Starting phenix.real_space_refine on Thu Dec 7 22:35:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orm_17129/12_2023/8orm_17129_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orm_17129/12_2023/8orm_17129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orm_17129/12_2023/8orm_17129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orm_17129/12_2023/8orm_17129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orm_17129/12_2023/8orm_17129_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orm_17129/12_2023/8orm_17129_updated.pdb" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 Cl 1 4.86 5 C 3307 2.51 5 N 874 2.21 5 O 1127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 254": "OE1" <-> "OE2" Residue "H TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I GLU 145": "OE1" <-> "OE2" Residue "I GLU 278": "OE1" <-> "OE2" Residue "J TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 216": "OD1" <-> "OD2" Residue "J GLU 227": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5341 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: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2297 Classifications: {'peptide': 288} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 269} Chain breaks: 2 Chain: "J" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'V0G': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "I" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "J" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Time building chain proxies: 3.51, per 1000 atoms: 0.66 Number of scatterers: 5341 At special positions: 0 Unit cell: (85.5, 93.3375, 68.4, 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) Cl 1 17.00 S 32 16.00 O 1127 8.00 N 874 7.00 C 3307 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 944.1 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 2 sheets defined 54.1% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'H' and resid 263 through 269 removed outlier: 4.591A pdb=" N GLY H 267 " --> pdb=" O LEU H 263 " (cutoff:3.500A) removed outlier: 4.701A 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: 3.532A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 removed outlier: 3.979A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 153 removed outlier: 4.671A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.591A 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: 4.624A pdb=" N LYS I 189 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 209 through 223 Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 238 through 240 No H-bonds generated for 'chain 'I' and resid 238 through 240' 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: 4.064A 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 192 through 208 removed outlier: 4.287A pdb=" N TRP J 197 " --> pdb=" O VAL J 194 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU J 208 " --> pdb=" O GLU J 205 " (cutoff:3.500A) 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 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: 6.658A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY J 82 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG J 30 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS J 14 " --> pdb=" O ARG J 30 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 143 through 145 217 hydrogen bonds defined for protein. 570 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: 1.57 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 825 1.31 - 1.43: 1414 1.43 - 1.56: 2966 1.56 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 5256 Sorted by residual: bond pdb=" C11 V0G J 401 " pdb=" N10 V0G J 401 " ideal model delta sigma weight residual 1.358 1.460 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C05 V0G J 401 " pdb=" N06 V0G J 401 " ideal model delta sigma weight residual 1.362 1.463 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C17 V0G J 401 " pdb=" N16 V0G J 401 " ideal model delta sigma weight residual 1.363 1.464 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C32 V0G J 401 " pdb=" C33 V0G J 401 " ideal model delta sigma weight residual 1.450 1.532 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C15 V0G J 401 " pdb=" N16 V0G J 401 " ideal model delta sigma weight residual 1.391 1.470 -0.079 2.00e-02 2.50e+03 1.58e+01 ... (remaining 5251 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.73: 135 105.73 - 112.83: 2760 112.83 - 119.94: 1835 119.94 - 127.04: 2315 127.04 - 134.15: 69 Bond angle restraints: 7114 Sorted by residual: angle pdb=" C09 V0G J 401 " pdb=" N10 V0G J 401 " pdb=" C11 V0G J 401 " ideal model delta sigma weight residual 129.31 121.44 7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" CB MET J 94 " pdb=" CG MET J 94 " pdb=" SD MET J 94 " ideal model delta sigma weight residual 112.70 119.92 -7.22 3.00e+00 1.11e-01 5.79e+00 angle pdb=" CA ILE I 186 " pdb=" CB ILE I 186 " pdb=" CG1 ILE I 186 " ideal model delta sigma weight residual 110.40 114.26 -3.86 1.70e+00 3.46e-01 5.15e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.95 3.95 1.80e+00 3.09e-01 4.82e+00 angle pdb=" C VAL J 173 " pdb=" N VAL J 174 " pdb=" CA VAL J 174 " ideal model delta sigma weight residual 121.97 125.54 -3.57 1.80e+00 3.09e-01 3.93e+00 ... (remaining 7109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2803 17.97 - 35.93: 251 35.93 - 53.90: 83 53.90 - 71.86: 20 71.86 - 89.83: 10 Dihedral angle restraints: 3167 sinusoidal: 1314 harmonic: 1853 Sorted by residual: dihedral pdb=" CG ARG J 298 " pdb=" CD ARG J 298 " pdb=" NE ARG J 298 " pdb=" CZ ARG J 298 " ideal model delta sinusoidal sigma weight residual -90.00 -42.52 -47.48 2 1.50e+01 4.44e-03 1.16e+01 dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU I 61 " pdb=" CG GLU I 61 " pdb=" CD GLU I 61 " pdb=" OE1 GLU I 61 " ideal model delta sinusoidal sigma weight residual 0.00 89.83 -89.83 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 450 0.026 - 0.052: 190 0.052 - 0.077: 79 0.077 - 0.103: 41 0.103 - 0.129: 17 Chirality restraints: 777 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 2.38 0.13 2.00e-01 2.50e+01 4.15e-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 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA VAL J 210 " pdb=" N VAL J 210 " pdb=" C VAL J 210 " pdb=" CB VAL J 210 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 774 not shown) Planarity restraints: 910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 44 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO I 45 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO I 45 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 45 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 298 " 0.128 9.50e-02 1.11e+02 5.75e-02 2.40e+00 pdb=" NE ARG J 298 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG J 298 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG J 298 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG J 298 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 193 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C ASP I 193 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP I 193 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE I 194 " 0.008 2.00e-02 2.50e+03 ... (remaining 907 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1101 2.77 - 3.30: 5495 3.30 - 3.83: 10220 3.83 - 4.37: 12120 4.37 - 4.90: 19513 Nonbonded interactions: 48449 Sorted by model distance: nonbonded pdb=" O GLU I 145 " pdb=" O HOH I 401 " model vdw 2.236 2.440 nonbonded pdb=" O ARG J 283 " pdb=" O HOH J 501 " model vdw 2.264 2.440 nonbonded pdb=" O HOH J 556 " pdb=" O HOH J 566 " model vdw 2.270 2.440 nonbonded pdb=" O HOH J 584 " pdb=" O HOH J 591 " model vdw 2.272 2.440 nonbonded pdb=" O HOH I 432 " pdb=" O HOH I 469 " model vdw 2.280 2.440 ... (remaining 48444 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: 3.010 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: 12.500 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.040 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 0.102 5256 Z= 0.290 Angle : 0.576 7.875 7114 Z= 0.282 Chirality : 0.040 0.129 777 Planarity : 0.005 0.058 910 Dihedral : 16.750 89.831 1967 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.61 % Favored : 98.23 % Rotamer: Outliers : 0.90 % Allowed : 14.39 % Favored : 84.71 % 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: 1.88 (0.33), residues: 620 helix: 1.92 (0.28), residues: 338 sheet: -0.24 (0.94), residues: 25 loop : 0.62 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS H 274 PHE 0.015 0.002 PHE I 30 TYR 0.015 0.001 TYR I 91 ARG 0.011 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.585 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 91 average time/residue: 1.4907 time to fit residues: 140.4400 Evaluate side-chains 90 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.8360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5256 Z= 0.248 Angle : 0.575 5.503 7114 Z= 0.301 Chirality : 0.042 0.135 777 Planarity : 0.005 0.042 910 Dihedral : 5.869 59.450 702 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.39 % Rotamer: Outliers : 2.16 % Allowed : 12.59 % Favored : 85.25 % 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: 620 helix: 1.67 (0.28), residues: 336 sheet: 1.07 (1.07), residues: 15 loop : 0.58 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.006 0.002 HIS H 274 PHE 0.017 0.002 PHE I 30 TYR 0.019 0.002 TYR I 2 ARG 0.007 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.669 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 94 average time/residue: 1.4865 time to fit residues: 144.7865 Evaluate side-chains 90 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.6893 time to fit residues: 2.2198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.0214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5256 Z= 0.155 Angle : 0.489 5.018 7114 Z= 0.255 Chirality : 0.039 0.128 777 Planarity : 0.005 0.045 910 Dihedral : 5.707 59.273 702 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.39 % Rotamer: Outliers : 1.80 % Allowed : 12.95 % Favored : 85.25 % 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: 1.98 (0.33), residues: 620 helix: 1.95 (0.28), residues: 336 sheet: 1.70 (1.26), residues: 15 loop : 0.60 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS H 274 PHE 0.016 0.002 PHE I 30 TYR 0.015 0.001 TYR I 91 ARG 0.008 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.676 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 1.4386 time to fit residues: 145.3403 Evaluate side-chains 92 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.662 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0557 time to fit residues: 0.9782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 0.0870 chunk 29 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 0.0270 chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.0429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5256 Z= 0.122 Angle : 0.454 5.510 7114 Z= 0.233 Chirality : 0.038 0.126 777 Planarity : 0.004 0.046 910 Dihedral : 5.510 58.627 702 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.39 % Rotamer: Outliers : 2.16 % Allowed : 12.95 % Favored : 84.89 % 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: 2.25 (0.34), residues: 620 helix: 2.19 (0.28), residues: 338 sheet: 2.38 (1.45), residues: 15 loop : 0.64 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 11 HIS 0.003 0.001 HIS H 274 PHE 0.014 0.001 PHE I 110 TYR 0.013 0.001 TYR I 60 ARG 0.007 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.673 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 95 average time/residue: 1.4634 time to fit residues: 144.2066 Evaluate side-chains 91 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.4481 time to fit residues: 2.4026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.0452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5256 Z= 0.247 Angle : 0.575 8.404 7114 Z= 0.299 Chirality : 0.042 0.133 777 Planarity : 0.005 0.054 910 Dihedral : 5.682 58.817 702 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.39 % Rotamer: Outliers : 1.26 % Allowed : 13.31 % Favored : 85.43 % 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: 1.77 (0.33), residues: 620 helix: 1.83 (0.28), residues: 336 sheet: -0.36 (0.91), residues: 25 loop : 0.60 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 237 HIS 0.006 0.002 HIS H 274 PHE 0.016 0.002 PHE I 30 TYR 0.017 0.002 TYR I 2 ARG 0.009 