Starting phenix.real_space_refine on Thu Nov 14 09:17:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6y_17511/11_2024/8p6y_17511.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6y_17511/11_2024/8p6y_17511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6y_17511/11_2024/8p6y_17511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6y_17511/11_2024/8p6y_17511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6y_17511/11_2024/8p6y_17511.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6y_17511/11_2024/8p6y_17511.cif" } resolution = 1.9 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 3279 2.51 5 N 869 2.21 5 O 1082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5266 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "J" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 4.87, per 1000 atoms: 0.92 Number of scatterers: 5266 At special positions: 0 Unit cell: (84.7875, 94.7625, 68.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 3 15.00 Mg 1 11.99 O 1082 8.00 N 869 7.00 C 3279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.37 Conformation dependent library (CDL) restraints added in 633.8 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 3 sheets defined 63.0% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 270 through 275 Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.883A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 removed outlier: 3.546A pdb=" N LEU I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.983A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.703A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 removed outlier: 3.622A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.571A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 Processing helix chain 'I' and resid 187 through 200 Processing helix chain 'I' and resid 201 through 206 removed outlier: 4.519A pdb=" N TYR I 204 " --> pdb=" O THR I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.743A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 240 removed outlier: 3.539A pdb=" N GLU I 240 " --> pdb=" O MET I 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 237 through 240' Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 284 Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 155 through 159 removed outlier: 4.435A pdb=" N LEU J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.886A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.824A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 19 removed outlier: 7.149A pdb=" N LEU J 15 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ARG J 30 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 274 hydrogen bonds defined for protein. 759 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: 1.30 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 1669 1.36 - 1.50: 1384 1.50 - 1.64: 2120 1.64 - 1.78: 7 1.78 - 1.91: 50 Bond restraints: 5230 Sorted by residual: bond pdb=" C6 AGS J 401 " pdb=" N6 AGS J 401 " ideal model delta sigma weight residual 1.335 1.457 -0.122 1.00e-02 1.00e+04 1.48e+02 bond pdb=" C1' AGS J 401 " pdb=" N9 AGS J 401 " ideal model delta sigma weight residual 1.459 1.319 0.140 1.40e-02 5.10e+03 1.00e+02 bond pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.94e+01 bond pdb=" O3B AGS J 401 " pdb=" PG AGS J 401 " ideal model delta sigma weight residual 1.559 1.656 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C4 AGS J 401 " pdb=" C5 AGS J 401 " ideal model delta sigma weight residual 1.386 1.338 0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 5225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 6949 1.77 - 3.53: 105 3.53 - 5.30: 22 5.30 - 7.06: 5 7.06 - 8.83: 4 Bond angle restraints: 7085 Sorted by residual: angle pdb=" N1 AGS J 401 " pdb=" C2 AGS J 401 " pdb=" N3 AGS J 401 " ideal model delta sigma weight residual 128.80 120.14 8.66 8.41e-01 1.41e+00 1.06e+02 angle pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " pdb=" C8 AGS J 401 " ideal model delta sigma weight residual 103.67 107.94 -4.27 4.26e-01 5.51e+00 1.01e+02 angle pdb=" C5 AGS J 401 " pdb=" C4 AGS J 401 " pdb=" N3 AGS J 401 " ideal model delta sigma weight residual 126.80 119.81 6.99 7.41e-01 1.82e+00 8.90e+01 angle pdb=" N7 AGS J 401 " pdb=" C8 AGS J 401 " pdb=" N9 AGS J 401 " ideal model delta sigma weight residual 114.03 108.21 5.82 6.99e-01 2.05e+00 6.93e+01 angle pdb=" C4 AGS J 401 " pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " ideal model delta sigma weight residual 110.73 108.03 2.70 4.52e-01 4.89e+00 3.57e+01 ... (remaining 7080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 2818 19.94 - 39.88: 257 39.88 - 59.81: 73 59.81 - 79.75: 11 79.75 - 99.69: 8 Dihedral angle restraints: 3167 sinusoidal: 1320 harmonic: 1847 Sorted by residual: dihedral pdb=" O1B AGS J 401 " pdb=" O3B AGS J 401 " pdb=" PB AGS J 401 " pdb=" PG AGS J 401 " ideal model delta sinusoidal sigma weight residual 68.91 168.60 -99.69 1 3.00e+01 1.11e-03 1.25e+01 dihedral pdb=" CB GLU I 145 " pdb=" CG GLU I 145 " pdb=" CD GLU I 145 " pdb=" OE1 GLU I 145 " ideal model delta sinusoidal sigma weight residual 0.00 90.26 -90.26 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.97e+00 ... (remaining 3164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 613 0.047 - 0.094: 131 0.094 - 0.142: 34 0.142 - 0.189: 1 0.189 - 0.236: 2 Chirality restraints: 781 Sorted by residual: chirality pdb=" C1' AGS J 401 " pdb=" C2' AGS J 401 " pdb=" N9 AGS J 401 " pdb=" O4' AGS J 401 " both_signs ideal model delta sigma weight residual False 2.41 2.17 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C2' AGS J 401 " pdb=" C1' AGS J 401 " pdb=" C3' AGS J 401 " pdb=" O2' AGS J 401 " both_signs ideal model delta sigma weight residual False -2.67 -2.87 