Starting phenix.real_space_refine on Fri Apr 5 19:56:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p75_17518/04_2024/8p75_17518_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p75_17518/04_2024/8p75_17518.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p75_17518/04_2024/8p75_17518_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p75_17518/04_2024/8p75_17518_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p75_17518/04_2024/8p75_17518_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p75_17518/04_2024/8p75_17518.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p75_17518/04_2024/8p75_17518.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p75_17518/04_2024/8p75_17518_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p75_17518/04_2024/8p75_17518_updated.pdb" } resolution = 2.0 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 31 5.16 5 C 3289 2.51 5 N 869 2.21 5 O 991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 25": "OD1" <-> "OD2" Residue "I GLU 137": "OE1" <-> "OE2" Residue "I GLU 141": "OE1" <-> "OE2" Residue "I PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 229": "OE1" <-> "OE2" Residue "J PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 147": "OE1" <-> "OE2" Residue "J PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 5181 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'X3Z': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Time building chain proxies: 3.42, per 1000 atoms: 0.66 Number of scatterers: 5181 At special positions: 0 Unit cell: (83.3625, 93.3375, 66.2625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 31 16.00 O 991 8.00 N 869 7.00 C 3289 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: 2.34 Conformation dependent library (CDL) restraints added in 886.5 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: 34 helices and 2 sheets defined 53.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'H' and resid 263 through 269 removed outlier: 4.471A pdb=" N GLY H 267 " --> 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: 3.722A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 removed outlier: 3.972A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 153 removed outlier: 4.718A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.536A 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: 4.613A pdb=" N LYS I 189 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.758A 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 283 Processing helix chain 'J' and resid 57 through 68 removed outlier: 4.031A 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 156 through 158 No H-bonds generated for 'chain 'J' and resid 156 through 158' 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 228 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 290 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: 6.815A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY J 82 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 143 through 145 219 hydrogen bonds defined for protein. 603 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: 1.18 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 1673 1.37 - 1.51: 1484 1.51 - 1.65: 2021 1.65 - 1.80: 22 1.80 - 1.94: 28 Bond restraints: 5228 Sorted by residual: bond pdb=" C10 X3Z J 401 " pdb=" C11 X3Z J 401 " ideal model delta sigma weight residual 1.612 1.531 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C22 X3Z J 401 " pdb=" O23 X3Z J 401 " ideal model delta sigma weight residual 1.459 1.399 0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" C29 X3Z J 401 " pdb=" N07 X3Z J 401 " ideal model delta sigma weight residual 1.349 1.300 0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C21 X3Z J 401 " pdb=" C22 X3Z J 401 " ideal model delta sigma weight residual 1.489 1.527 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C08 X3Z J 401 " pdb=" C18 X3Z J 401 " ideal model delta sigma weight residual 1.359 1.392 -0.033 2.00e-02 2.50e+03 2.77e+00 ... (remaining 5223 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.01: 146 106.01 - 112.99: 2777 112.99 - 119.98: 1819 119.98 - 126.96: 2261 126.96 - 133.94: 73 Bond angle restraints: 7076 Sorted by residual: angle pdb=" C11 X3Z J 401 " pdb=" C16 X3Z J 401 " pdb="BR17 X3Z J 401 " ideal model delta sigma weight residual 142.95 119.67 23.28 3.00e+00 1.11e-01 6.02e+01 angle pdb=" C15 X3Z J 401 " pdb=" C16 X3Z J 401 " pdb="BR17 X3Z J 401 " ideal model delta sigma weight residual 96.85 120.12 -23.27 3.00e+00 1.11e-01 6.02e+01 angle pdb=" N07 X3Z J 401 " pdb=" C08 X3Z J 401 " pdb=" N09 X3Z J 401 " ideal model delta sigma weight residual 110.61 120.69 -10.08 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CA ARG J 11 " pdb=" CB ARG J 11 " pdb=" CG ARG J 11 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" C18 X3Z J 401 " pdb=" C08 X3Z J 401 " pdb=" N09 X3Z J 401 " ideal model delta sigma weight residual 129.14 