Starting phenix.real_space_refine on Fri Apr 5 20:26:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p78_17521/04_2024/8p78_17521_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p78_17521/04_2024/8p78_17521.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p78_17521/04_2024/8p78_17521_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p78_17521/04_2024/8p78_17521_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p78_17521/04_2024/8p78_17521_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p78_17521/04_2024/8p78_17521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p78_17521/04_2024/8p78_17521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p78_17521/04_2024/8p78_17521_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p78_17521/04_2024/8p78_17521_updated.pdb" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 3311 2.51 5 N 876 2.21 5 O 1086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5304 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 58 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 29 Unusual residues: {'1QK': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 29 Unusual residues: {'1QK': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "I" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C01A1QK J 401 " occ=0.54 ... (56 atoms not shown) pdb=" O29B1QK J 401 " occ=0.46 Time building chain proxies: 3.48, per 1000 atoms: 0.66 Number of scatterers: 5304 At special positions: 0 Unit cell: (84.7875, 94.05, 68.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1086 8.00 N 876 7.00 C 3311 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 918.6 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 2 sheets defined 54.1% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'H' and resid 263 through 269 removed outlier: 3.607A pdb=" N LEU H 266 " --> pdb=" O LEU H 263 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 274 Processing helix chain 'H' and resid 280 through 285 Processing helix chain 'H' and resid 289 through 301 Processing helix chain 'I' and resid 2 through 4 No H-bonds generated for 'chain 'I' and resid 2 through 4' Processing helix chain 'I' and resid 6 through 10 Processing helix chain 'I' and resid 16 through 37 Processing helix chain 'I' and resid 50 through 69 Processing helix chain 'I' and resid 77 through 92 Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.711A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 removed outlier: 3.981A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 153 removed outlier: 4.617A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.529A 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: 4.644A pdb=" N LYS I 189 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.959A 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 224 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 260 Processing helix chain 'I' and resid 267 through 282 Processing helix chain 'J' and resid 57 through 68 removed outlier: 4.061A pdb=" N GLU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 103 Processing helix chain 'J' and resid 111 through 130 Processing helix chain 'J' and resid 140 through 142 No H-bonds generated for 'chain 'J' and resid 140 through 142' Processing helix chain 'J' and resid 156 through 158 No H-bonds generated for 'chain 'J' and resid 156 through 158' Processing helix chain 'J' and resid 176 through 178 No H-bonds generated for 'chain 'J' and resid 176 through 178' Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 218 through 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: 6.821A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLY J 82 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU J 89 " --> pdb=" O LYS J 41 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG J 30 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 6.351A 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 145 215 hydrogen bonds defined for protein. 597 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: 1.32 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1648 1.34 - 1.46: 1040 1.46 - 1.58: 2524 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 5261 Sorted by residual: bond pdb=" C03B1QK J 401 " pdb=" C07B1QK J 401 " ideal model delta sigma weight residual 1.384 1.431 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" C23B1QK J 401 " pdb=" C24B1QK J 401 " ideal model delta sigma weight residual 1.489 1.443 0.046 2.00e-02 2.50e+03 5.29e+00 bond pdb=" C03A1QK J 401 " pdb=" C07A1QK J 401 " ideal model delta sigma weight residual 1.384 1.429 -0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C24B1QK J 401 " pdb=" C25B1QK J 401 " ideal model delta sigma weight residual 1.491 1.447 0.044 2.00e-02 2.50e+03 4.86e+00 bond pdb=" C07A1QK J 401 " pdb=" N06A1QK J 401 " ideal model delta sigma weight residual 1.340 1.296 0.044 2.00e-02 2.50e+03 4.83e+00 ... (remaining 5256 not shown) Histogram of bond angle deviations from ideal: 97.23 - 104.58: 104 104.58 - 111.93: 2518 111.93 - 119.27: 1792 119.27 - 126.62: 2625 126.62 - 133.96: 82 Bond angle restraints: 7121 Sorted by residual: angle pdb=" C02A1QK J 401 " pdb=" C03A1QK J 401 " pdb=" C04A1QK J 401 " ideal model delta sigma weight residual 104.51 125.52 -21.01 3.00e+00 1.11e-01 4.90e+01 angle pdb=" C02B1QK J 401 " pdb=" C03B1QK J 401 " pdb=" C04B1QK J 401 " ideal model delta sigma weight residual 104.51 124.96 -20.45 3.00e+00 1.11e-01 4.64e+01 angle pdb=" C02A1QK J 401 " pdb=" C03A1QK J 401 " pdb=" C07A1QK J 401 " ideal model delta sigma weight residual 145.34 128.51 16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C02B1QK J 401 " pdb=" C03B1QK J 401 " pdb=" C07B1QK J 401 " ideal model delta sigma weight residual 145.34 129.09 16.25 3.00e+00 1.11e-01 2.94e+01 angle pdb=" C09A1QK J 401 " pdb=" N21A1QK J 401 " pdb=" C26A1QK J 401 " ideal model delta sigma weight residual 109.48 121.93 -12.45 3.00e+00 1.11e-01 1.72e+01 ... (remaining 7116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.48: 2853 20.48 - 40.97: 243 40.97 - 61.45: 57 61.45 - 81.93: 10 81.93 - 102.42: 6 Dihedral angle restraints: 3169 sinusoidal: 1322 harmonic: 1847 Sorted by residual: dihedral pdb=" C23B1QK J 401 " pdb=" C22B1QK J 401 " pdb=" N21B1QK J 401 " pdb=" C26B1QK J 401 " ideal model delta sinusoidal sigma weight residual -52.98 49.44 -102.42 1 3.00e+01 1.11e-03 1.30e+01 dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" C22B1QK J 401 " pdb=" C26B1QK J 401 " pdb=" N21B1QK J 401 " pdb=" C25B1QK J 401 " ideal model delta sinusoidal sigma weight residual -52.99 42.59 -95.58 1 3.00e+01 1.11e-03 1.17e+01 ... (remaining 3166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 469 0.030 - 0.060: 193 0.060 - 0.090: 77 0.090 - 0.120: 31 0.120 - 0.150: 7 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 2.36 0.15 2.00e-01 2.50e+01 5.60e-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 4.24e-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 4.23e-01 ... (remaining 774 not shown) Planarity restraints: 905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.35e+00 pdb=" N PRO J 140 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 287 " 0.016 2.00e-02 2.50e+03 1.01e-02 2.04e+00 pdb=" CG TYR H 287 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR H 287 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR H 287 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR H 287 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR H 287 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR H 287 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 287 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 195 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.00e+00 pdb=" C LEU I 195 " 0.024 2.00e-02 2.50e+03 pdb=" O LEU I 195 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN I 196 " -0.008 2.00e-02 2.50e+03 ... (remaining 902 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 677 2.75 - 3.28: 5574 3.28 - 3.82: 10028 3.82 - 4.36: 12194 4.36 - 4.90: 19700 Nonbonded interactions: 48173 Sorted by model distance: nonbonded pdb=" OG1 THR J 233 " pdb=" OE1 GLU J 235 " model vdw 2.208 2.440 nonbonded pdb=" O GLY H 286 " pdb=" O HOH H 401 " model vdw 2.211 2.440 nonbonded pdb=" O HOH H 413 " pdb=" O HOH H 422 " model vdw 2.240 2.440 nonbonded pdb=" OD1 ASN J 141 " pdb=" O HOH J 501 " model vdw 2.242 2.440 nonbonded pdb=" O ASN I 128 " pdb=" O HOH I 401 " model vdw 2.243 2.440 ... (remaining 48168 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=0.46 max=1.00 mean=0.99 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: 10.900 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: 8.890 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.440 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: 0.010 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 0.047 5261 Z= 0.282 Angle : 0.842 21.011 7121 Z= 0.361 Chirality : 0.042 0.150 777 Planarity : 0.005 0.038 905 Dihedral : 16.579 102.416 1973 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 0.72 % Allowed : 12.82 % Favored : 86.46 % 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: 1.79 (0.33), residues: 618 helix: 1.85 (0.28), residues: 338 sheet: -0.28 (1.01), residues: 18 loop : 0.56 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.015 0.002 PHE J 295 TYR 0.023 0.002 TYR H 287 ARG 0.003 0.000 ARG I 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.627 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 95 average time/residue: 1.4307 time to fit residues: 141.0987 Evaluate side-chains 93 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 305 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 0.0470 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 36 optimal weight: 0.0270 chunk 56 optimal weight: 6.