Starting phenix.real_space_refine on Fri Apr 5 20:09:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6w_17509/04_2024/8p6w_17509_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6w_17509/04_2024/8p6w_17509.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6w_17509/04_2024/8p6w_17509_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/8p6w_17509/04_2024/8p6w_17509_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6w_17509/04_2024/8p6w_17509_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6w_17509/04_2024/8p6w_17509.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6w_17509/04_2024/8p6w_17509.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6w_17509/04_2024/8p6w_17509_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6w_17509/04_2024/8p6w_17509_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= 0.001 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 3291 2.51 5 N 870 2.21 5 O 1051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 247": "OE1" <-> "OE2" Residue "H GLU 254": "OE1" <-> "OE2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "I GLU 234": "OE1" <-> "OE2" Residue "J ASP 53": "OD1" <-> "OD2" Residue "J ASP 79": "OD1" <-> "OD2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "J ASP 216": "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: 5243 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'X2H': 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "J" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Time building chain proxies: 3.30, per 1000 atoms: 0.63 Number of scatterers: 5243 At special positions: 0 Unit cell: (84.7875, 92.625, 68.4, 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 1051 8.00 N 870 7.00 C 3291 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: 2.23 Conformation dependent library (CDL) restraints added in 886.4 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... running ksdssp... Secondary structure from input PDB file: 33 helices and 2 sheets defined 53.3% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'H' and resid 263 through 269 removed outlier: 4.579A pdb=" N GLY H 267 " --> pdb=" O LEU H 263 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG H 268 " --> pdb=" O GLU H 264 " (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: 3.674A 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: 4.713A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.652A 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 199 removed outlier: 4.955A pdb=" N LYS I 189 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 206 No H-bonds generated for 'chain 'I' and resid 203 through 206' 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 68 removed outlier: 4.141A pdb=" N GLU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) 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 77 through 83 removed outlier: 6.711A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY J 82 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 143 through 145 218 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: 1.39 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1639 1.34 - 1.46: 1098 1.46 - 1.58: 2441 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 5227 Sorted by residual: bond pdb=" C28 X2H J 401 " pdb=" N07 X2H J 401 " ideal model delta sigma weight residual 1.340 1.294 0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" C08 X2H J 401 " pdb=" C17 X2H J 401 " ideal model delta sigma weight residual 1.357 1.393 -0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C17 X2H J 401 " pdb=" C18 X2H J 401 " ideal model delta sigma weight residual 1.359 1.395 -0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C04 X2H J 401 " pdb=" C28 X2H J 401 " ideal model delta sigma weight residual 1.384 1.418 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C ACE I 0 " pdb=" O ACE I 0 " ideal model delta sigma weight residual 1.199 1.223 -0.024 2.00e-02 2.50e+03 1.49e+00 ... (remaining 5222 not shown) Histogram of bond angle deviations from ideal: 97.01 - 104.40: 99 104.40 - 111.79: 2459 111.79 - 119.18: 1773 119.18 - 126.57: 2663 126.57 - 133.96: 78 Bond angle restraints: 7072 Sorted by residual: angle pdb=" CB MET H 265 " pdb=" CG MET H 265 " pdb=" SD MET H 265 " ideal model delta sigma weight residual 112.70 123.88 -11.18 3.00e+00 1.11e-01 1.39e+01 angle pdb=" N07 X2H J 401 " pdb=" C08 X2H J 401 " pdb=" N09 X2H J 401 " ideal model delta sigma weight residual 108.93 118.92 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C17 X2H J 401 " pdb=" C18 X2H J 401 " pdb=" N19 X2H J 401 " ideal model delta sigma weight residual 111.48 120.53 -9.05 3.00e+00 1.11e-01 9.10e+00 angle pdb=" N19 X2H J 401 " pdb=" C18 X2H J 401 " pdb=" N27 X2H J 401 " ideal model delta sigma weight residual 128.54 119.58 8.96 3.00e+00 1.11e-01 8.92e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 108.63 5.27 