_final: 0.6216 (ttm) REVERT: A 102 TRP cc_start: 0.6628 (m-10) cc_final: 0.6050 (m100) REVERT: B 101 ARG cc_start: 0.6236 (mmm160) cc_final: 0.4854 (mmm160) REVERT: C 2 ILE cc_start: 0.8862 (mm) cc_final: 0.8546 (mm) REVERT: C 52 ILE cc_start: 0.9431 (mm) cc_final: 0.9164 (mm) REVERT: C 162 ASN cc_start: 0.8137 (t0) cc_final: 0.7822 (t0) REVERT: D 144 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8190 (pp) REVERT: E 195 GLU cc_start: 0.7614 (pp20) cc_final: 0.7275 (pp20) outliers start: 27 outliers final: 23 residues processed: 139 average time/residue: 0.1750 time to fit residues: 34.4639 Evaluate side-chains 142 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 34 ILE 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 67 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 147 GLN Chi-restraints excluded: chain E residue 151 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 GLN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.169957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140022 restraints weight = 9714.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139776 restraints weight = 7961.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141687 restraints weight = 8094.297| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7652 Z= 0.161 Angle : 0.694 10.877 10424 Z= 0.353 Chirality : 0.045 0.157 1172 Planarity : 0.005 0.044 1327 Dihedral : 5.031 21.037 1048 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.48 % Favored : 91.21 % Rotamer: Outliers : 3.17 % Allowed : 19.39 % Favored : 77.44 % 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: -2.06 (0.27), residues: 967 helix: 0.21 (1.14), residues: 22 sheet: -0.80 (0.29), residues: 333 loop : -1.83 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 52 HIS 0.006 0.001 HIS C 38 PHE 0.023 0.002 PHE B 79 TYR 0.028 0.002 TYR B 102 ARG 0.009 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.02919 ( 173) hydrogen bonds : angle 6.39844 ( 411) SS BOND : bond 0.00352 ( 16) SS BOND : angle 0.96243 ( 32) covalent geometry : bond 0.00382 ( 7636) covalent geometry : angle 0.69287 (10392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2351.20 seconds wall clock time: 41 minutes 48.68 seconds (2508.68 seconds total)