Starting phenix.real_space_refine on Thu Dec 7 22:22:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/12_2023/8p6v_17508_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/12_2023/8p6v_17508.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/8p6v_17508/12_2023/8p6v_17508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/12_2023/8p6v_17508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/12_2023/8p6v_17508_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/12_2023/8p6v_17508_updated.pdb" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 3291 2.51 5 N 870 2.21 5 O 1051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 17": "OE1" <-> "OE2" Residue "I ASP 250": "OD1" <-> "OD2" Residue "I GLU 268": "OE1" <-> "OE2" Residue "I GLU 278": "OE1" <-> "OE2" Residue "J ASP 92": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5243 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'I74': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Time building chain proxies: 3.54, per 1000 atoms: 0.68 Number of scatterers: 5243 At special positions: 0 Unit cell: (84.7875, 94.05, 69.1125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1051 8.00 N 870 7.00 C 3291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 822.0 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 54.4% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'H' and resid 263 through 269 removed outlier: 4.122A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 269 " --> pdb=" O LEU H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 274 Processing helix chain 'H' and resid 280 through 284 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 70 Processing helix chain 'I' and resid 77 through 92 Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.827A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 removed outlier: 4.034A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 153 removed outlier: 4.570A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.402A 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: 4.920A pdb=" N LYS I 189 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA I 191 " --> pdb=" O ARG I 188 " (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 234 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 283 Processing helix chain 'J' and resid 57 through 66 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: 4.123A pdb=" N TRP J 197 " --> pdb=" O VAL J 194 " (cutoff:3.500A) removed outlier: 3.818A 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 291 Processing helix chain 'J' and resid 293 through 296 No H-bonds generated for 'chain 'J' and resid 293 through 296' Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing sheet with id= A, first strand: chain 'J' and resid 77 through 83 removed outlier: 6.797A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY J 82 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR J 25 " --> pdb=" O LYS J 42 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 143 through 145 220 hydrogen bonds defined for protein. 576 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: 1.20 Time building geometry restraints manager: 2.25 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: 1637 1.34 - 1.46: 969 1.46 - 1.58: 2572 1.58 - 1.69: 2 1.69 - 1.81: 49 Bond restraints: 5229 Sorted by residual: bond pdb=" C3 I74 J 401 " pdb=" N10 I74 J 401 " ideal model delta sigma weight residual 1.335 1.489 -0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" C26 I74 J 401 " pdb=" C8 I74 J 401 " ideal model delta sigma weight residual 1.497 1.602 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C5 I74 J 401 " pdb=" N18 I74 J 401 " ideal model delta sigma weight residual 1.350 1.453 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C41 I74 J 401 " pdb=" C46 I74 J 401 " ideal model delta sigma weight residual 1.532 1.456 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C40 I74 J 401 " pdb=" C41 I74 J 401 " ideal model delta sigma weight residual 1.524 1.592 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 5224 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.68: 139 105.68 - 112.74: 2729 112.74 - 119.81: 1750 119.81 - 126.87: 2388 126.87 - 133.93: 71 Bond angle restraints: 7077 Sorted by residual: angle pdb=" CA LYS I 260 " pdb=" CB LYS I 260 " pdb=" CG LYS I 260 " ideal model delta sigma weight residual 114.10 120.32 -6.22 2.00e+00 2.50e-01 9.68e+00 angle pdb=" CB LYS J 293 " pdb=" CG LYS J 293 " pdb=" CD LYS J 293 " ideal model delta sigma weight residual 111.30 118.04 -6.74 2.30e+00 1.89e-01 8.59e+00 angle pdb=" CA GLU I 268 " pdb=" CB GLU I 268 " pdb=" CG GLU I 268 " ideal model delta sigma weight residual 114.10 119.75 -5.65 2.00e+00 2.50e-01 7.97e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.45 4.45 1.80e+00 3.09e-01 6.10e+00 angle pdb=" CB LYS I 260 " pdb=" CG LYS I 260 " pdb=" CD LYS I 260 " ideal model delta sigma weight residual 111.30 116.85 -5.55 2.30e+00 1.89e-01 5.82e+00 ... (remaining 7072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 2791 17.41 - 34.83: 270 34.83 - 52.24: 73 52.24 - 69.65: 17 69.65 - 87.06: 13 Dihedral angle restraints: 3164 sinusoidal: 1317 harmonic: 1847 Sorted by residual: dihedral pdb=" CA THR J 175 " pdb=" C THR J 175 " pdb=" N ARG J 176 " pdb=" CA ARG J 176 " ideal model delta harmonic sigma weight residual 180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CG ARG J 176 " pdb=" CD ARG J 176 " pdb=" NE ARG J 176 " pdb=" CZ ARG J 176 " ideal model delta sinusoidal sigma weight residual 180.00 136.01 43.99 2 1.50e+01 4.44e-03 1.03e+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 180.00 164.41 15.59 0 5.00e+00 4.00e-02 9.72e+00 ... (remaining 3161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 445 0.028 - 0.057: 210 0.057 - 0.085: 75 0.085 - 0.114: 39 0.114 - 0.142: 8 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 2.37 0.14 2.00e-01 2.50e+01 5.05e-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 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA VAL H 260 " pdb=" N VAL H 260 " pdb=" C VAL H 260 " pdb=" CB VAL H 260 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 774 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 14 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C LYS J 14 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS J 14 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU J 15 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 162 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO I 163 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS J 201 " 0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C CYS J 201 " -0.021 2.00e-02 2.50e+03 pdb=" O CYS J 201 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE J 202 " 0.007 2.00e-02 2.50e+03 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 846 2.76 - 3.29: 5347 3.29 - 3.83: 9809 3.83 - 4.36: 11859 4.36 - 4.90: 19012 Nonbonded interactions: 46873 Sorted by model distance: nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 401 " model vdw 2.221 2.440 nonbonded pdb=" O LEU I 236 " pdb=" O HOH I 401 " model vdw 2.225 2.440 nonbonded pdb=" O MET J 189 " pdb=" O HOH J 501 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR I 178 " pdb=" OG SER I 230 " model vdw 2.238 2.440 nonbonded pdb=" O HOH J 567 " pdb=" O HOH J 571 " model vdw 2.243 2.440 ... (remaining 46868 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.270 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.670 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.005 0.154 5229 Z= 0.287 Angle : 0.616 8.587 7077 Z= 0.309 Chirality : 0.041 0.142 777 Planarity : 0.004 0.031 903 Dihedral : 16.303 87.063 1968 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.26 % Allowed : 13.90 % Favored : 84.84 % 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: 1.53 (0.34), residues: 618 helix: 1.80 (0.28), residues: 337 sheet: 0.43 (1.28), residues: 20 loop : 0.10 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.007 0.001 HIS H 259 PHE 0.015 0.002 PHE I 110 TYR 0.015 0.002 TYR I 91 ARG 0.007 0.000 ARG H 268 *********************** 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 93 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.611 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 1.3169 time to fit residues: 125.9421 Evaluate side-chains 89 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.8062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5229 Z= 0.188 Angle : 0.543 8.251 7077 Z= 0.280 Chirality : 0.041 0.135 777 Planarity : 0.005 0.033 903 Dihedral : 7.375 87.877 706 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.79 % Allowed : 12.45 % Favored : 83.75 % 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: 1.53 (0.34), residues: 618 helix: 1.78 (0.28), residues: 337 sheet: 0.43 (1.25), residues: 20 loop : 0.14 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 132 HIS 0.006 0.001 HIS H 259 PHE 0.014 0.002 PHE I 110 TYR 0.016 0.002 TYR I 91 ARG 0.005 0.000 ARG H 268 *********************** 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 108 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.566 Fit side-chains outliers start: 21 outliers final: 9 residues processed: 101 average time/residue: 1.3248 time to fit residues: 138.8898 Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.0447 time to fit residues: 0.9267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.0470 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5229 Z= 0.169 Angle : 0.522 7.995 7077 Z= 0.267 Chirality : 0.040 0.136 777 Planarity : 0.004 0.030 903 Dihedral : 7.341 88.862 706 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.07 % Allowed : 13.00 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.34), residues: 618 helix: 1.78 (0.28), residues: 337 sheet: 0.51 (1.35), residues: 20 loop : 0.17 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.005 0.001 HIS H 259 PHE 0.013 0.001 PHE I 110 TYR 0.015 0.002 TYR I 91 ARG 0.003 0.000 ARG H 268 *********************** 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 105 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.711 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 98 average time/residue: 1.4070 time to fit residues: 143.0301 Evaluate side-chains 93 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.5032 time to fit residues: 3.0421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5229 Z= 0.167 Angle : 0.519 7.802 7077 Z= 0.266 Chirality : 0.040 0.137 777 Planarity : 0.004 0.029 903 Dihedral : 7.320 89.340 706 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.43 % Allowed : 13.18 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.34), residues: 618 helix: 1.82 (0.29), residues: 337 sheet: 0.55 (1.33), residues: 20 loop : 0.16 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.005 0.001 HIS H 259 PHE 0.012 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.002 0.000 ARG I 242 *********************** 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 108 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.649 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 101 average time/residue: 1.4562 time to fit residues: 152.5818 Evaluate side-chains 92 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.0534 time to fit residues: 1.1389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 258 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5229 Z= 0.246 Angle : 0.595 8.483 7077 Z= 0.306 Chirality : 0.043 0.140 777 Planarity : 0.005 0.030 903 Dihedral : 7.427 88.845 706 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.43 % Allowed : 12.82 % Favored : 83.75 % 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: 1.27 (0.34), residues: 618 helix: 1.57 (0.28), residues: 336 sheet: -0.00 (1.18), residues: 20 loop : 0.06 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.006 0.002 HIS H 259 PHE 0.013 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.004 0.001 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.650 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 96 average time/residue: 1.5104 time to fit