1.80e+00 3.09e-01 8.57e+00 ... (remaining 7067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.00: 2956 26.00 - 51.99: 166 51.99 - 77.99: 26 77.99 - 103.98: 6 103.98 - 129.98: 2 Dihedral angle restraints: 3156 sinusoidal: 1309 harmonic: 1847 Sorted by residual: dihedral pdb=" C08 X2H J 401 " pdb=" C10 X2H J 401 " pdb=" N09 X2H J 401 " pdb=" C11 X2H J 401 " ideal model delta sinusoidal sigma weight residual 190.08 60.10 129.98 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C21 X2H J 401 " pdb=" C22 X2H J 401 " pdb=" C23 X2H J 401 " pdb=" C24 X2H J 401 " ideal model delta sinusoidal sigma weight residual 184.06 64.24 119.82 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" CA THR I 176 " pdb=" C THR I 176 " pdb=" N ARG I 177 " pdb=" CA ARG I 177 " ideal model delta harmonic sigma weight residual -180.00 -161.29 -18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 436 0.029 - 0.057: 217 0.057 - 0.086: 74 0.086 - 0.115: 37 0.115 - 0.144: 11 Chirality restraints: 775 Sorted by residual: 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 5.16e-01 chirality pdb=" CA PRO J 238 " pdb=" N PRO J 238 " pdb=" C PRO J 238 " pdb=" CB PRO J 238 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CG LEU I 65 " pdb=" CB LEU I 65 " pdb=" CD1 LEU I 65 " pdb=" CD2 LEU I 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 772 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 71 " -0.015 2.00e-02 2.50e+03 1.08e-02 2.03e+00 pdb=" CG PHE I 71 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE I 71 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE I 71 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE I 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 71 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE I 71 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO J 140 " -0.058 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 delta sigma weight rms_deltas residual plane pdb=" C THR J 231 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO J 232 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO J 232 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 232 " 0.019 5.00e-02 4.00e+02 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1134 2.77 - 3.30: 5369 3.30 - 3.84: 10007 3.84 - 4.37: 11899 4.37 - 4.90: 19105 Nonbonded interactions: 47514 Sorted by model distance: nonbonded pdb=" OE2 GLU J 62 " pdb=" O HOH J 501 " model vdw 2.239 2.440 nonbonded pdb=" O LEU J 290 " pdb=" O HOH J 502 " model vdw 2.248 2.440 nonbonded pdb=" O GLU I 145 " pdb=" O HOH I 401 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR J 233 " pdb=" OE1 GLU J 235 " model vdw 2.261 2.440 nonbonded pdb=" O HOH H 405 " pdb=" O HOH J 555 " model vdw 2.263 2.440 ... (remaining 47509 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: 3.640 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: 12.290 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.900 Find NCS groups from input model: 0.160 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:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.004 0.046 5227 Z= 0.286 Angle : 0.691 11.179 7072 Z= 0.338 Chirality : 0.042 0.144 775 Planarity : 0.005 0.035 903 Dihedral : 16.839 129.980 1960 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 0.90 % Allowed : 14.98 % 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: 1.39 (0.33), residues: 618 helix: 1.60 (0.27), residues: 344 sheet: 1.06 (2.27), residues: 5 loop : 0.12 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP J 132 HIS 0.006 0.002 HIS H 274 PHE 0.023 0.003 PHE I 71 TYR 0.021 0.002 TYR I 91 ARG 0.005 0.001 ARG I 77 *********************** 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 104 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.613 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 104 average time/residue: 1.4325 time to fit residues: 154.4011 Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 244 CYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.0492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5227 Z= 0.155 Angle : 0.502 5.636 7072 Z= 0.257 Chirality : 0.039 0.139 775 Planarity : 0.004 0.032 903 Dihedral : 9.441 126.244 704 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % 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: 1.82 (0.34), residues: 618 helix: 2.02 (0.28), residues: 344 sheet: 0.37 (1.27), residues: 14 loop : 0.23 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.005 0.001 HIS H 274 PHE 0.012 0.002 PHE I 71 TYR 0.018 0.002 TYR I 91 ARG 0.005 0.000 ARG I 77 *********************** 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 105 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.612 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 102 average time/residue: 1.4128 time to fit residues: 150.3039 Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 244 