Starting phenix.real_space_refine on Sun Mar 10 23:25:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hry_34982/03_2024/8hry_34982.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hry_34982/03_2024/8hry_34982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hry_34982/03_2024/8hry_34982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hry_34982/03_2024/8hry_34982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hry_34982/03_2024/8hry_34982.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hry_34982/03_2024/8hry_34982.pdb" } resolution = 3.11 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= 0.002 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 42 5.16 5 C 3880 2.51 5 N 976 2.21 5 O 1118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 185": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2322 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 16, 'TRANS': 285} Chain: "B" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 371 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 7, 'TRANS': 39} Chain: "H" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1666 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 14, 'TRANS': 205} Chain: "L" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1657 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Time building chain proxies: 3.54, per 1000 atoms: 0.59 Number of scatterers: 6016 At special positions: 0 Unit cell: (70.965, 73.455, 144.42, 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 42 16.00 O 1118 8.00 N 976 7.00 C 3880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.3 seconds 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1446 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 11 sheets defined 35.8% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 58 through 84 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.643A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 removed outlier: 3.699A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 180 removed outlier: 3.548A pdb=" N VAL A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 211 removed outlier: 4.949A pdb=" N LYS A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 4.065A pdb=" N ALA A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix removed outlier: 3.562A pdb=" N PHE A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.609A pdb=" N GLY A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 removed outlier: 4.252A pdb=" N CYS A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 284 through 312 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.873A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.716A pdb=" N THR L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 189 removed outlier: 4.155A pdb=" N HIS L 189 " --> pdb=" O TYR L 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.590A pdb=" N ILE H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.683A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.532A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N TYR H 182 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.532A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N TYR H 182 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 158 through 160 Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.501A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.434A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.780A pdb=" N ASN L 137 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 145 through 149 removed outlier: 5.680A pdb=" N HIS L 198 " --> pdb=" O SER L 203 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER L 203 " --> pdb=" O HIS L 198 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 864 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: 1.72 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1856 1.34 - 1.46: 1385 1.46 - 1.58: 2863 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 6168 Sorted by residual: bond pdb=" CB ASP H 73 " pdb=" CG ASP H 73 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.41e+00 bond pdb=" CG ARG A 143 " pdb=" CD ARG A 143 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CA TYR A 146 " pdb=" C TYR A 146 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.11e+00 bond pdb=" CB PRO A 181 " pdb=" CG PRO A 181 " ideal model delta sigma weight residual 1.492 1.543 -0.051 5.00e-02 4.00e+02 1.04e+00 bond pdb=" C VAL A 187 " pdb=" O VAL A 187 " ideal model delta sigma weight residual 