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" C4' AGS J 401 " pdb=" C3' AGS J 401 " pdb=" C5' AGS J 401 " pdb=" O4' AGS J 401 " both_signs ideal model delta sigma weight residual False -2.49 -2.63 0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 778 not shown) Planarity restraints: 902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I 66 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" CD GLU I 66 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU I 66 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU I 66 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 183 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO I 184 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO I 184 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 184 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO J 140 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.019 5.00e-02 4.00e+02 ... (remaining 899 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 186 2.70 - 3.25: 5265 3.25 - 3.80: 9244 3.80 - 4.35: 12178 4.35 - 4.90: 19355 Nonbonded interactions: 46228 Sorted by model distance: nonbonded pdb="MG MG J 402 " pdb=" O HOH J 551 " model vdw 2.148 2.170 nonbonded pdb=" O ARG I 242 " pdb=" NH1 ARG I 242 " model vdw 2.203 3.120 nonbonded pdb=" O HOH J 535 " pdb=" O HOH J 561 " model vdw 2.246 3.040 nonbonded pdb=" O HOH I 402 " pdb=" O HOH I 467 " model vdw 2.255 3.040 nonbonded pdb=" O HOH J 505 " pdb=" O HOH J 539 " model vdw 2.260 3.040 ... (remaining 46223 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 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.350 Find NCS groups from input model: 0.070 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:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.005 0.140 5230 Z= 0.353 Angle : 0.600 8.826 7085 Z= 0.400 Chirality : 0.042 0.236 781 Planarity : 0.004 0.036 902 Dihedral : 17.032 99.688 1971 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 0.36 % Allowed : 15.34 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.34), residues: 618 helix: 2.21 (0.29), residues: 331 sheet: -0.61 (1.27), residues: 19 loop : 0.43 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 11 HIS 0.009 0.001 HIS J 258 PHE 0.013 0.002 PHE I 110 TYR 0.016 0.001 TYR I 91 ARG 0.002 0.000 ARG I 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.681 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 1.6957 time to fit residues: 157.4802 Evaluate side-chains 87 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5230 Z= 0.243 Angle : 0.639 8.309 7085 Z= 0.328 Chirality : 0.044 0.169 781 Planarity : 0.005 0.035 902 Dihedral : 8.191 90.930 712 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.62 % Allowed : 13.54 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.34), residues: 618 helix: 2.13 (0.28), residues: 338 sheet: -0.46 (0.99), residues: 25 loop : 0.27 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.010 0.002 HIS J 131 PHE 0.016 0.002 PHE J 295 TYR 0.019 0.002 TYR I 2 ARG 0.004 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.672 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 92 average time/residue: 1.6668 time to fit residues: 158.5661 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5230 Z= 0.240 Angle : 0.633 8.326 7085 Z= 0.325 Chirality : 0.044 0.152 781 Planarity : 0.005 0.036 902 Dihedral : 7.823 83.658 710 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 1.44 % Allowed : 13.54 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.34), residues: 618 helix: 2.08 (0.27), residues: 338 sheet: -0.51 (0.97), residues: 25 loop : 0.18 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.010 0.002 HIS J 131 PHE 0.016 0.002 PHE J 295 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.660 Fit side-chains REVERT: I 18 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: J 52 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6541 (mmtm) outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 1.6858 time to fit residues: 160.3203 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 0.0070 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5230 Z= 0.175 Angle : 0.566 8.490 7085 Z= 0.289 Chirality : 0.042 0.141 781 Planarity : 0.004 0.035 902 Dihedral : 7.550 81.389 709 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 1.08 % Allowed : 13.90 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.34), residues: 618 helix: 2.26 (0.28), residues: 338 sheet: -0.38 (0.96), residues: 25 loop : 0.21 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.009 0.002 HIS J 258 PHE 0.014 0.002 PHE I 110 TYR 0.016 0.002 TYR I 91 ARG 0.004 0.000 ARG J 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.654 Fit side-chains REVERT: I 18 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: J 52 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6223 (mmtm) outliers start: 6 outliers final: 2 residues processed: 98 average time/residue: 1.6942 time to fit residues: 171.3789 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 124 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 5230 Z= 0.352 Angle : 0.742 8.145 7085 Z= 0.380 Chirality : 0.048 0.192 781 Planarity : 0.006 0.038 902 Dihedral : 7.794 80.150 709 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.62 % Allowed : 13.18 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.33), residues: 618 helix: 1.85 (0.27), residues: 338 sheet: -0.74 (1.20), residues: 19 loop : 0.16 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP J 132 HIS 0.012 0.003 HIS J 131 PHE 0.020 0.003 PHE I 13 TYR 0.021 0.003 TYR I 91 ARG 0.006 0.001 ARG J 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.623 Fit side-chains REVERT: I 18 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: J 