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN J 258 HIS J 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.0506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5261 Z= 0.132 Angle : 0.496 5.539 7121 Z= 0.242 Chirality : 0.039 0.135 777 Planarity : 0.004 0.037 905 Dihedral : 8.987 101.907 715 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.44 % Allowed : 12.09 % Favored : 86.46 % 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: 2.32 (0.34), residues: 618 helix: 2.28 (0.29), residues: 338 sheet: 0.13 (1.04), residues: 18 loop : 0.78 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 132 HIS 0.003 0.001 HIS H 274 PHE 0.013 0.001 PHE I 110 TYR 0.016 0.001 TYR I 91 ARG 0.002 0.000 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.630 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 100 average time/residue: 1.4158 time to fit residues: 147.0727 Evaluate side-chains 89 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.0170 chunk 55 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN J 258 HIS J 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.0458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5261 Z= 0.167 Angle : 0.530 6.109 7121 Z= 0.260 Chirality : 0.039 0.139 777 Planarity : 0.004 0.037 905 Dihedral : 9.008 100.139 711 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 12.45 % Favored : 86.46 % 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: 2.23 (0.34), residues: 618 helix: 2.19 (0.28), residues: 338 sheet: -0.00 (1.06), residues: 18 loop : 0.77 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.013 0.002 PHE I 110 TYR 0.019 0.002 TYR I 91 ARG 0.002 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.641 Fit side-chains REVERT: I 25 ASP cc_start: 0.7634 (t0) cc_final: 0.7423 (t0) REVERT: I 260 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6663 (ttmt) REVERT: J 240 MET cc_start: 0.7791 (ttp) cc_final: 0.7588 (ttp) outliers start: 6 outliers final: 1 residues processed: 96 average time/residue: 1.4345 time to fit residues: 143.2441 Evaluate side-chains 88 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain J residue 216 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN J 258 HIS J 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5261 Z= 0.286 Angle : 0.659 7.798 7121 Z= 0.323 Chirality : 0.044 0.174 777 Planarity : 0.005 0.046 905 Dihedral : 9.191 99.204 711 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.44 % Allowed : 12.09 % Favored : 86.46 % 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: 1.74 (0.33), residues: 618 helix: 1.78 (0.28), residues: 338 sheet: -0.39 (1.04), residues: 18 loop : 0.59 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.018 0.002 PHE J 295 TYR 0.021 0.002 TYR I 91 ARG 0.004 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.631 Fit side-chains REVERT: J 52 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.6016 (ptpp) outliers start: 8 outliers final: 2 residues processed: 96 average time/residue: 1.4544 time to fit residues: 144.7632 Evaluate side-chains 88 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 237 MET Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 216 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 183 ASN J 258 HIS J 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.0467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5261 Z= 0.312 Angle : 0.687 8.029 7121 Z= 0.336 Chirality : 0.045 0.162 777 Planarity : 0.005 0.045 905 Dihedral : 9.216 98.250 711 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 2.17 % Allowed : 11.55 % Favored : 86.28 % 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: 1.46 (0.33), residues: 618 helix: 1.57 (0.28), residues: 338 sheet: -0.55 (1.01), residues: 18 loop : 0.43 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.018 0.002 PHE J 295 TYR 0.023 0.003 TYR H 287 ARG 0.004 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.649 Fit side-chains REVERT: J 13 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5738 (pt0) REVERT: J 52 LYS cc_start: 0.6471 (OUTLIER) cc_final: 0.6036 (ptpp) outliers start: 12 outliers final: 6 residues processed: 97 average time/residue: 1.4864 time to fit residues: 149.4740 Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain I residue 237 MET Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 86 ASN Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 0.0870 chunk 6 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN J 258 HIS J 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5261 Z= 0.226 Angle : 0.605 6.813 7121 Z= 0.297 Chirality : 0.042 0.149 777 Planarity : 0.005 0.040 905 Dihedral : 9.159 97.907 711 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 12.45 % Favored : 85.56 % 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: 1.68 (0.33), residues: 618 helix: 1.77 (0.28), residues: 338 sheet: -0.56 (0.98), residues: 18 loop : 0.51 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.016 0.002 PHE J 295 TYR 0.022 0.002 TYR H 287 ARG 0.003 0.000 ARG I 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.625 Fit side-chains REVERT: I 260 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6631 (ttmt) REVERT: J 13 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5743 (pt0) REVERT: J 52 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.5978 (ptpp) outliers start: 11 outliers final: 5 residues processed: 99 average time/residue: 1.4964 time to fit residues: 153.6649 Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain I residue 237 MET Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 86 ASN Chi-restraints excluded: chain J residue 216 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 59 optimal weight: 0.0060 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 183 ASN J 258 HIS J 