Starting phenix.real_space_refine on Fri Apr 5 20:04:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p72_17515/04_2024/8p72_17515_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p72_17515/04_2024/8p72_17515.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p72_17515/04_2024/8p72_17515_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p72_17515/04_2024/8p72_17515_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p72_17515/04_2024/8p72_17515_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p72_17515/04_2024/8p72_17515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p72_17515/04_2024/8p72_17515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p72_17515/04_2024/8p72_17515_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p72_17515/04_2024/8p72_17515_updated.pdb" } 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 3290 2.51 5 N 870 2.21 5 O 1036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 141": "OE1" <-> "OE2" Residue "J GLU 68": "OE1" <-> "OE2" Residue "J PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "J ASP 245": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5227 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'X2Z': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "I" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "J" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Time building chain proxies: 3.21, per 1000 atoms: 0.61 Number of scatterers: 5227 At special positions: 0 Unit cell: (82.65, 94.05, 67.6875, 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 31 16.00 O 1036 8.00 N 870 7.00 C 3290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.0 seconds 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... running ksdssp... Secondary structure from input PDB file: 33 helices and 2 sheets defined 53.0% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'H' and resid 264 through 269 removed outlier: 4.042A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU H 269 " --> pdb=" O LEU H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 274 Processing helix chain 'H' and resid 280 through 285 Processing helix chain 'H' and resid 289 through 301 Processing helix chain 'I' and resid 2 through 4 No H-bonds generated for 'chain 'I' and resid 2 through 4' Processing helix chain 'I' and resid 6 through 10 Processing helix chain 'I' and resid 16 through 37 Processing helix chain 'I' and resid 50 through 69 Processing helix chain 'I' and resid 77 through 92 Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.931A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 Processing helix chain 'I' and resid 133 through 153 removed outlier: 4.707A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 177 Processing helix chain 'I' and resid 184 through 200 removed outlier: 4.467A pdb=" N LYS I 189 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 209 through 223 Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 242 through 261 Processing helix chain 'I' and resid 267 through 282 Processing helix chain 'J' and resid 57 through 67 Processing helix chain 'J' and resid 98 through 103 Processing helix chain 'J' and resid 111 through 130 Processing helix chain 'J' and resid 140 through 142 No H-bonds generated for 'chain 'J' and resid 140 through 142' Processing helix chain 'J' and resid 176 through 178 No H-bonds generated for 'chain 'J' and resid 176 through 178' Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 218 through 229 Processing helix chain 'J' and resid 240 through 242 No H-bonds generated for 'chain 'J' and resid 240 through 242' Processing helix chain 'J' and resid 257 through 260 No H-bonds generated for 'chain 'J' and resid 257 through 260' Processing helix chain 'J' and resid 266 through 275 Processing helix chain 'J' and resid 286 through 291 Processing helix chain 'J' and resid 293 through 296 No H-bonds generated for 'chain 'J' and resid 293 through 296' Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing sheet with id= A, first strand: chain 'J' and resid 26 through 29 removed outlier: 7.044A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 143 through 145 220 hydrogen bonds defined for protein. 612 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: 1.51 Time building geometry restraints manager: 2.37 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: 1641 1.34 - 1.46: 1038 1.46 - 1.58: 2499 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 5227 Sorted by residual: bond pdb=" C04 X2Z J 401 " pdb=" C27 X2Z J 401 " ideal model delta sigma weight residual 1.384 1.426 -0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" C27 X2Z J 401 " pdb=" N07 X2Z J 401 " ideal model delta sigma weight residual 1.340 1.302 0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" C17 X2Z J 401 " pdb=" C18 X2Z J 401 " ideal model delta sigma weight residual 1.360 1.393 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C08 X2Z J 401 " pdb=" C17 X2Z J 401 " ideal model delta sigma weight residual 1.357 1.388 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C ACE I 0 " pdb=" O ACE I 0 " ideal model delta sigma weight residual 1.199 1.228 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 5222 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.77: 143 105.77 - 