52 LYS cc_start: 0.6797 (OUTLIER) cc_final: 0.6530 (mmtm) outliers start: 9 outliers final: 6 residues processed: 92 average time/residue: 1.6607 time to fit residues: 157.9452 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5230 Z= 0.157 Angle : 0.559 9.168 7085 Z= 0.284 Chirality : 0.041 0.139 781 Planarity : 0.004 0.035 902 Dihedral : 7.480 80.446 709 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 1.08 % Allowed : 14.62 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.34), residues: 618 helix: 2.29 (0.28), residues: 338 sheet: -0.29 (0.95), residues: 25 loop : 0.16 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 132 HIS 0.010 0.001 HIS J 258 PHE 0.014 0.002 PHE I 30 TYR 0.015 0.001 TYR I 91 ARG 0.002 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.567 Fit side-chains REVERT: I 18 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: J 52 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6053 (mmtm) outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 1.7506 time to fit residues: 168.0143 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 124 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5230 Z= 0.319 Angle : 0.714 9.506 7085 Z= 0.365 Chirality : 0.047 0.179 781 Planarity : 0.006 0.038 902 Dihedral : 7.707 79.358 709 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.62 % Allowed : 13.90 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.34), residues: 618 helix: 1.94 (0.27), residues: 338 sheet: -0.60 (1.20), residues: 19 loop : 0.15 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.012 0.002 HIS J 131 PHE 0.019 0.003 PHE I 13 TYR 0.020 0.003 TYR I 91 ARG 0.005 0.001 ARG J 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.641 Fit side-chains REVERT: I 18 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: J 52 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6521 (mmtm) outliers start: 9 outliers final: 4 residues processed: 92 average time/residue: 1.7570 time to fit residues: 167.0132 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 124 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5230 Z= 0.380 Angle : 0.784 10.228 7085 Z= 0.401 Chirality : 0.049 0.200 781 Planarity : 0.006 0.044 902 Dihedral : 7.841 79.876 709 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.62 % Allowed : 13.90 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.33), residues: 618 helix: 1.60 (0.27), residues: 344 sheet: -0.73 (0.94), residues: 25 loop : -0.04 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP J 132 HIS 0.012 0.003 HIS J 131 PHE 0.022 0.003 PHE I 71 TYR 0.022 0.003 TYR I 91 ARG 0.007 0.001 ARG J 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.680 Fit side-chains REVERT: I 18 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: J 52 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6579 (mmtm) outliers start: 9 outliers final: 5 residues processed: 91 average time/residue: 1.7318 time to fit residues: 162.7264 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5230 Z= 0.188 Angle : 0.608 10.375 7085 Z= 0.310 Chirality : 0.043 0.144 781 Planarity : 0.005 0.037 902 Dihedral : 7.575 80.641 709 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.08 % Allowed : 14.44 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.34), residues: 618 helix: 2.14 (0.28), residues: 338 sheet: -0.31 (0.97), residues: 25 loop : 0.16 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.010 0.002 HIS J 258 PHE 0.015 0.002 PHE I 30 TYR 0.015 0.002 TYR I 2 ARG 0.002 0.000 ARG I 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.629 Fit side-chains REVERT: I 18 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: J 52 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6285 (mmtm) outliers start: 6 outliers final: 2 residues processed: 90 average time/residue: 1.7669 time to fit residues: 163.9988 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 7 optimal weight: 0.0040 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5230 Z= 0.201 Angle : 0.622 9.650 7085 Z= 0.317 Chirality : 0.043 0.146 781 Planarity : 0.005 0.037 902 Dihedral : 7.535 79.115 709 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 1.26 % Allowed : 14.62 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.34), residues: 618 helix: 2.15 (0.28), residues: 338 sheet: -0.26 (0.97), residues: 25 loop : 0.16 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.009 0.002 HIS J 258 PHE 0.016 0.002 PHE I 30 TYR 0.016 0.002 TYR I 2 ARG 0.002 0.000 ARG J 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.646 Fit side-chains REVERT: I 18 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: J 52 LYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6320 (mmtm) outliers start: 7 outliers final: 3 residues processed: 90 average time/residue: 1.7831 time to fit residues: 165.5824 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.157577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133319 restraints weight = 4448.765| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 0.82 r_work: 0.3403 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5230 Z= 0.249 Angle : 0.669 9.436 7085 Z= 0.341 Chirality : 0.045 0.152 781 Planarity : 0.005 0.037 902 Dihedral : 7.625 78.762 709 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.08 % Allowed : 14.98 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.34), residues: 618 helix: 2.04 (0.27), residues: 338 sheet: -0.40 (0.96), residues: 25 loop : 0.16 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.011 0.002 HIS J 131 PHE 0.018 0.002 PHE I 71 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.001 ARG J 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3049.14 seconds wall clock time: 55 minutes 8.10 seconds (3308.10 seconds total)