120.78 8.36 3.00e+00 1.11e-01 7.77e+00 ... (remaining 7071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 2750 17.58 - 35.16: 297 35.16 - 52.74: 83 52.74 - 70.32: 15 70.32 - 87.89: 9 Dihedral angle restraints: 3154 sinusoidal: 1307 harmonic: 1847 Sorted by residual: dihedral pdb=" CG ARG J 179 " pdb=" CD ARG J 179 " pdb=" NE ARG J 179 " pdb=" CZ ARG J 179 " ideal model delta sinusoidal sigma weight residual 180.00 135.86 44.14 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CB GLU I 137 " pdb=" CG GLU I 137 " pdb=" CD GLU I 137 " pdb=" OE1 GLU I 137 " ideal model delta sinusoidal sigma weight residual 0.00 85.05 -85.05 1 3.00e+01 1.11e-03 9.75e+00 dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 164.43 15.57 0 5.00e+00 4.00e-02 9.70e+00 ... (remaining 3151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 457 0.027 - 0.054: 196 0.054 - 0.081: 69 0.081 - 0.108: 39 0.108 - 0.135: 16 Chirality restraints: 777 Sorted by residual: 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 2.58 -0.14 2.00e-01 2.50e+01 4.56e-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 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE J 255 " pdb=" N ILE J 255 " pdb=" C ILE J 255 " pdb=" CB ILE J 255 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 774 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 132 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO I 133 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO I 133 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 133 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 194 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C PHE I 194 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE I 194 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU I 195 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 193 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C ASP I 193 " -0.020 2.00e-02 2.50e+03 pdb=" O ASP I 193 " 0.007 2.00e-02 2.50e+03 pdb=" N PHE I 194 " 0.007 2.00e-02 2.50e+03 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 420 2.74 - 3.28: 5417 3.28 - 3.82: 9686 3.82 - 4.36: 11479 4.36 - 4.90: 18848 Nonbonded interactions: 45850 Sorted by model distance: nonbonded pdb=" OD1 ASP J 137 " pdb=" NZ LYS J 139 " model vdw 2.198 2.520 nonbonded pdb=" N GLU J 147 " pdb=" OE1 GLU J 147 " model vdw 2.218 2.520 nonbonded pdb=" O LEU I 144 " pdb=" O HOH I 401 " model vdw 2.246 2.440 nonbonded pdb=" O HOH I 412 " pdb=" O HOH I 429 " model vdw 2.305 2.440 nonbonded pdb=" O HOH J 520 " pdb=" O HOH J 523 " model vdw 2.314 2.440 ... (remaining 45845 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: 7.170 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: 0.000 Extract box with map and model: 11.110 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.150 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 0.081 5228 Z= 0.246 Angle : 0.704 23.276 7076 Z= 0.322 Chirality : 0.040 0.135 777 Planarity : 0.004 0.042 903 Dihedral : 16.365 87.895 1958 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.90 % Allowed : 18.77 % Favored : 80.32 % 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: 1.61 (0.33), residues: 618 helix: 1.88 (0.28), residues: 340 sheet: 2.46 (1.28), residues: 15 loop : -0.06 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG J 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.593 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 1.3776 time to fit residues: 131.5229 Evaluate side-chains 89 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain J residue 216 ASP 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: 0.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 0.0670 chunk 18 optimal weight: 0.0770 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 136 GLN J 83 HIS ** J 142 ASN ** 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: 0.7604 moved from start: 0.0479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5228 Z= 0.141 Angle : 0.475 7.780 7076 Z= 0.242 Chirality : 0.038 0.132 777 Planarity : 0.004 0.043 903 Dihedral : 5.582 58.437 704 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.17 % Allowed : 16.25 % Favored : 81.59 % 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: 1.85 (0.34), residues: 618 helix: 2.11 (0.29), residues: 340 sheet: 2.45 (1.26), residues: 15 loop : 0.02 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.003 0.001 HIS I 281 PHE 0.014 0.001 PHE I 110 TYR 0.015 0.001 TYR I 91 ARG 0.002 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 112 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.661 Fit side-chains REVERT: J 99 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6481 (tp30) outliers start: 12 outliers final: 3 residues processed: 107 average time/residue: 1.4348 time to fit residues: 159.2064 Evaluate side-chains 91 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 292 MET 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: 6.