112.81: 2743 112.81 - 119.85: 1738 119.85 - 126.89: 2377 126.89 - 133.93: 73 Bond angle restraints: 7074 Sorted by residual: angle pdb=" C02 X2Z J 401 " pdb=" C04 X2Z J 401 " pdb=" C05 X2Z J 401 " ideal model delta sigma weight residual 116.66 126.65 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N07 X2Z J 401 " pdb=" C08 X2Z J 401 " pdb=" N09 X2Z J 401 " ideal model delta sigma weight residual 111.31 120.64 -9.33 3.00e+00 1.11e-01 9.67e+00 angle pdb=" CA LYS J 293 " pdb=" CB LYS J 293 " pdb=" CG LYS J 293 " ideal model delta sigma weight residual 114.10 119.95 -5.85 2.00e+00 2.50e-01 8.56e+00 angle pdb=" C02 X2Z J 401 " pdb=" C04 X2Z J 401 " pdb=" C27 X2Z J 401 " ideal model delta sigma weight residual 135.35 126.65 8.70 3.00e+00 1.11e-01 8.41e+00 angle pdb=" C17 X2Z J 401 " pdb=" C08 X2Z J 401 " pdb=" N09 X2Z J 401 " ideal model delta sigma weight residual 128.58 120.96 7.62 3.00e+00 1.11e-01 6.45e+00 ... (remaining 7069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.77: 2935 25.77 - 51.53: 192 51.53 - 77.30: 24 77.30 - 103.06: 5 103.06 - 128.83: 1 Dihedral angle restraints: 3157 sinusoidal: 1310 harmonic: 1847 Sorted by residual: dihedral pdb=" C08 X2Z J 401 " pdb=" C10 X2Z J 401 " pdb=" N09 X2Z J 401 " pdb=" C11 X2Z J 401 " ideal model delta sinusoidal sigma weight residual 179.50 50.67 128.83 1 3.00e+01 1.11e-03 1.74e+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 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG I 197 " pdb=" CD ARG I 197 " pdb=" NE ARG I 197 " pdb=" CZ ARG I 197 " ideal model delta sinusoidal sigma weight residual 180.00 -136.20 -43.80 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 3154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 460 0.028 - 0.055: 191 0.055 - 0.083: 75 0.083 - 0.110: 36 0.110 - 0.138: 14 Chirality restraints: 776 Sorted by residual: chirality pdb=" CG LEU I 236 " pdb=" CB LEU I 236 " pdb=" CD1 LEU I 236 " pdb=" CD2 LEU I 236 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA VAL J 210 " pdb=" N VAL J 210 " pdb=" C VAL J 210 " pdb=" CB VAL J 210 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 773 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU I 49 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO I 50 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO I 50 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 50 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU I 141 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" CD GLU I 141 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU I 141 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU I 141 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 162 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO I 163 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " -0.021 5.00e-02 4.00e+02 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 745 2.75 - 3.29: 5393 3.29 - 3.83: 9977 3.83 - 4.36: 11782 4.36 - 4.90: 19275 Nonbonded interactions: 47172 Sorted by model distance: nonbonded pdb=" O HOH J 501 " pdb=" O HOH J 537 " model vdw 2.215 2.440 nonbonded pdb=" OG SER I 78 " pdb=" OD2 ASP I 116 " model vdw 2.220 2.440 nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 401 " model vdw 2.225 2.440 nonbonded pdb=" O PRO J 280 " pdb=" O HOH J 501 " model vdw 2.256 2.440 nonbonded pdb=" O HOH J 544 " pdb=" O HOH J 550 " model vdw 2.273 2.440 ... (remaining 47167 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 18.490 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 17.590 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 0.042 5227 Z= 0.217 Angle : 0.629 9.989 7074 Z= 0.311 Chirality : 0.041 0.138 776 Planarity : 0.005 0.038 903 Dihedral : 16.828 128.827 1961 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 0.54 % Allowed : 18.23 % Favored : 81.23 % 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: 1.51 (0.33), residues: 618 helix: 1.91 (0.28), residues: 339 sheet: -0.00 (1.28), residues: 16 loop : -0.09 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 11 HIS 0.004 0.001 HIS I 161 PHE 0.019 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.003 0.000 ARG I 256 *********************** 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 93 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.921 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 92 average time/residue: 2.0370 time to fit residues: 193.6497 Evaluate side-chains 89 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS ** J 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.0542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5227 Z= 0.284 Angle : 0.631 5.693 7074 Z= 0.325 Chirality : 0.043 0.137 776 Planarity : 0.005 0.038 903 Dihedral : 7.348 126.367 702 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.53 % Allowed : 16.06 % Favored : 81.41 % 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: 1.29 (0.32), residues: 618 helix: 1.67 (0.27), residues: 331 sheet: 0.43 (1.33), residues: 15 loop : -0.07 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 11 HIS 0.006 0.001 HIS I 281 PHE 0.019 0.002 PHE I 71 TYR 0.018 0.002 TYR I 91 ARG 0.004 0.001 ARG J 136 *********************** 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 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.608 