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 45 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 273 ASN H 281 GLN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5227 Z= 0.141 Angle : 0.481 6.685 7072 Z= 0.245 Chirality : 0.038 0.135 775 Planarity : 0.004 0.036 903 Dihedral : 9.174 125.127 699 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.26 % Allowed : 14.44 % 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: 2.01 (0.34), residues: 618 helix: 2.19 (0.28), residues: 344 sheet: 0.46 (1.29), residues: 14 loop : 0.28 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.004 0.001 HIS H 274 PHE 0.011 0.002 PHE I 110 TYR 0.017 0.001 TYR I 91 ARG 0.004 0.000 ARG I 77 *********************** 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 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.536 Fit side-chains REVERT: J 13 GLU cc_start: 0.5863 (OUTLIER) cc_final: 0.5523 (pt0) outliers start: 7 outliers final: 1 residues processed: 107 average time/residue: 1.4695 time to fit residues: 163.0087 Evaluate side-chains 99 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain J residue 13 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.0270 chunk 29 optimal weight: 0.3980 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.002 0.021 5227 Z= 0.136 Angle : 0.484 8.398 7072 Z= 0.243 Chirality : 0.038 0.134 775 Planarity : 0.004 0.036 903 Dihedral : 9.021 124.738 698 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 0.54 % Allowed : 16.06 % Favored : 83.39 % 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: 2.01 (0.34), residues: 618 helix: 2.25 (0.28), residues: 342 sheet: 0.44 (1.30), residues: 14 loop : 0.21 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.004 0.001 HIS H 274 PHE 0.011 0.002 PHE I 110 TYR 0.017 0.001 TYR I 91 ARG 0.006 0.000 ARG I 77 *********************** 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 fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.580 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 98 average time/residue: 1.5187 time to fit residues: 154.3296 Evaluate side-chains 97 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 189 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN H 273 ASN H 281 GLN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.0535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5227 Z= 0.399 Angle : 0.716 9.405 7072 Z= 0.372 Chirality : 0.046 0.164 775 Planarity : 0.006 0.040 903 Dihedral : 9.887 127.830 698 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % 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: 1.18 (0.33), residues: 618 helix: 1.40 (0.27), residues: 344 sheet: 1.59 (2.33), residues: 5 loop : 0.06 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP J 237 HIS 0.007 0.002 HIS J 131 PHE 0.027 0.004 PHE I 71 TYR 0.023 0.003 TYR I 91 ARG 0.005 0.001 ARG I 9 *********************** 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 111 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.620 Fit side-chains REVERT: I 137 GLU cc_start: 0.6694 (tp30) cc_final: 0.6310 (tp30) outliers start: 6 outliers final: 3 residues processed: 108 average time/residue: 1.4991 time to fit residues: 167.6801 Evaluate side-chains 104 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 247 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 189 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.0552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5227 Z= 0.186 Angle : 0.571 10.330 7072 Z= 0.289 Chirality : 0.040 0.142 775 Planarity : 0.004 0.032 903 Dihedral : 9.445 125.154 698 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 0.90 % Allowed : 15.16 % 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: 1.56 (0.33), residues: 618 helix: 1.83 (0.28), residues: 342 sheet: 1.62 (2.33), residues: 5 loop : 0.08 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.005 0.001 HIS H 274 PHE 0.014 0.002 PHE I 71 TYR 0.019 0.002 TYR I 91 ARG 0.005 0.000 ARG I 77 *********************** 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 107 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.548 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 104 average time/residue: 1.4405 time to fit residues: 155.2836 Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 247 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain J residue 158 LEU 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: 0.7980 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5227 Z= 0.175 Angle : 0.540 11.202 7072 Z= 0.273 Chirality : 0.039 0.142 775 Planarity : 0.004 0.032 903 Dihedral : 9.324 125.528 698 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 0.72 % Allowed : 15.70 % 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: 1.70 (0.33), residues: 618 helix: 1.95 (0.28), residues: 342 sheet: 1.65 (2.11), residues: 5 loop : 0.11 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.005 