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 136 GLN I 275 GLN J 83 HIS J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.0393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5228 Z= 0.193 Angle : 0.529 8.330 7076 Z= 0.270 Chirality : 0.040 0.137 777 Planarity : 0.004 0.045 903 Dihedral : 5.423 59.585 696 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 2.53 % Allowed : 16.61 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.34), residues: 618 helix: 2.11 (0.28), residues: 333 sheet: 2.52 (1.28), residues: 15 loop : 0.03 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.013 0.002 PHE I 30 TYR 0.019 0.002 TYR I 207 ARG 0.002 0.000 ARG J 136 *********************** 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 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.656 Fit side-chains REVERT: I 229 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5975 (tm-30) outliers start: 14 outliers final: 5 residues processed: 99 average time/residue: 1.5401 time to fit residues: 158.1348 Evaluate side-chains 91 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 0.0020 chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 136 GLN I 275 GLN J 83 HIS J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.0431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5228 Z= 0.195 Angle : 0.535 9.302 7076 Z= 0.273 Chirality : 0.040 0.137 777 Planarity : 0.004 0.045 903 Dihedral : 5.450 59.277 696 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.35 % Allowed : 17.51 % Favored : 80.14 % 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: 1.62 (0.34), residues: 618 helix: 1.93 (0.28), residues: 339 sheet: 2.56 (1.29), residues: 15 loop : -0.09 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.014 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.002 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 106 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.483 Fit side-chains REVERT: I 186 ILE cc_start: 0.7709 (pp) cc_final: 0.7294 (pp) outliers start: 13 outliers final: 5 residues processed: 100 average time/residue: 1.3944 time to fit residues: 144.5162 Evaluate side-chains 93 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 136 GLN I 275 GLN J 83 HIS J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 0.041 5228 Z= 0.249 Angle : 0.585 10.502 7076 Z= 0.300 Chirality : 0.042 0.143 777 Planarity : 0.004 0.044 903 Dihedral : 5.626 59.989 696 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 2.17 % Allowed : 18.23 % Favored : 79.60 % 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: 1.41 (0.33), residues: 618 helix: 1.74 (0.28), residues: 341 sheet: 3.01 (1.46), residues: 9 loop : -0.13 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 306 HIS 0.005 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.003 0.000 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 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.614 Fit side-chains REVERT: I 186 ILE cc_start: 0.7781 (pp) cc_final: 0.7306 (pp) outliers start: 12 outliers final: 6 residues processed: 97 average time/residue: 1.4558 time to fit residues: 146.4851 Evaluate side-chains 92 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP 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: 6.9990 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 136 GLN I 275 GLN J 83 HIS J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5228 Z= 0.304 Angle : 0.647 12.231 7076 Z= 0.331 Chirality : 0.044 0.147 777 Planarity : 0.005 0.039 903 Dihedral : 5.809 59.466 696 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.17 % Allowed : 18.59 % Favored : 79.24 % 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: 1.14 (0.33), residues: 618 helix: 1.51 (0.28), residues: 341 sheet: 2.96 (1.47), residues: 9 loop : -0.25 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.021 0.002 TYR I 91 ARG 0.003 0.001 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 99 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.669 Fit side-chains REVERT: I 186 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7370 (pp) outliers start: 12 outliers final: 6 residues processed: 93 average time/residue: 1.4515 time to fit residues: 140.2051 Evaluate side-chains 90 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 216 ASP 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: 3.9990 chunk 33 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 0.0770 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 136 GLN I 275 GLN J 83 HIS J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.0439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5228 Z= 0.177 Angle : 0.550 14.806 7076 Z= 0.277 Chirality : 0.040 0.135 777 Planarity : 0.004 0.043 903 Dihedral : 5.498 59.343 696 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.62 % Allowed : 19.31 % Favored : 79.06 % 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 (0.34), residues: 618 helix: 1.83 (0.28), residues: 340 sheet: 2.66 (1.26), residues: 15 loop : -0.10 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.017 0.001 PHE I 110 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG J 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.573 Fit side-chains REVERT: J 189 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7150 (tpt) outliers start: 9 outliers final: 7 residues processed: 95 average time/residue: 1.4182 time to fit residues: 139.8882 Evaluate side-chains 92 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 189 MET Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 46 optimal weight: 0.0980 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 136 GLN J 83 HIS J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.0497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5228 Z= 0.203 Angle : 0.580 16.039 7076 Z= 0.291 Chirality : 0.040 0.139 777 Planarity : 0.004 0.043 903 Dihedral : 5.510 59.789 696 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 2.17 % Allowed : 18.77 % Favored : 79.06 % 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 (0.34), residues: 618 helix: 1.81 (0.28), residues: 340 sheet: 2.66 (1.28), residues: 15 loop : -0.07 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.016 0.002 PHE I 110 TYR 0.019 0.002 TYR I 91 ARG 0.004 0.000 ARG I 279 *********************** 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 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.601 Fit side-chains REVERT: I 186 ILE cc_start: 0.7745 (pp) cc_final: 0.7313 (pp) outliers start: 12 outliers final: 7 residues processed: 97 average time/residue: 1.3883 time to fit residues: 139.7446 Evaluate side-chains 92 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET 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: 1.9990 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 136 GLN I 275 GLN J 83 HIS J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.0466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5228 Z= 0.182 Angle : 0.538 6.548 7076 Z= 0.279 Chirality : 0.040 0.136 777 Planarity : 0.004 0.043 903 Dihedral : 5.449 59.397 696 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.81 % Allowed : 18.95 % Favored : 79.24 % 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: 1.62 (0.34), residues: 618 helix: 1.86 (0.28), residues: 340 sheet: 2.65 (1.25), residues: 15 loop : -0.00 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.017 0.002 PHE I 110 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 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 97 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.607 Fit side-chains REVERT: I 186 ILE cc_start: 0.7721 (pp) cc_final: 0.7325 (pp) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 1.4286 time to fit residues: 137.8780 Evaluate side-chains 90 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 136 GLN I 275 GLN J 83 HIS J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.0504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5228 Z= 0.194 Angle : 0.593 14.533 7076 Z= 0.295 Chirality : 0.040 0.137 777 Planarity : 0.004 0.039 903 Dihedral : 5.449 59.367 696 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.26 % Allowed : 19.49 % Favored : 79.24 % 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: 1.59 (0.34), residues: 618 helix: 1.82 (0.28), residues: 340 sheet: 2.63 (1.26), residues: 15 loop : 0.01 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.016 0.002 PHE I 110 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG J 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.601 Fit side-chains REVERT: I 186 ILE cc_start: 0.7723 (pp) cc_final: 0.7324 (pp) outliers start: 7 outliers final: 6 residues processed: 91 average time/residue: 1.4298 time to fit residues: 135.0311 Evaluate side-chains 92 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 33 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 136 GLN J 83 HIS J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.175203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.154616 restraints weight = 3961.019| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 0.90 r_work: 0.3737 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 5228 Z= 0.416 Angle : 0.782 18.056 7076 Z= 0.397 Chirality : 0.049 0.157 777 Planarity : 0.006 0.048 903 Dihedral : 6.013 59.326 696 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.44 % Allowed : 19.86 % Favored : 78.70 % 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: 0.81 (0.33), residues: 618 helix: 1.20 (0.28), residues: 341 sheet: 2.90 (1.45), residues: 9 loop : -0.34 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.018 0.003 PHE J 17 TYR 0.022 0.003 TYR I 91 ARG 0.005 0.001 ARG I 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2954.55 seconds wall clock time: 53 minutes 43.49 seconds (3223.49 seconds total)