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 5261 Z= 0.442 Angle : 0.808 9.704 7121 Z= 0.398 Chirality : 0.050 0.236 777 Planarity : 0.006 0.054 905 Dihedral : 9.348 98.428 711 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.43 % Favored : 97.41 % Rotamer: Outliers : 2.35 % Allowed : 12.27 % Favored : 85.38 % 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: 1.02 (0.32), residues: 618 helix: 1.20 (0.27), residues: 338 sheet: -0.78 (0.96), residues: 18 loop : 0.24 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP J 237 HIS 0.012 0.002 HIS J 131 PHE 0.022 0.003 PHE J 295 TYR 0.028 0.003 TYR H 287 ARG 0.006 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.620 Fit side-chains REVERT: J 13 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5738 (pt0) REVERT: J 52 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.6108 (ptpp) REVERT: J 219 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7079 (mm) outliers start: 13 outliers final: 8 residues processed: 95 average time/residue: 1.5160 time to fit residues: 149.3352 Evaluate side-chains 93 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain I residue 237 MET Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 86 ASN Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 248 THR 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: 2.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN J 258 HIS J 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5261 Z= 0.168 Angle : 0.561 6.611 7121 Z= 0.274 Chirality : 0.040 0.146 777 Planarity : 0.004 0.042 905 Dihedral : 9.063 99.540 711 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.08 % Allowed : 13.54 % Favored : 85.38 % 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: 618 helix: 1.94 (0.28), residues: 338 sheet: -0.47 (0.97), residues: 18 loop : 0.54 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.004 0.001 HIS J 131 PHE 0.015 0.002 PHE I 110 TYR 0.019 0.002 TYR H 287 ARG 0.003 0.000 ARG I 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.638 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 100 average time/residue: 1.4157 time to fit residues: 146.9331 Evaluate side-chains 92 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN J 258 HIS J 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5261 Z= 0.333 Angle : 0.725 8.375 7121 Z= 0.355 Chirality : 0.045 0.182 777 Planarity : 0.006 0.041 905 Dihedral : 9.238 99.033 711 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 0.90 % Allowed : 13.54 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.33), residues: 618 helix: 1.55 (0.28), residues: 338 sheet: -0.68 (1.01), residues: 18 loop : 0.38 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP H 306 HIS 0.009 0.002 HIS J 131 PHE 0.020 0.003 PHE J 295 TYR 0.030 0.003 TYR H 287 ARG 0.004 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.632 Fit side-chains REVERT: J 13 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5723 (pt0) outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 1.4369 time to fit residues: 132.7857 Evaluate side-chains 88 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN J 258 HIS J 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.0607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5261 Z= 0.317 Angle : 0.711 9.098 7121 Z= 0.348 Chirality : 0.045 0.170 777 Planarity : 0.005 0.041 905 Dihedral : 9.266 98.926 711 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 0.72 % Allowed : 13.54 % Favored : 85.74 % 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: 1.30 (0.33), residues: 618 helix: 1.48 (0.27), residues: 338 sheet: -0.68 (1.02), residues: 18 loop : 0.30 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP H 306 HIS 0.009 0.002 HIS J 131 PHE 0.019 0.003 PHE J 295 TYR 0.030 0.003 TYR H 287 ARG 0.004 0.001 ARG I 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.608 Fit side-chains REVERT: J 13 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5736 (pt0) outliers start: 4 outliers final: 3 residues processed: 89 average time/residue: 1.4286 time to fit residues: 132.0253 Evaluate side-chains 88 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 0.0040 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN J 258 HIS J 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.174938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146327 restraints weight = 10483.708| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.40 r_work: 0.3514 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5261 Z= 0.211 Angle : 0.615 8.600 7121 Z= 0.300 Chirality : 0.042 0.146 777 Planarity : 0.004 0.041 905 Dihedral : 9.139 97.506 711 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 0.54 % Allowed : 14.08 % Favored : 85.38 % 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: 1.68 (0.33), residues: 618 helix: 1.80 (0.28), residues: 338 sheet: -0.54 (1.02), residues: 18 loop : 0.45 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 306 HIS 0.006 0.001 HIS J 131 PHE 0.016 0.002 PHE J 295 TYR 0.023 0.002 TYR H 287 ARG 0.003 0.000 ARG I 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3065.57 seconds wall clock time: 55 minutes 25.16 seconds (3325.16 seconds total)