1.233 1.243 -0.010 1.02e-02 9.61e+03 9.41e-01 ... (remaining 6163 not shown) Histogram of bond angle deviations from ideal: 98.97 - 105.99: 179 105.99 - 113.00: 3367 113.00 - 120.02: 2027 120.02 - 127.04: 2734 127.04 - 134.06: 85 Bond angle restraints: 8392 Sorted by residual: angle pdb=" C ASN H 140 " pdb=" CA ASN H 140 " pdb=" CB ASN H 140 " ideal model delta sigma weight residual 116.54 110.42 6.12 1.15e+00 7.56e-01 2.83e+01 angle pdb=" N ILE L 75 " pdb=" CA ILE L 75 " pdb=" C ILE L 75 " ideal model delta sigma weight residual 113.42 108.86 4.56 1.17e+00 7.31e-01 1.52e+01 angle pdb=" CA ASN H 140 " pdb=" C ASN H 140 " pdb=" N SER H 141 " ideal model delta sigma weight residual 119.52 116.78 2.74 7.90e-01 1.60e+00 1.20e+01 angle pdb=" CA LEU A 197 " pdb=" CB LEU A 197 " pdb=" CG LEU A 197 " ideal model delta sigma weight residual 116.30 128.41 -12.11 3.50e+00 8.16e-02 1.20e+01 angle pdb=" CG ARG A 143 " pdb=" CD ARG A 143 " pdb=" NE ARG A 143 " ideal model delta sigma weight residual 112.00 118.15 -6.15 2.20e+00 2.07e-01 7.82e+00 ... (remaining 8387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 3098 16.20 - 32.40: 432 32.40 - 48.59: 113 48.59 - 64.79: 17 64.79 - 80.99: 5 Dihedral angle restraints: 3665 sinusoidal: 1408 harmonic: 2257 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.21 41.79 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual 93.00 60.92 32.08 1 1.00e+01 1.00e-02 1.47e+01 dihedral pdb=" CA PRO A 181 " pdb=" C PRO A 181 " pdb=" N GLN A 182 " pdb=" CA GLN A 182 " ideal model delta harmonic sigma weight residual -180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 3662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 660 0.037 - 0.075: 209 0.075 - 0.112: 83 0.112 - 0.149: 7 0.149 - 0.187: 2 Chirality restraints: 961 Sorted by residual: chirality pdb=" CB ILE A 291 " pdb=" CA ILE A 291 " pdb=" CG1 ILE A 291 " pdb=" CG2 ILE A 291 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CB ILE A 93 " pdb=" CA ILE A 93 " pdb=" CG1 ILE A 93 " pdb=" CG2 ILE A 93 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ASP H 90 " pdb=" N ASP H 90 " pdb=" C ASP H 90 " pdb=" CB ASP H 90 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 958 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 180 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO A 181 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 82 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" CG ASP L 82 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP L 82 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP L 82 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU L 185 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" CD GLU L 185 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU L 185 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU L 185 " -0.012 2.00e-02 2.50e+03 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1042 2.76 - 3.30: 5747 3.30 - 3.83: 9895 3.83 - 4.37: 11414 4.37 - 4.90: 20185 Nonbonded interactions: 48283 Sorted by model distance: nonbonded pdb=" OG1 THR H 28 " pdb=" OD1 ASN H 31 " model vdw 2.228 2.440 nonbonded pdb=" O SER H 179 " pdb=" OG SER H 179 " model vdw 2.243 2.440 nonbonded pdb=" NZ LYS L 149 " pdb=" OE2 GLU L 195 " model vdw 2.254 2.520 nonbonded pdb=" OD1 ASN A 106 " pdb=" OG SER A 119 " model vdw 2.270 2.440 nonbonded pdb=" N GLU L 154 " pdb=" OE1 GLU L 154 " model vdw 2.276 2.520 ... (remaining 48278 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 2.080 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.190 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 0.051 6168 Z= 0.202 Angle : 0.661 12.108 8392 Z= 0.339 Chirality : 0.042 0.187 961 Planarity : 0.006 0.124 1050 Dihedral : 15.757 80.986 2210 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.74 % Allowed : 28.74 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.31), residues: 774 helix: 1.85 (0.33), residues: 240 sheet: 0.63 (0.36), residues: 218 loop : -1.51 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS L 189 PHE 0.006 0.001 PHE A 283 TYR 0.014 0.001 TYR A 307 ARG 0.015 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 172 time to evaluate : 0.683 Fit side-chains REVERT: A 180 ARG cc_start: 0.7410 (ptp-170) cc_final: 0.7098 (ptp-110) REVERT: A 183 TYR cc_start: 0.7114 (m-80) cc_final: 0.6799 (m-80) outliers start: 5 outliers final: 4 residues processed: 172 average time/residue: 0.1596 time to fit residues: 36.6687 Evaluate