Fit side-chains REVERT: I 49 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5827 (mp0) REVERT: J 10 LYS cc_start: 0.4723 (OUTLIER) cc_final: 0.4503 (tptp) outliers start: 14 outliers final: 2 residues processed: 95 average time/residue: 1.5437 time to fit residues: 151.7018 Evaluate side-chains 88 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.0565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5227 Z= 0.277 Angle : 0.624 6.890 7074 Z= 0.321 Chirality : 0.043 0.137 776 Planarity : 0.005 0.039 903 Dihedral : 7.308 126.913 701 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.81 % Allowed : 15.88 % Favored : 82.31 % 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: 1.19 (0.32), residues: 618 helix: 1.60 (0.27), residues: 331 sheet: 0.45 (1.34), residues: 15 loop : -0.15 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 11 HIS 0.005 0.001 HIS I 281 PHE 0.017 0.002 PHE I 71 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.001 ARG J 188 *********************** 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 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.651 Fit side-chains REVERT: J 10 LYS cc_start: 0.4725 (OUTLIER) cc_final: 0.4493 (tptp) outliers start: 10 outliers final: 3 residues processed: 93 average time/residue: 1.6998 time to fit residues: 163.3073 Evaluate side-chains 86 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 29 optimal weight: 0.0370 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 142 GLN I 183 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.0450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5227 Z= 0.216 Angle : 0.574 6.002 7074 Z= 0.294 Chirality : 0.041 0.133 776 Planarity : 0.005 0.038 903 Dihedral : 7.124 125.525 701 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.81 % Allowed : 14.62 % Favored : 83.57 % 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: 1.35 (0.33), residues: 618 helix: 1.75 (0.27), residues: 339 sheet: 0.46 (1.33), residues: 15 loop : -0.14 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.004 0.001 HIS I 161 PHE 0.017 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG J 136 *********************** 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 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.667 Fit side-chains REVERT: I 49 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5809 (mp0) REVERT: J 97 ASP cc_start: 0.7585 (p0) cc_final: 0.7305 (p0) outliers start: 10 outliers final: 3 residues processed: 94 average time/residue: 1.5554 time to fit residues: 151.3754 Evaluate side-chains 88 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5227 Z= 0.236 Angle : 0.594 5.661 7074 Z= 0.305 Chirality : 0.042 0.134 776 Planarity : 0.005 0.038 903 Dihedral : 7.133 126.041 701 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 15.34 % Favored : 82.67 % 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: 1.38 (0.33), residues: 618 helix: 1.79 (0.28), residues: 332 sheet: 0.50 (1.34), residues: 15 loop : -0.10 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.004 0.001 HIS I 281 PHE 0.017 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.004 0.001 ARG J 136 *********************** 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 100 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.528 Fit side-chains REVERT: I 49 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5811 (mp0) REVERT: I 252 MET cc_start: 0.6989 (mtm) cc_final: 0.6759 (mtm) REVERT: J 10 LYS cc_start: 0.4721 (OUTLIER) cc_final: 0.4515 (tptp) REVERT: J 292 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7352 (mtt) outliers start: 11 outliers final: 2 residues processed: 94 average time/residue: 1.6721 time to fit residues: 162.5803 Evaluate side-chains 89 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 142 GLN I 183 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.0423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5227 Z= 0.215 Angle : 0.576 5.155 7074 Z= 0.297 Chirality : 0.041 0.134 776 Planarity : 0.005 0.038 903 Dihedral : 6.971 125.013 699 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.17 % Allowed : 15.52 % Favored : 82.31 % 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: 1.39 (0.33), residues: 618 helix: 1.81 (0.27), residues: 339 sheet: 0.18 (1.27), residues: 16 loop : -0.15 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.004 0.001 HIS I 161 PHE 0.018 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG J 136 *********************** 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 100 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.566 Fit side-chains REVERT: I 49 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5807 (mp0) REVERT: J 10 LYS cc_start: 0.4732 (OUTLIER) cc_final: 0.4505 (tptp) REVERT: J 97 ASP cc_start: 0.7580 (p0) cc_final: 0.7291 (p0) REVERT: J 292 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7333 (mtt) outliers start: 12 outliers final: 3 residues processed: 95 average time/residue: 1.5540 time to fit residues: 152.7042 Evaluate side-chains 92 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.0270 chunk 59 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.0629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5227 Z= 0.290 Angle : 0.648 