Starting phenix.real_space_refine on Fri Apr 5 20:13:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8plz_17754/04_2024/8plz_17754_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8plz_17754/04_2024/8plz_17754.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8plz_17754/04_2024/8plz_17754_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/8plz_17754/04_2024/8plz_17754_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8plz_17754/04_2024/8plz_17754_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8plz_17754/04_2024/8plz_17754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8plz_17754/04_2024/8plz_17754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8plz_17754/04_2024/8plz_17754_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8plz_17754/04_2024/8plz_17754_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 3292 2.51 5 N 870 2.21 5 O 1078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 254": "OE1" <-> "OE2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "I GLU 16": "OE1" <-> "OE2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I GLU 141": "OE1" <-> "OE2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "I GLU 229": "OE1" <-> "OE2" Residue "I GLU 240": "OE1" <-> "OE2" Residue "I GLU 269": "OE1" <-> "OE2" Residue "I GLU 278": "OE1" <-> "OE2" Residue "J TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "J TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 147": "OE1" <-> "OE2" Residue "J GLU 227": "OE1" <-> "OE2" 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: 5271 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZQ6': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "I" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "J" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Time building chain proxies: 3.42, per 1000 atoms: 0.65 Number of scatterers: 5271 At special positions: 0 Unit cell: (83.3625, 94.05, 67.6875, 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 1078 8.00 N 870 7.00 C 3292 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: 2.25 Conformation dependent library (CDL) restraints added in 876.3 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: 33 helices and 3 sheets defined 52.4% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... 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 69 Processing helix chain 'I' and resid 77 through 92 Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.596A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS I 114 " --> pdb=" O PHE I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 removed outlier: 4.097A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 153 removed outlier: 4.765A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.691A 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: 4.400A pdb=" N LYS I 189 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP I 193 " --> pdb=" O THR I 190 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA I 199 " --> pdb=" O ASN I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 209 through 223 Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 238 through 240 No H-bonds generated for 'chain 'I' and resid 238 through 240' Processing helix chain 'I' and resid 242 through 260 Processing helix chain 'I' and resid 267 through 282 Processing helix chain 'J' and resid 57 through 68 removed outlier: 3.995A 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 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: 4.337A pdb=" N TRP J 197 " --> pdb=" O VAL J 194 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU J 208 " --> pdb=" O GLU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 229 Processing helix chain 'J' and resid 240 through 242 No H-bonds generated for 'chain 'J' and resid 240 through 242' Processing helix chain 'J' and resid 257 through 260 No H-bonds generated for 'chain 'J' and resid 257 through 260' Processing helix chain 'J' and resid 266 through 275 Processing helix chain 'J' and resid 286 through 290 Processing helix chain 'J' and resid 293 through 296 No H-bonds generated for 'chain 'J' and resid 293 through 296' Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing sheet with id= A, first strand: chain 'J' and resid 19 through 21 removed outlier: 3.638A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 143 through 145 Processing sheet with id= C, first strand: chain 'J' and resid 14 through 17 removed outlier: 6.467A pdb=" N LYS J 28 " --> pdb=" O LEU J 15 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 567 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: 1.40 Time building geometry restraints manager: 2.39 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: 1641 1.34 - 1.46: 1145 1.46 - 1.58: 2395 1.58 - 1.70: 1 1.70 - 1.82: 49 Bond restraints: 5231 Sorted by residual: bond pdb=" C24 ZQ6 J 401 " pdb=" N28 ZQ6 J 401 " ideal model delta sigma weight residual 1.340 1.296 0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C24 ZQ6 J 401 " pdb=" C25 ZQ6 J 401 " ideal model delta sigma weight residual 1.384 1.428 -0.044 2.00e-02 2.50e+03 4.81e+00 bond pdb=" C12 ZQ6 J 401 " pdb=" C13 ZQ6 J 401 " ideal model delta sigma weight residual 1.361 1.393 -0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" C ACE I 0 " pdb=" O ACE I 0 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C11 