side-chains 172 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 168 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.0370 chunk 31 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6168 Z= 0.194 Angle : 0.605 11.390 8392 Z= 0.295 Chirality : 0.043 0.147 961 Planarity : 0.005 0.079 1050 Dihedral : 4.704 36.652 837 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.59 % Allowed : 25.48 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.31), residues: 774 helix: 2.02 (0.33), residues: 242 sheet: 0.63 (0.36), residues: 217 loop : -1.49 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 161 HIS 0.003 0.001 HIS L 198 PHE 0.008 0.001 PHE A 310 TYR 0.016 0.001 TYR L 49 ARG 0.005 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 0.701 Fit side-chains REVERT: A 180 ARG cc_start: 0.7353 (ptp-170) cc_final: 0.6933 (ptp-110) REVERT: A 183 TYR cc_start: 0.7103 (m-80) cc_final: 0.6771 (m-80) REVERT: H 73 ASP cc_start: 0.8401 (t0) cc_final: 0.8148 (t0) outliers start: 31 outliers final: 24 residues processed: 197 average time/residue: 0.1398 time to fit residues: 37.5541 Evaluate side-chains 195 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain L residue 176 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 0.0060 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6168 Z= 0.196 Angle : 0.591 12.223 8392 Z= 0.288 Chirality : 0.043 0.152 961 Planarity : 0.004 0.066 1050 Dihedral : 4.117 18.985 829 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.33 % Allowed : 26.22 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.31), residues: 774 helix: 2.07 (0.33), residues: 242 sheet: 0.55 (0.36), residues: 217 loop : -1.49 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS L 91 PHE 0.007 0.001 PHE H 153 TYR 0.012 0.001 TYR L 49 ARG 0.007 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 180 time to evaluate : 0.737 Fit side-chains REVERT: A 180 ARG cc_start: 0.7371 (ptp-170) cc_final: 0.6741 (ptp-110) REVERT: A 183 TYR cc_start: 0.7367 (m-80) cc_final: 0.6890 (m-80) REVERT: A 254 VAL cc_start: 0.8863 (t) cc_final: 0.8637 (p) REVERT: H 73 ASP cc_start: 0.8344 (t0) cc_final: 0.7973 (t0) REVERT: L 134 CYS cc_start: 0.8177 (t) cc_final: 0.7925 (t) REVERT: L 193 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8422 (t) outliers start: 36 outliers final: 26 residues processed: 204 average time/residue: 0.1558 time to fit residues: 42.4651 Evaluate side-chains 196 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 210 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 203 ASN L 38 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6168 Z= 0.171 Angle : 0.579 12.168 8392 Z= 0.281 Chirality : 0.042 0.151 961 Planarity : 0.004 0.060 1050 Dihedral : 4.052 19.403 829 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.22 % Allowed : 25.63 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.31), residues: 774 helix: 1.93 (0.33), residues: 254 sheet: 0.64 (0.36), residues: 215 loop : -1.63 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.000 HIS L 91 PHE 0.006 0.001 PHE L 135 TYR 0.017 0.001 TYR A 69 ARG 0.008 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 181 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 180 ARG cc_start: 0.7401 (ptp-170) cc_final: 0.6663 (ptp-110) REVERT: A 183 TYR cc_start: 0.7483 (m-80) cc_final: 0.6946 (m-80) REVERT: A 254 VAL cc_start: 0.8879 (t) cc_final: 0.8629 (p) REVERT: H 73 ASP cc_start: 0.8334 (t0) cc_final: 0.7921 (t0) REVERT: L 193 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8429 (t) outliers start: 42 outliers final: 28 residues processed: 213 average time/residue: 0.1559 time to fit residues: 44.4119 Evaluate side-chains 207 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 210 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.0170 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 203 ASN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 6168 Z= 0.365 Angle : 0.677 12.806 8392 Z= 0.330 Chirality : 0.045 0.159 961 Planarity : 0.005 0.053 1050 Dihedral : 4.469 21.131 829 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 8.00 % Allowed : 25.78 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.31), residues: 774 helix: 1.72 (0.33), residues: 255 sheet: 0.64 (0.37), residues: 214 loop : -1.70 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.006 0.001 HIS L 91 PHE 0.013 0.002 PHE H 153 TYR 0.018 0.002 TYR A 69 ARG 0.011 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 