Starting phenix.real_space_refine on Fri Jul 19 00:54:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p77_17520/07_2024/8p77_17520.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p77_17520/07_2024/8p77_17520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p77_17520/07_2024/8p77_17520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p77_17520/07_2024/8p77_17520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p77_17520/07_2024/8p77_17520.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p77_17520/07_2024/8p77_17520.cif" } resolution = 1.8 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 3313 2.51 5 N 876 2.21 5 O 1051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 247": "OE1" <-> "OE2" Residue "I ASP 116": "OD1" <-> "OD2" Residue "J ASP 79": "OD1" <-> "OD2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 58 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 29 Unusual residues: {'I73': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 29 Unusual residues: {'I73': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C11AI73 J 401 " occ=0.50 ... (56 atoms not shown) pdb=" O1 BI73 J 401 " occ=0.50 Time building chain proxies: 4.72, per 1000 atoms: 0.90 Number of scatterers: 5271 At special positions: 0 Unit cell: (84.7875, 93.3375, 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 1051 8.00 N 876 7.00 C 3313 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 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... Secondary structure from input PDB file: 34 helices and 3 sheets defined 61.9% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.513A pdb=" N ASN H 273 " --> pdb=" O GLY H 270 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.796A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.908A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.669A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 removed outlier: 3.687A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.805A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.738A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 225 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.631A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 262 Processing helix chain 'I' and resid 266 through 283 Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 155 through 159 removed outlier: 4.298A pdb=" N LEU J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.851A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.738A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 20 removed outlier: 7.333A pdb=" N LEU J 15 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ARG J 30 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 273 hydrogen bonds defined for protein. 768 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: 1.68 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1642 1.34 - 1.46: 1170 1.46 - 1.58: 2398 1.58 - 1.69: 2 1.69 - 1.81: 49 Bond restraints: 5261 Sorted by residual: bond pdb=" C3 AI73 J 401 " pdb=" N10AI73 J 401 " ideal model delta sigma weight residual 1.339 1.517 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" C3 BI73 J 401 " pdb=" N10BI73 J 401 " ideal model delta sigma weight residual 1.339 1.516 -0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" C5 BI73 J 401 " pdb=" N18BI73 J 401 " ideal model delta sigma weight residual 1.349 1.480 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" C5 AI73 J 401 " pdb=" N18AI73 J 401 " ideal model delta sigma weight residual 1.349 1.480 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" N1 AI73 J 401 " pdb=" N2 AI73 J 401 " ideal model delta sigma weight residual 1.343 1.415 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 5256 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.22: 171 106.22 - 113.15: 2805 113.15 - 120.07: 1854 120.07 - 127.00: 2219 127.00 - 133.93: 72 Bond angle restraints: 7121 Sorted by residual: angle pdb=" C4 BI73 J 401 " pdb=" C3 BI73 J 401 " pdb=" N10BI73 J 401 " ideal model delta sigma weight residual 127.16 119.93 7.23 3.00e+00 1.11e-01 5.81e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.65 4.25 1.80e+00 3.09e-01 5.58e+00 angle pdb=" C4 AI73 J 401 " pdb=" C3 AI73 J 401 " pdb=" N10AI73 J 401 " ideal model delta sigma weight residual 127.16 120.17 6.99 3.00e+00 1.11e-01 5.44e+00 angle pdb=" CB MET J 189 " pdb=" CG MET J 189 " pdb=" SD MET J 189 " ideal model delta sigma weight residual 112.70 119.39 -6.69 3.00e+00 1.11e-01 4.97e+00 angle pdb=" C8 BI73 J 401 " pdb=" C9 BI73 J 401 " pdb=" N1 BI73 J 401 " ideal model delta sigma weight residual 113.59 107.37 6.22 3.00e+00 1.11e-01 4.30e+00 ... (remaining 7116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.84: 2806 18.84 - 37.68: 287 37.68 - 56.51: 63 56.51 - 75.35: 19 75.35 - 94.19: 6 Dihedral angle restraints: 3181 sinusoidal: 1334 harmonic: 1847 Sorted by residual: dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" C41AI73 J 401 " pdb=" C40AI73 J 401 " pdb=" N18AI73 J 401 " pdb=" C5 AI73 J 401 " ideal model delta sinusoidal sigma weight residual 166.20 -99.61 -94.19 1 3.00e+01 1.11e-03 1.14e+01 dihedral pdb=" CB GLU J 99 " pdb=" CG GLU J 99 " pdb=" CD GLU J 99 " pdb=" OE1 GLU J 99 " ideal model delta sinusoidal sigma weight residual 0.00 -88.27 88.27 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 3178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 495 0.028 - 0.057: 170 0.057 - 0.085: 72 0.085 - 0.114: 36 0.114 - 0.142: 6 Chirality restraints: 779 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 5.06e-01 chirality pdb=" CA ILE J 74 " pdb=" N ILE J 74 " pdb=" C ILE J 74 " pdb=" CB ILE J 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-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 