7.679 7074 Z= 0.334 Chirality : 0.043 0.138 776 Planarity : 0.005 0.038 903 Dihedral : 7.153 127.254 699 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.81 % Allowed : 16.43 % Favored : 81.77 % 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: 1.16 (0.32), residues: 618 helix: 1.58 (0.27), residues: 331 sheet: 0.57 (1.35), residues: 15 loop : -0.17 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.006 0.001 HIS I 281 PHE 0.017 0.002 PHE I 71 TYR 0.018 0.002 TYR I 91 ARG 0.005 0.001 ARG J 136 *********************** 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 100 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.597 Fit side-chains REVERT: I 49 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5823 (mp0) REVERT: J 10 LYS cc_start: 0.4736 (OUTLIER) cc_final: 0.4487 (tptp) outliers start: 10 outliers final: 3 residues processed: 95 average time/residue: 1.5412 time to fit residues: 151.4860 Evaluate side-chains 90 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 0.0980 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 183 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.0476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5227 Z= 0.237 Angle : 0.606 7.670 7074 Z= 0.312 Chirality : 0.042 0.134 776 Planarity : 0.005 0.037 903 Dihedral : 7.022 125.608 699 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.26 % Allowed : 17.33 % Favored : 81.41 % 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: 1.33 (0.33), residues: 618 helix: 1.75 (0.28), residues: 332 sheet: 0.46 (1.33), residues: 15 loop : -0.13 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.004 0.001 HIS I 281 PHE 0.017 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.001 ARG J 136 *********************** 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 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.611 Fit side-chains REVERT: J 10 LYS cc_start: 0.4715 (OUTLIER) cc_final: 0.4495 (tptp) outliers start: 7 outliers final: 3 residues processed: 93 average time/residue: 1.6308 time to fit residues: 156.7897 Evaluate side-chains 88 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 52 optimal weight: 0.1980 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.0619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5227 Z= 0.283 Angle : 0.654 7.747 7074 Z= 0.337 Chirality : 0.043 0.142 776 Planarity : 0.005 0.038 903 Dihedral : 7.148 126.775 699 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.44 % Allowed : 17.51 % Favored : 81.05 % 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: 1.13 (0.32), residues: 618 helix: 1.58 (0.27), residues: 331 sheet: 0.50 (1.35), residues: 15 loop : -0.21 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 11 HIS 0.005 0.001 HIS I 281 PHE 0.019 0.002 PHE I 71 TYR 0.018 0.002 TYR I 91 ARG 0.005 0.001 ARG J 136 *********************** 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 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.620 Fit side-chains REVERT: J 10 LYS cc_start: 0.4732 (OUTLIER) cc_final: 0.4495 (tptp) outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 1.5538 time to fit residues: 147.8541 Evaluate side-chains 91 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 183 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5227 Z= 0.320 Angle : 0.699 8.001 7074 Z= 0.361 Chirality : 0.045 0.188 776 Planarity : 0.006 0.038 903 Dihedral : 7.221 127.473 699 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.26 % Allowed : 18.05 % Favored : 80.69 % 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: 0.97 (0.32), residues: 618 helix: 1.43 (0.27), residues: 331 sheet: 0.50 (1.35), residues: 15 loop : -0.27 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 11 HIS 0.006 0.001 HIS I 281 PHE 0.020 0.003 PHE J 185 TYR 0.020 0.003 TYR I 164 ARG 0.005 0.001 ARG J 136 ********************** 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 fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.618 Fit side-chains REVERT: J 10 LYS cc_start: 0.4747 (OUTLIER) cc_final: 0.4500 (tptp) outliers start: 7 outliers final: 3 residues processed: 90 average time/residue: 1.5444 time to fit residues: 143.9858 Evaluate side-chains 89 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 183 ASN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.186217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.164704 restraints weight = 4537.696| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 0.88 r_work: 0.3844 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.0545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5227 Z= 0.258 Angle : 0.655 7.755 7074 Z= 0.336 Chirality : 0.043 0.146 776 Planarity : 0.005 0.038 903 Dihedral : 7.113 126.193 699 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 0.90 % Allowed : 18.59 % Favored : 80.51 % 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: 1.13 (0.32), residues: 618 helix: 1.61 (0.27), residues: 332 sheet: 0.09 (1.29), residues: 16 loop : -0.23 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.005 0.001 HIS I 281 PHE 0.018 0.002 PHE I 30 TYR 0.019 0.002 TYR I 164 ARG 0.004 0.001 ARG J 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3142.98 seconds wall clock time: 56 minutes 53.99 seconds (3413.99 seconds total)