162 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9237 (mt) cc_final: 0.9017 (mt) REVERT: A 180 ARG cc_start: 0.7601 (ptp-170) cc_final: 0.6634 (ptp-170) REVERT: A 183 TYR cc_start: 0.7537 (m-80) cc_final: 0.6914 (m-80) REVERT: A 254 VAL cc_start: 0.8927 (t) cc_final: 0.8678 (p) REVERT: H 73 ASP cc_start: 0.8534 (t0) cc_final: 0.8077 (t0) REVERT: L 193 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8386 (t) outliers start: 54 outliers final: 46 residues processed: 202 average time/residue: 0.1494 time to fit residues: 40.9414 Evaluate side-chains 205 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 158 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6168 Z= 0.181 Angle : 0.609 12.924 8392 Z= 0.290 Chirality : 0.042 0.157 961 Planarity : 0.004 0.051 1050 Dihedral : 4.162 20.642 829 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.78 % Allowed : 28.74 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.31), residues: 774 helix: 1.90 (0.33), residues: 254 sheet: 0.64 (0.37), residues: 214 loop : -1.71 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 35 HIS 0.001 0.000 HIS L 90 PHE 0.007 0.001 PHE A 310 TYR 0.013 0.001 TYR A 69 ARG 0.010 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9271 (mt) cc_final: 0.9044 (mt) REVERT: A 180 ARG cc_start: 0.7634 (ptp-170) cc_final: 0.6652 (ptp-170) REVERT: A 183 TYR cc_start: 0.7551 (m-80) cc_final: 0.6980 (m-80) REVERT: A 254 VAL cc_start: 0.8919 (t) cc_final: 0.8652 (p) REVERT: H 73 ASP cc_start: 0.8414 (t0) cc_final: 0.7931 (t0) REVERT: L 193 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8398 (t) outliers start: 39 outliers final: 31 residues processed: 201 average time/residue: 0.1560 time to fit residues: 41.9713 Evaluate side-chains 199 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 210 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.0570 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6168 Z= 0.177 Angle : 0.611 12.785 8392 Z= 0.289 Chirality : 0.042 0.177 961 Planarity : 0.004 0.052 1050 Dihedral : 4.043 18.817 829 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 6.67 % Allowed : 28.15 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.31), residues: 774 helix: 1.95 (0.33), residues: 253 sheet: 0.66 (0.36), residues: 216 loop : -1.70 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 106 HIS 0.002 0.000 HIS L 91 PHE 0.007 0.001 PHE A 310 TYR 0.011 0.001 TYR L 49 ARG 0.011 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 180 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9357 (mt) cc_final: 0.9143 (mt) REVERT: A 180 ARG cc_start: 0.7588 (ptp-170) cc_final: 0.6554 (ptp-170) REVERT: A 183 TYR cc_start: 0.7388 (m-80) cc_final: 0.6830 (m-80) REVERT: A 229 MET cc_start: 0.8847 (ttm) cc_final: 0.8598 (ttt) REVERT: A 254 VAL cc_start: 0.8929 (t) cc_final: 0.8650 (p) REVERT: H 73 ASP cc_start: 0.8531 (t0) cc_final: 0.7922 (t0) REVERT: L 132 VAL cc_start: 0.9069 (t) cc_final: 0.8846 (t) REVERT: L 193 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8293 (t) outliers start: 45 outliers final: 36 residues processed: 212 average time/residue: 0.1458 time to fit residues: 41.8619 Evaluate side-chains 213 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 176 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 0.0980 chunk 50 optimal weight: 0.0020 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 0.0770 chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 overall best weight: 0.3146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6168 Z= 0.150 Angle : 0.609 13.545 8392 Z= 0.285 Chirality : 0.042 0.185 961 Planarity : 0.004 0.053 1050 Dihedral : 3.903 18.069 829 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.78 % Allowed : 29.48 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.31), residues: 774 helix: 1.96 (0.33), residues: 253 sheet: 0.73 (0.36), residues: 216 loop : -1.69 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.001 0.000 HIS L 91 PHE 0.006 0.001 PHE A 310 TYR 0.023 0.001 TYR H 152 ARG 0.011 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9379 (mt) cc_final: 0.9178 (mt) REVERT: A 180 ARG cc_start: 0.7521 (ptp-170) cc_final: 0.6558 (ptp-110) REVERT: A 183 TYR cc_start: 0.7450 (m-80) cc_final: 0.6846 (m-80) REVERT: A 254 VAL cc_start: 0.8898 (t) cc_final: 0.8613 (p) REVERT: B 39 ASP cc_start: 0.8664 (t0) cc_final: 0.8271 (t0) REVERT: H 73 ASP cc_start: 0.8474 (t0) cc_final: 0.8030 (t0) REVERT: H 182 TYR cc_start: 