residues: 150.3149 Evaluate side-chains 94 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.703 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.4579 time to fit residues: 2.8761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 258 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5229 Z= 0.206 Angle : 0.564 8.035 7077 Z= 0.288 Chirality : 0.041 0.142 777 Planarity : 0.004 0.031 903 Dihedral : 7.387 89.356 706 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 3.61 % Allowed : 13.54 % Favored : 82.85 % 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: 1.34 (0.34), residues: 618 helix: 1.64 (0.28), residues: 336 sheet: 0.00 (1.17), residues: 20 loop : 0.07 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.006 0.001 HIS H 259 PHE 0.013 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.005 0.000 ARG I 279 *********************** 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: 20 poor density : 83 time to evaluate : 0.647 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 97 average time/residue: 1.3533 time to fit residues: 136.5236 Evaluate side-chains 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.0530 time to fit residues: 1.1627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS I 142 GLN J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5229 Z= 0.167 Angle : 0.527 7.177 7077 Z= 0.270 Chirality : 0.040 0.140 777 Planarity : 0.004 0.030 903 Dihedral : 7.332 89.770 706 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.71 % Allowed : 14.08 % Favored : 83.21 % 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: 1.52 (0.34), residues: 618 helix: 1.78 (0.28), residues: 336 sheet: 0.34 (1.30), residues: 20 loop : 0.13 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.007 0.001 HIS H 259 PHE 0.013 0.001 PHE I 110 TYR 0.015 0.002 TYR I 91 ARG 0.004 0.000 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.605 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 99 average time/residue: 1.4873 time to fit residues: 152.5215 Evaluate side-chains 89 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.0524 time to fit residues: 1.0987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS I 142 GLN J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5229 Z= 0.240 Angle : 0.581 8.416 7077 Z= 0.300 Chirality : 0.042 0.139 777 Planarity : 0.005 0.030 903 Dihedral : 7.406 89.233 706 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.89 % Allowed : 14.98 % Favored : 82.13 % 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: 1.25 (0.34), residues: 618 helix: 1.54 (0.28), residues: 336 sheet: -0.10 (1.16), residues: 20 loop : 0.07 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.006 0.002 HIS H 259 PHE 0.013 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.001 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.683 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 94 average time/residue: 1.4357 time to fit residues: 139.9633 Evaluate side-chains 94 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.662 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.4372 time to fit residues: 2.7280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 0.0170 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5229 Z= 0.136 Angle : 0.514 10.905 7077 Z= 0.258 Chirality : 0.039 0.138 777 Planarity : 0.004 0.029 903 Dihedral : 7.191 87.870 706 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.99 % Allowed : 15.52 % Favored : 82.49 % 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: 1.71 (0.34), residues: 618 helix: 1.91 (0.29), residues: 338 sheet: 0.52 (1.33), residues: 20 loop : 0.24 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.007 0.001 HIS H 259 PHE 0.014 0.001 PHE I 110 TYR 0.016 0.001 TYR I 60 ARG 0.004 0.000 ARG I 279 *********************** 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 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.599 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 94 average time/residue: 1.3845 time to fit residues: 135.1216 Evaluate side-chains 89 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.5207 time to fit residues: 1.9350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5229 Z= 0.180 Angle : 0.539 8.592 7077 Z= 0.274 Chirality : 0.040 0.136 777 Planarity : 0.004 0.033 903 Dihedral : 7.272 89.765 706 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.44 % Allowed : 16.79 % Favored : 81.77 % 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 (0.34), residues: 618 helix: 1.81 (0.28), residues: 336 sheet: 0.43 (1.31), residues: 20 loop : 0.18 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.007 0.001 HIS H 259 PHE 0.012 0.002 PHE I 110 TYR 0.016 0.002 TYR I 91 ARG 0.005 0.000 ARG I 279 ********************** 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 91 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.630 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 90 average time/residue: 1.4502 time to fit residues: 135.4470 Evaluate side-chains 90 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0524 time to fit residues: 0.9418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.175534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.152845 restraints weight = 4744.908| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 0.98 r_work: 0.3745 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5229 Z= 0.250 Angle : 0.614 10.666 7077 Z= 0.313 Chirality : 0.043 0.139 777 Planarity : 0.005 0.040 903 Dihedral : 7.380 89.375 706 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.17 % Allowed : 15.88 % Favored : 81.95 % 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: 1.22 (0.34), residues: 618 helix: 1.51 (0.28), residues: 336 sheet: -0.07 (1.12), residues: 20 loop : 0.07 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.008 0.002 HIS H 259 PHE 0.013 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.004 0.001 ARG I 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3001.58 seconds wall clock time: 53 minutes 46.20 seconds (3226.20 seconds total)