ZQ6 J 401 " pdb=" C12 ZQ6 J 401 " ideal model delta sigma weight residual 1.357 1.387 -0.030 2.00e-02 2.50e+03 2.28e+00 ... (remaining 5226 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.95: 144 105.95 - 112.94: 2743 112.94 - 119.92: 1849 119.92 - 126.91: 2270 126.91 - 133.90: 74 Bond angle restraints: 7080 Sorted by residual: angle pdb=" CB MET J 189 " pdb=" CG MET J 189 " pdb=" SD MET J 189 " ideal model delta sigma weight residual 112.70 122.88 -10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CB ARG I 102 " pdb=" CG ARG I 102 " pdb=" CD ARG I 102 " ideal model delta sigma weight residual 111.30 118.90 -7.60 2.30e+00 1.89e-01 1.09e+01 angle pdb=" CA GLU I 17 " pdb=" CB GLU I 17 " pdb=" CG GLU I 17 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.91e+00 angle pdb=" C LEU I 65 " pdb=" N GLU I 66 " pdb=" CA GLU I 66 " ideal model delta sigma weight residual 121.14 115.74 5.40 1.75e+00 3.27e-01 9.53e+00 angle pdb=" C PHE I 90 " pdb=" N TYR I 91 " pdb=" CA TYR I 91 " ideal model delta sigma weight residual 122.38 116.95 5.43 1.81e+00 3.05e-01 9.01e+00 ... (remaining 7075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.54: 3042 32.54 - 65.07: 98 65.07 - 97.61: 18 97.61 - 130.14: 0 130.14 - 162.68: 1 Dihedral angle restraints: 3159 sinusoidal: 1312 harmonic: 1847 Sorted by residual: dihedral pdb=" C17 ZQ6 J 401 " pdb=" C15 ZQ6 J 401 " pdb=" C16 ZQ6 J 401 " pdb=" N14 ZQ6 J 401 " ideal model delta sinusoidal sigma weight residual 228.12 65.44 162.68 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA ILE I 180 " pdb=" C ILE I 180 " pdb=" N LEU I 181 " pdb=" CA LEU I 181 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLU J 20 " pdb=" C GLU J 20 " pdb=" N GLY J 21 " pdb=" CA GLY J 21 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 3156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 400 0.029 - 0.058: 227 0.058 - 0.087: 94 0.087 - 0.116: 40 0.116 - 0.145: 16 Chirality restraints: 777 Sorted by residual: 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 2.57 0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA GLU I 66 " pdb=" N GLU I 66 " pdb=" C GLU I 66 " pdb=" CB GLU I 66 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA VAL I 120 " pdb=" N VAL I 120 " pdb=" C VAL I 120 " pdb=" CB VAL I 120 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 774 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 ZQ6 J 401 " -0.000 2.00e-02 2.50e+03 1.07e-02 3.47e+00 pdb=" C12 ZQ6 J 401 " -0.007 2.00e-02 2.50e+03 pdb=" C13 ZQ6 J 401 " 0.007 2.00e-02 2.50e+03 pdb=" C24 ZQ6 J 401 " -0.004 2.00e-02 2.50e+03 pdb=" C25 ZQ6 J 401 " 0.031 2.00e-02 2.50e+03 pdb=" C26 ZQ6 J 401 " -0.006 2.00e-02 2.50e+03 pdb=" C29 ZQ6 J 401 " -0.016 2.00e-02 2.50e+03 pdb=" N10 ZQ6 J 401 " 0.000 2.00e-02 2.50e+03 pdb=" N14 ZQ6 J 401 " -0.001 2.00e-02 2.50e+03 pdb=" N23 ZQ6 J 401 " -0.000 2.00e-02 2.50e+03 pdb=" N27 ZQ6 J 401 " -0.003 2.00e-02 2.50e+03 pdb=" N28 ZQ6 J 401 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 162 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO I 163 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS J 201 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C CYS J 201 " -0.026 2.00e-02 2.50e+03 pdb=" O CYS J 201 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE J 202 " 0.009 2.00e-02 2.50e+03 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 698 2.75 - 3.29: 5467 3.29 - 3.82: 9916 3.82 - 4.36: 12059 4.36 - 4.90: 19222 Nonbonded interactions: 47362 Sorted by model distance: nonbonded pdb=" O HOH J 567 " pdb=" O HOH J 573 " model vdw 2.212 2.440 nonbonded pdb=" O HOH J 577 " pdb=" O HOH J 581 " model vdw 2.218 2.440 nonbonded pdb=" O HOH H 413 " pdb=" O HOH H 417 " model vdw 2.250 2.440 nonbonded pdb=" OD1 ASN J 279 " pdb=" O HOH J 501 " model vdw 2.256 2.440 nonbonded pdb=" O ARG J 283 " pdb=" O HOH J 502 " model vdw 2.267 2.440 ... (remaining 47357 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: 5.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 12.030 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.110 Find NCS groups from input model: 0.150 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:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 0.044 5231 Z= 0.269 Angle : 0.756 10.185 7080 Z= 0.396 Chirality : 0.046 0.145 777 Planarity : 0.006 0.043 903 Dihedral : 16.734 162.677 1963 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.90 % Allowed : 13.36 % 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: 0.88 (0.32), residues: 618 helix: 1.23 (0.28), residues: 337 sheet: 0.74 (0.96), residues: 15 loop : -0.17 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.006 0.001 ARG I 102 *********************** 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 88 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.736 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 86 average time/residue: 1.4994 time to fit residues: 133.9827 Evaluate side-chains 85 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 236 GLN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5231 Z= 0.160 Angle : 0.550 7.037 7080 Z= 0.281 Chirality : 0.041 0.139 777 Planarity : 0.004 0.038 903 Dihedral : 9.224 163.600 708 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % 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: 1.22 (0.33), residues: 618 helix: 1.60 (0.28), residues: 341 sheet: 0.80 (0.99), residues: 15 loop : -0.18 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.003 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.017 0.001 TYR I 91 ARG 0.004 0.000 ARG I 63 *********************** 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 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.646 Fit side-chains REVERT: I 192 ASP cc_start: 0.7155 (t70) cc_final: 0.6817 (t70) REVERT: I 255 MET cc_start: 0.8012 (mtp) cc_final: 0.7688 (ttm) REVERT: J 169 TYR cc_start: 0.6394 (OUTLIER) cc_final: 0.5159 (m-80) outliers start: 8 outliers final: 2 residues processed: 91 average time/residue: 1.5484 time to fit residues: 145.8850 Evaluate side-chains 84 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 169 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.0670 chunk 50 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 247 GLN J 236 GLN J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5231 Z= 0.221 Angle : 0.608 6.599 7080 Z= 0.309 Chirality : 0.043 0.142 777 Planarity : 0.005 0.038 903 Dihedral : 9.246 163.572 704 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.44 % Allowed : 12.82 % 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: 1.20 (0.33), residues: 618 helix: 1.54 (0.28), residues: 341 sheet: 0.90 (1.07), residues: 15 loop : -0.11 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.004 0.001 ARG J 30 *********************** 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 91 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.652 Fit side-chains REVERT: I 138 LYS cc_start: 0.7485 (ttpt) cc_final: 0.6936 (tptt) REVERT: I 255 MET cc_start: 0.8006 (mtp) cc_final: 0.7714 (ttm) outliers start: 8 outliers final: 3 residues processed: 86 average time/residue: 1.4510 time to fit residues: 129.4601 Evaluate side-chains 84 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 129 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN J 236 GLN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.0621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5231 Z= 0.245 Angle : 0.622 6.411 7080 Z= 0.316 Chirality : 0.044 0.142 777 Planarity : 0.005 0.038 903 Dihedral : 9.313 162.893 704 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.44 % Allowed : 13.18 % 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: 1.20 (0.33), residues: 618 helix: 1.49 (0.28), residues: 340 sheet: 1.08 (1.10), residues: 15 loop : -0.05 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.018 0.002 PHE J 81 TYR 0.021 0.002 TYR I 91 ARG 0.003 0.001 ARG J 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.619 Fit side-chains REVERT: I 138 LYS cc_start: 0.7445 (ttpt) cc_final: 0.6908 (tptt) REVERT: I 192 ASP cc_start: 0.7240 (t70) cc_final: 0.6895 (t70) outliers start: 8 outliers final: 3 residues processed: 88 average time/residue: 1.4217 time to fit residues: 129.7904 Evaluate side-chains 87 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 129 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 236 GLN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5231 Z= 0.245 Angle : 0.623 6.562 7080 Z= 0.317 Chirality : 0.044 0.143 777 Planarity : 0.005 0.038 903 Dihedral : 9.332 162.734 704 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.62 % Allowed : 13.90 % Favored : 84.48 % 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: 1.23 (0.33), residues: 618 helix: 1.50 (0.28), residues: 339 sheet: 1.45 (1.28), residues: 15 loop : -0.03 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.021 0.002 PHE J 81 TYR 0.020 0.002 TYR I 91 ARG 0.003 0.001 ARG I 102 *********************** 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 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.633 Fit side-chains REVERT: H 307 GLN cc_start: 0.7596 (mm110) cc_final: 0.7384 (mm110) REVERT: I 102 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.7081 (ttt180) REVERT: I 138 LYS cc_start: 0.7455 (ttpt) cc_final: 0.6919 (tptt) REVERT: I 192 ASP cc_start: 0.7251 (t70) cc_final: 0.6902 (t70) outliers start: 9 outliers final: 4 residues processed: 91 average time/residue: 1.6020 time to fit residues: 150.8883 Evaluate side-chains 92 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 113 HIS J 236 GLN J 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5231 Z= 0.163 Angle : 0.540 7.051 7080 Z= 0.276 Chirality : 0.041 0.136 777 Planarity : 0.004 0.037 903 Dihedral : 8.998 162.863 704 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.44 % Allowed : 14.80 % 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: 1.44 (0.33), residues: 618 helix: 1.73 (0.29), residues: 341 sheet: 1.42 (1.29), residues: 15 loop : -0.04 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.003 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.018 0.001 TYR I 91 ARG 0.005 0.000 ARG I 63 *********************** 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 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.572 Fit side-chains REVERT: I 138 LYS cc_start: 0.7430 (ttpt) cc_final: 0.6897 (tptt) REVERT: I 192 ASP cc_start: 0.7152 (t70) cc_final: 0.6813 (t70) outliers start: 8 outliers final: 1 residues processed: 93 average time/residue: 1.6142 time to fit residues: 155.2366 Evaluate side-chains 86 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 