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.667 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 90 average time/residue: 1.4801 time to fit residues: 138.1699 Evaluate side-chains 89 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.626 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.7389 time to fit residues: 2.4144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5256 Z= 0.178 Angle : 0.513 5.060 7114 Z= 0.268 Chirality : 0.040 0.129 777 Planarity : 0.005 0.055 910 Dihedral : 5.555 58.950 702 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.61 % Favored : 98.23 % Rotamer: Outliers : 1.44 % Allowed : 13.67 % Favored : 84.89 % 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 (0.33), residues: 620 helix: 1.91 (0.28), residues: 336 sheet: -0.28 (0.95), residues: 25 loop : 0.62 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.005 0.001 HIS H 274 PHE 0.016 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.010 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.665 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 93 average time/residue: 1.4928 time to fit residues: 144.0037 Evaluate side-chains 92 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.5567 time to fit residues: 2.5165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 50 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.0505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5256 Z= 0.252 Angle : 0.584 6.027 7114 Z= 0.306 Chirality : 0.042 0.133 777 Planarity : 0.006 0.061 910 Dihedral : 5.610 59.259 702 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.39 % Rotamer: Outliers : 1.62 % Allowed : 13.31 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.33), residues: 620 helix: 1.62 (0.28), residues: 338 sheet: -0.68 (0.82), residues: 25 loop : 0.58 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 237 HIS 0.006 0.002 HIS H 274 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 2 ARG 0.010 0.001 ARG J 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.620 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 90 average time/residue: 1.4483 time to fit residues: 135.2914 Evaluate side-chains 89 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.635 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.7187 time to fit residues: 2.3868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.0514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5256 Z= 0.249 Angle : 0.585 8.184 7114 Z= 0.305 Chirality : 0.042 0.133 777 Planarity : 0.006 0.060 910 Dihedral : 5.587 59.527 702 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.26 % Allowed : 13.67 % Favored : 85.07 % 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: 1.49 (0.33), residues: 620 helix: 1.57 (0.28), residues: 338 sheet: -0.77 (0.79), residues: 25 loop : 0.55 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.006 0.002 HIS H 274 PHE 0.017 0.002 PHE I 30 TYR 0.018 0.002 TYR I 2 ARG 0.009 0.001 ARG H 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.639 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 89 average time/residue: 1.4434 time to fit residues: 133.3354 Evaluate side-chains 89 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.4382 time to fit residues: 2.2727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5256 Z= 0.267 Angle : 0.604 9.324 7114 Z= 0.315 Chirality : 0.043 0.154 777 Planarity : 0.006 0.057 910 Dihedral : 5.584 59.759 702 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 1.08 % Allowed : 14.03 % Favored : 84.89 % 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: 620 helix: 1.49 (0.27), residues: 338 sheet: -0.82 (0.78), residues: 25 loop : 0.54 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.006 0.002 HIS H 274 PHE 0.017 0.002 PHE I 30 TYR 0.019 0.002 TYR I 2 ARG 0.009 0.001 ARG H 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.653 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 90 average time/residue: 1.4784 time to fit residues: 138.0281 Evaluate side-chains 88 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.7814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.0050 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.002 0.022 5256 Z= 0.147 Angle : 0.500 8.182 7114 Z= 0.259 Chirality : 0.039 0.139 777 Planarity : 0.005 0.047 910 Dihedral : 5.349 58.983 702 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.77 % Favored : 98.06 % Rotamer: Outliers : 1.26 % Allowed : 14.03 % Favored : 84.71 % 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: 1.98 (0.33), residues: 620 helix: 1.98 (0.28), residues: 336 sheet: 1.75 (1.20), residues: 15 loop : 0.56 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.004 0.001 HIS H 274 PHE 0.016 0.002 PHE I 30 TYR 0.014 0.001 TYR I 207 ARG 0.010 0.001 ARG H 276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.648 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 1.4300 time to fit residues: 135.2392 Evaluate side-chains 89 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 1.6735 time to fit residues: 2.6447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN I 183 ASN I 247 GLN I 275 GLN J 148 ASN J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.170498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148409 restraints weight = 3491.831| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 0.62 r_work: 0.3480 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work: 0.3279 rms_B_bonded: 3.63 restraints_weight: 0.1250 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 5256 Z= 0.501 Angle : 0.810 13.476 7114 Z= 0.423 Chirality : 0.051 0.219 777 Planarity : 0.007 0.083 910 Dihedral : 5.722 58.324 702 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % Rotamer: Outliers : 1.44 % Allowed : 13.67 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.32), residues: 620 helix: 1.09 (0.27), residues: 338 sheet: -1.02 (0.78), residues: 25 loop : 0.41 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP J 237 HIS 0.008 0.003 HIS J 131 PHE 0.020 0.004 PHE I 13 TYR 0.027 0.004 TYR J 178 ARG 0.013 0.002 ARG J 298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2979.59 seconds wall clock time: 53 minutes 15.35 seconds (3195.35 seconds total)