0.001 HIS H 274 PHE 0.015 0.002 PHE J 185 TYR 0.018 0.002 TYR I 91 ARG 0.006 0.000 ARG I 77 *********************** 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 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.634 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 100 average time/residue: 1.5215 time to fit residues: 157.3892 Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 247 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain J residue 158 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.0536 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= 0.226 Angle : 0.573 6.436 7072 Z= 0.294 Chirality : 0.041 0.140 775 Planarity : 0.005 0.033 903 Dihedral : 9.471 126.311 698 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 0.90 % Allowed : 16.06 % Favored : 83.03 % 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: 1.54 (0.33), residues: 618 helix: 1.79 (0.27), residues: 343 sheet: 1.61 (1.97), residues: 5 loop : 0.08 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.005 0.001 HIS H 274 PHE 0.020 0.003 PHE I 71 TYR 0.020 0.002 TYR I 91 ARG 0.008 0.001 ARG I 77 *********************** 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 104 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.646 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 101 average time/residue: 1.4967 time to fit residues: 156.6226 Evaluate side-chains 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 247 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain J residue 158 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.0481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5227 Z= 0.282 Angle : 0.639 10.591 7072 Z= 0.327 Chirality : 0.042 0.143 775 Planarity : 0.005 0.035 903 Dihedral : 9.657 126.888 698 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 0.90 % Allowed : 15.70 % Favored : 83.39 % 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: 1.65 (0.27), residues: 341 sheet: 1.51 (1.93), residues: 5 loop : 0.04 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP J 132 HIS 0.006 0.002 HIS J 131 PHE 0.026 0.003 PHE J 185 TYR 0.021 0.002 TYR I 91 ARG 0.006 0.001 ARG I 77 *********************** 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 106 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.600 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 103 average time/residue: 1.4632 time to fit residues: 156.1370 Evaluate side-chains 104 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 247 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 210 VAL 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: 5.9990 chunk 49 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.0670 chunk 7 optimal weight: 0.6980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5227 Z= 0.181 Angle : 0.544 6.561 7072 Z= 0.279 Chirality : 0.040 0.143 775 Planarity : 0.004 0.032 903 Dihedral : 9.403 125.545 698 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 0.90 % Allowed : 16.06 % Favored : 83.03 % 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: 1.58 (0.33), residues: 618 helix: 1.79 (0.28), residues: 347 sheet: 1.59 (2.01), residues: 5 loop : 0.12 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 11 HIS 0.005 0.001 HIS H 274 PHE 0.023 0.002 PHE J 185 TYR 0.018 0.002 TYR I 91 ARG 0.008 0.000 ARG I 77 ********************** 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 105 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.589 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 102 average time/residue: 1.5083 time to fit residues: 159.3572 Evaluate side-chains 104 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 247 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain J residue 158 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 273 ASN H 307 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.190006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.172487 restraints weight = 3641.656| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 0.58 r_work: 0.3790 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work: 0.3606 rms_B_bonded: 4.08 restraints_weight: 0.1250 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.0522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5227 Z= 0.243 Angle : 0.609 11.228 7072 Z= 0.311 Chirality : 0.041 0.142 775 Planarity : 0.005 0.038 903 Dihedral : 9.538 126.543 698 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 16.25 % 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: 1.48 (0.33), residues: 618 helix: 1.75 (0.27), residues: 341 sheet: 1.50 (1.93), residues: 5 loop : 0.06 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.030 0.003 PHE J 185 TYR 0.020 0.002 TYR I 91 ARG 0.007 0.001 ARG J 298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3120.25 seconds wall clock time: 56 minutes 6.11 seconds (3366.11 seconds total)