0.8989 (m-80) cc_final: 0.8435 (m-80) REVERT: L 32 TYR cc_start: 0.9203 (m-10) cc_final: 0.8976 (m-10) REVERT: L 132 VAL cc_start: 0.9038 (t) cc_final: 0.8821 (t) REVERT: L 193 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8304 (t) REVERT: L 207 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7849 (mptt) outliers start: 39 outliers final: 32 residues processed: 223 average time/residue: 0.1464 time to fit residues: 44.0992 Evaluate side-chains 223 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 189 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 207 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.0060 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6168 Z= 0.156 Angle : 0.620 13.483 8392 Z= 0.289 Chirality : 0.042 0.185 961 Planarity : 0.005 0.057 1050 Dihedral : 3.865 17.924 829 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.59 % Allowed : 30.37 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.31), residues: 774 helix: 1.90 (0.33), residues: 259 sheet: 0.80 (0.37), residues: 216 loop : -1.59 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 195 HIS 0.001 0.000 HIS L 91 PHE 0.007 0.001 PHE A 310 TYR 0.012 0.001 TYR H 129 ARG 0.014 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 180 ARG cc_start: 0.7523 (ptp-170) cc_final: 0.6553 (ptp-110) REVERT: A 183 TYR cc_start: 0.7438 (m-80) cc_final: 0.6866 (m-80) REVERT: A 254 VAL cc_start: 0.8871 (t) cc_final: 0.8555 (p) REVERT: B 39 ASP cc_start: 0.8664 (t0) cc_final: 0.8252 (t0) REVERT: H 73 ASP cc_start: 0.8488 (t0) cc_final: 0.8015 (t0) REVERT: H 182 TYR cc_start: 0.9051 (m-80) cc_final: 0.8518 (m-80) REVERT: L 32 TYR cc_start: 0.9211 (m-10) cc_final: 0.8970 (m-10) REVERT: L 132 VAL cc_start: 0.9043 (t) cc_final: 0.8828 (t) REVERT: L 193 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8295 (t) REVERT: L 207 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7866 (mptt) outliers start: 31 outliers final: 27 residues processed: 212 average time/residue: 0.1504 time to fit residues: 42.9011 Evaluate side-chains 215 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 186 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 207 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6168 Z= 0.269 Angle : 0.656 13.709 8392 Z= 0.311 Chirality : 0.044 0.182 961 Planarity : 0.005 0.059 1050 Dihedral : 4.140 18.444 829 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.19 % Allowed : 29.78 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.31), residues: 774 helix: 1.90 (0.33), residues: 253 sheet: 0.75 (0.37), residues: 216 loop : -1.76 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS L 91 PHE 0.011 0.001 PHE A 37 TYR 0.017 0.001 TYR A 69 ARG 0.014 0.001 ARG A 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 180 ARG cc_start: 0.7574 (ptp-170) cc_final: 0.6574 (ptp-110) REVERT: A 183 TYR cc_start: 0.7412 (m-80) cc_final: 0.6850 (m-80) REVERT: A 229 MET cc_start: 0.9030 (ttm) cc_final: 0.8681 (ttt) REVERT: A 254 VAL cc_start: 0.8876 (t) cc_final: 0.8542 (p) REVERT: H 73 ASP cc_start: 0.8476 (t0) cc_final: 0.7788 (t0) REVERT: L 193 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8381 (t) REVERT: L 207 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7995 (mptt) outliers start: 35 outliers final: 31 residues processed: 194 average time/residue: 0.1499 time to fit residues: 39.2109 Evaluate side-chains 201 residues out of total 675 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 CYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 207 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 0.0670 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.092771 restraints weight = 9610.971| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.74 r_work: 0.2909 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6168 Z= 0.172 Angle : 0.634 13.908 8392 Z= 0.296 Chirality : 0.043 0.186 961 Planarity : 0.005 0.061 1050 Dihedral : 4.011 18.287 829 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.44 % Allowed : 30.52 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.31), residues: 774 helix: 1.82 (0.33), residues: 259 sheet: 0.77 (0.37), residues: 216 loop : -1.64 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 195 HIS 0.001 0.000 HIS L 91 PHE 0.009 0.001 PHE L 96 TYR 0.015 0.001 TYR A 69 ARG 0.016 0.001 ARG A 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1881.55 seconds wall clock time: 34 minutes 52.48 seconds (2092.48 seconds total)