Starting phenix.real_space_refine on Sun Mar 10 21:47:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orm_17129/03_2024/8orm_17129_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orm_17129/03_2024/8orm_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_17129/03_2024/8orm_17129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orm_17129/03_2024/8orm_17129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orm_17129/03_2024/8orm_17129_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orm_17129/03_2024/8orm_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-dev-5265/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: 3.66, per 1000 atoms: 0.69 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: 2.01 Conformation dependent library (CDL) restraints added in 833.4 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: 0.98 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: 1.59 Time building geometry restraints manager: 2.20 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: 2.880 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: 12.610 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 18.530 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.450 ------------------------------------------------------------------------------- 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= 0.291 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 : 0.566 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 91 average time/residue: 1.5317 time to fit residues: 144.2109 Evaluate side-chains 90 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 170 THR 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: 3.9990 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: 0.0368 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 : 0.576 5.522 7114 Z= 0.301 Chirality : 0.042 0.136 777 Planarity : 0.005 0.042 910 Dihedral : 7.302 64.041 714 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 : 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: 1.70 (0.33), residues: 620 helix: 1.67 (0.28), residues: 336 sheet: 1.06 (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 94 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.576 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 92 average time/residue: 1.5457 time to fit residues: 147.1547 Evaluate side-chains 87 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 106 SER 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: 0.0870 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 55 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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: 0.0237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5256 Z= 0.140 Angle : 0.471 4.994 7114 Z= 0.245 Chirality : 0.039 0.128 777 Planarity : 0.004 0.042 910 Dihedral : 6.603 71.142 707 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.61 % Favored : 98.23 % Rotamer: Outliers : 1.62 % Allowed : 13.13 % 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: 2.07 (0.34), residues: 620 helix: 2.04 (0.28), residues: 336 sheet: 1.87 (1.31), 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 0.004 0.001 HIS H 274 PHE 0.015 0.001 PHE I 30 TYR 0.014 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 97 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.665 Fit side-chains REVERT: J 94 MET cc_start: 0.8312 (mmm) cc_final: 0.8087 (mmm) outliers start: 9 outliers final: 4 residues processed: 94 average time/residue: 1.5166 time to fit residues: 147.8110 Evaluate side-chains 91 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 0.0870 chunk 59 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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: 0.7955 moved from start: 0.0310 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= 0.147 Angle : 0.477 5.000 7114 Z= 0.248 Chirality : 0.039 0.126 777 Planarity : 0.005 0.047 910 Dihedral : 5.835 59.728 704 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.39 % Rotamer: Outliers : 1.44 % Allowed : 13.31 % 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: 2.13 (0.34), residues: 620 helix: 2.09 (0.28), residues: 336 sheet: 2.01 (1.32), residues: 15 loop : 0.62 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS H 274 PHE 0.015 0.002 PHE I 30 TYR 0.015 0.001 TYR I 91 ARG 0.009 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 96 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.621 Fit side-chains REVERT: I 77 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6526 (ttm170) outliers start: 8 outliers final: 4 residues processed: 93 average time/residue: 1.4498 time to fit residues: 139.8924 Evaluate side-chains 91 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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: 0.7951 moved from start: 0.0331 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= 0.145 Angle : 0.474 5.010 7114 Z= 0.246 Chirality : 0.039 0.126 777 Planarity : 0.005 0.048 910 Dihedral : 5.779 59.952 704 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.77 % Favored : 98.06 % 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: 2.15 (0.34), residues: 620 helix: 2.08 (0.28), residues: 338 sheet: 2.06 (1.34), residues: 15 loop : 0.66 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS H 274 PHE 0.014 0.002 PHE I 30 TYR 0.015 0.001 TYR I 91 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 93 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.575 Fit side-chains REVERT: I 77 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6519 (ttm170) REVERT: J 94 MET cc_start: 0.8327 (mmm) cc_final: 0.8125 (mmm) outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 1.4334 time to fit residues: 133.9964 Evaluate side-chains 91 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 57 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7954 moved from start: 0.0322 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= 0.148 Angle : 0.479 5.012 7114 Z= 0.249 Chirality : 0.039 0.126 777 Planarity : 0.005 0.052 910 Dihedral : 5.723 59.498 704 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.61 % Favored : 98.23 % Rotamer: Outliers : 1.08 % Allowed : 13.85 % 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: 2.15 (0.34), residues: 620 helix: 2.07 (0.28), residues: 338 sheet: 1.98 (1.30), residues: 15 loop : 0.67 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS H 274 PHE 0.014 0.002 PHE I 30 TYR 0.015 0.001 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 93 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.626 Fit side-chains REVERT: I 77 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6533 (ttm170) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 1.4448 time to fit residues: 134.7603 Evaluate side-chains 90 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.7993 moved from start: 0.0461 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= 0.255 Angle : 0.588 8.258 7114 Z= 0.305 Chirality : 0.042 0.134 777 Planarity : 0.005 0.059 910 Dihedral : 5.839 59.743 704 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.39 % 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: 1.73 (0.33), residues: 620 helix: 1.67 (0.28), residues: 338 sheet: 1.18 (1.48), residues: 9 loop : 0.63 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 0.011 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 93 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.601 Fit side-chains REVERT: I 62 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7462 (mmtp) REVERT: I 77 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6606 (ttm170) outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 1.5032 time to fit residues: 140.1574 Evaluate side-chains 88 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 251 SER 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: 5.9990 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.5122 ------------------------------------------------------------------------------- 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: 0.7989 moved from start: 0.0444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5256 Z= 0.230 Angle : 0.563 5.378 7114 Z= 0.294 Chirality : 0.041 0.131 777 Planarity : 0.005 0.059 910 Dihedral : 5.786 59.500 704 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.39 % Rotamer: Outliers : 1.62 % Allowed : 13.67 % 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: 1.57 (0.33), residues: 620 helix: 1.64 (0.28), residues: 338 sheet: -0.66 (0.81), residues: 25 loop : 0.57 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.006 0.001 HIS H 274 PHE 0.015 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.009 0.001 ARG J 298 *********************** 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 92 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.619 Fit side-chains REVERT: I 62 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7484 (mmtp) REVERT: I 77 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6570 (ttm170) outliers start: 9 outliers final: 4 residues processed: 89 average time/residue: 1.4986 time to fit residues: 138.2530 Evaluate side-chains 88 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 251 SER 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: 5.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 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 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: 0.8000 moved from start: 0.0587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5256 Z= 0.276 Angle : 0.612 8.067 7114 Z= 0.318 Chirality : 0.043 0.136 777 Planarity : 0.005 0.057 910 Dihedral : 5.798 59.223 704 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.55 % 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 (0.28), residues: 338 sheet: -0.83 (0.78), residues: 25 loop : 0.55 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 237 HIS 0.006 0.002 HIS H 274 PHE 0.017 0.002 PHE I 30 TYR 0.020 0.002 TYR I 2 ARG 0.008 0.001 ARG J 298 *********************** 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 91 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.607 Fit side-chains REVERT: I 62 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7485 (mmtp) REVERT: I 77 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6609 (ttm170) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 1.5224 time to fit residues: 138.7957 Evaluate side-chains 89 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7985 moved from start: 0.0476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5256 Z= 0.213 Angle : 0.559 8.631 7114 Z= 0.291 Chirality : 0.041 0.141 777 Planarity : 0.005 0.053 910 Dihedral : 5.710 59.420 704 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.39 % Rotamer: Outliers : 1.08 % Allowed : 14.39 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.33), residues: 620 helix: 1.68 (0.28), residues: 336 sheet: -0.72 (0.80), residues: 25 loop : 0.55 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.006 0.001 HIS H 274 PHE 0.017 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.009 0.001 ARG J 298 ********************** 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 88 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.661 Fit side-chains REVERT: I 62 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7494 (mmtp) REVERT: I 77 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6555 (ttm170) outliers start: 6 outliers final: 4 residues processed: 85 average time/residue: 1.5281 time to fit residues: 134.5514 Evaluate side-chains 87 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.170869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148900 restraints weight = 3489.888| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 0.61 r_work: 0.3482 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work: 0.3288 rms_B_bonded: 3.57 restraints_weight: 0.1250 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5256 Z= 0.401 Angle : 0.732 12.075 7114 Z= 0.381 Chirality : 0.048 0.204 777 Planarity : 0.007 0.080 910 Dihedral : 5.893 58.737 704 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.44 % Allowed : 14.03 % Favored : 84.53 % 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: 1.06 (0.32), residues: 620 helix: 1.16 (0.27), residues: 338 sheet: -1.03 (0.77), residues: 25 loop : 0.45 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP J 237 HIS 0.008 0.002 HIS J 131 PHE 0.019 0.003 PHE I 30 TYR 0.025 0.003 TYR I 2 ARG 0.012 0.001 ARG J 298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2954.60 seconds wall clock time: 52 minutes 55.65 seconds (3175.65 seconds total)