129 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.0050 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 23 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 148 ASN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5231 Z= 0.199 Angle : 0.580 7.380 7080 Z= 0.295 Chirality : 0.042 0.140 777 Planarity : 0.005 0.037 903 Dihedral : 8.907 163.004 703 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.26 % Allowed : 15.52 % 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: 1.35 (0.33), residues: 618 helix: 1.64 (0.28), residues: 341 sheet: 1.33 (1.28), residues: 15 loop : -0.05 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.018 0.002 PHE J 81 TYR 0.019 0.002 TYR I 91 ARG 0.006 0.000 ARG I 21 *********************** 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 93 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.619 Fit side-chains REVERT: I 138 LYS cc_start: 0.7432 (ttpt) cc_final: 0.6880 (tptt) REVERT: I 192 ASP cc_start: 0.7212 (t70) cc_final: 0.6859 (t70) outliers start: 7 outliers final: 2 residues processed: 88 average time/residue: 1.5245 time to fit residues: 138.9921 Evaluate side-chains 85 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 129 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 0.0670 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 148 ASN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5231 Z= 0.231 Angle : 0.621 8.048 7080 Z= 0.314 Chirality : 0.043 0.141 777 Planarity : 0.005 0.038 903 Dihedral : 8.936 162.794 703 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.44 % Allowed : 15.52 % Favored : 83.03 % 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 (0.33), residues: 618 helix: 1.54 (0.28), residues: 341 sheet: 1.29 (1.30), residues: 15 loop : -0.06 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.005 0.001 ARG I 21 *********************** 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 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.607 Fit side-chains REVERT: I 138 LYS cc_start: 0.7426 (ttpt) cc_final: 0.6898 (tptt) REVERT: I 192 ASP cc_start: 0.7224 (t70) cc_final: 0.6870 (t70) outliers start: 8 outliers final: 3 residues processed: 93 average time/residue: 1.5375 time to fit residues: 148.0087 Evaluate side-chains 88 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 148 ASN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5231 Z= 0.333 Angle : 0.728 9.214 7080 Z= 0.367 Chirality : 0.047 0.152 777 Planarity : 0.006 0.044 903 Dihedral : 9.202 162.596 703 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 0.72 % Allowed : 16.61 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.33), residues: 618 helix: 1.29 (0.28), residues: 338 sheet: 1.40 (1.30), residues: 15 loop : 0.02 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP J 132 HIS 0.007 0.002 HIS J 131 PHE 0.026 0.003 PHE J 81 TYR 0.022 0.002 TYR I 91 ARG 0.005 0.001 ARG H 268 *********************** 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 89 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.599 Fit side-chains REVERT: I 138 LYS cc_start: 0.7476 (ttpt) cc_final: 0.6945 (tptt) outliers start: 4 outliers final: 3 residues processed: 87 average time/residue: 1.4843 time to fit residues: 133.8279 Evaluate side-chains 84 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 148 ASN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5231 Z= 0.199 Angle : 0.614 10.461 7080 Z= 0.309 Chirality : 0.042 0.142 777 Planarity : 0.005 0.037 903 Dihedral : 8.992 162.323 703 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.08 % Allowed : 15.88 % Favored : 83.03 % 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: 1.23 (0.33), residues: 618 helix: 1.51 (0.28), residues: 341 sheet: 1.36 (1.32), residues: 15 loop : -0.05 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.005 0.000 ARG I 21 ********************** 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 92 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.622 Fit side-chains REVERT: I 138 LYS cc_start: 0.7418 (ttpt) cc_final: 0.6892 (tptt) REVERT: I 192 ASP cc_start: 0.7201 (t70) cc_final: 0.6852 (t70) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 1.4854 time to fit residues: 135.6461 Evaluate side-chains 88 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 170 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 148 ASN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.177568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155616 restraints weight = 4703.357| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 0.94 r_work: 0.3710 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5231 Z= 0.314 Angle : 0.718 10.855 7080 Z= 0.361 Chirality : 0.046 0.149 777 Planarity : 0.006 0.041 903 Dihedral : 9.134 162.768 703 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.44 % Allowed : 15.70 % 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: 1.02 (0.33), residues: 618 helix: 1.26 (0.28), residues: 338 sheet: 1.42 (1.31), residues: 15 loop : -0.01 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.006 0.002 HIS J 131 PHE 0.025 0.003 PHE J 81 TYR 0.022 0.002 TYR I 91 ARG 0.004 0.001 ARG J 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2931.69 seconds wall clock time: 52 minutes 51.93 seconds (3171.93 seconds total)