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 776 not shown) Planarity restraints: 905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO J 140 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 193 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.60e+00 pdb=" C ASP I 193 " -0.022 2.00e-02 2.50e+03 pdb=" O ASP I 193 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE I 194 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 199 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" C VAL J 199 " -0.021 2.00e-02 2.50e+03 pdb=" O VAL J 199 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY J 200 " 0.007 2.00e-02 2.50e+03 ... (remaining 902 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 973 2.76 - 3.30: 5275 3.30 - 3.83: 10028 3.83 - 4.37: 11749 4.37 - 4.90: 19327 Nonbonded interactions: 47352 Sorted by model distance: nonbonded pdb=" OD2 ASP J 97 " pdb=" O HOH J 501 " model vdw 2.228 2.440 nonbonded pdb=" O HOH J 514 " pdb=" O HOH J 552 " model vdw 2.255 2.440 nonbonded pdb=" O PHE J 295 " pdb=" O HOH J 502 " model vdw 2.263 2.440 nonbonded pdb=" O HOH I 403 " pdb=" O HOH I 445 " model vdw 2.265 2.440 nonbonded pdb=" O GLU I 145 " pdb=" O HOH I 401 " model vdw 2.277 2.440 ... (remaining 47347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.450 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.850 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:17.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 : 0.006 0.178 5261 Z= 0.406 Angle : 0.583 7.229 7121 Z= 0.275 Chirality : 0.039 0.142 779 Planarity : 0.004 0.035 905 Dihedral : 16.680 94.189 1985 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.08 % Allowed : 14.98 % 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: 2.01 (0.34), residues: 618 helix: 2.07 (0.29), residues: 339 sheet: 1.40 (1.58), residues: 10 loop : 0.48 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.003 0.001 HIS I 161 PHE 0.014 0.002 PHE I 110 TYR 0.016 0.002 TYR I 60 ARG 0.007 0.001 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 107 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.629 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 106 average time/residue: 1.3566 time to fit residues: 149.5419 Evaluate side-chains 106 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 124 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.0554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5261 Z= 0.181 Angle : 0.536 6.044 7121 Z= 0.277 Chirality : 0.041 0.138 779 Planarity : 0.005 0.034 905 Dihedral : 8.239 93.440 730 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 14.80 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.34), residues: 618 helix: 2.24 (0.29), residues: 339 sheet: 2.32 (1.25), residues: 15 loop : 0.54 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.014 0.002 PHE J 91 TYR 0.019 0.002 TYR I 91 ARG 0.004 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 113 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.719 Fit side-chains REVERT: J 92 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7124 (m-30) outliers start: 6 outliers final: 3 residues processed: 109 average time/residue: 1.3311 time to fit residues: 150.9942 Evaluate side-chains 106 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 56 optimal weight: 0.0870 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 124 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.002 0.024 5261 Z= 0.158 Angle : 0.506 5.945 7121 Z= 0.260 Chirality : 0.040 0.136 779 Planarity : 0.004 0.033 905 Dihedral : 7.745 92.628 724 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 2.71 % Allowed : 13.36 % 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: 2.28 (0.34), residues: 618 helix: 2.27 (0.28), residues: 339 sheet: 2.58 (1.29), residues: 15 loop : 0.54 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.013 0.002 PHE J 91 TYR 0.018 0.002 TYR I 91 ARG 0.005 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 119 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.617 Fit side-chains REVERT: J 42 LYS cc_start: 0.5786 (OUTLIER) cc_final: 0.5000 (mmmt) REVERT: J 92 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7108 (m-30) outliers start: 15 outliers final: 6 residues processed: 113 average time/residue: 1.3159 time to fit residues: 154.5518 Evaluate side-chains 111 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 169 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5261 Z= 0.188 Angle : 0.536 6.142 7121 Z= 0.276 Chirality : 0.041 0.141 779 Planarity : 0.005 0.034 905 Dihedral : 7.753 91.766 723 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.99 % Allowed : 13.90 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.34), residues: 618 helix: 2.13 (0.28), residues: 339 sheet: 2.72 (1.29), residues: 15 loop : 0.52 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.004 0.001 HIS I 281 PHE 0.013 0.002 PHE J 295 TYR 0.020 0.002 TYR I 91 ARG 0.005 0.000 ARG H 268 *********************** 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 117 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.646 Fit side-chains REVERT: J 42 LYS cc_start: 0.5814 (OUTLIER) cc_final: 0.5005 (mmmt) REVERT: J 92 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7171 (m-30) outliers start: 11 outliers final: 6 residues processed: 109 average time/residue: 1.3102 time to fit residues: 148.3952 Evaluate side-chains 111 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.0570 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5261 Z= 0.212 Angle : 0.558 6.261 7121 Z= 0.288 Chirality : 0.042 0.143 779 Planarity : 0.005 0.034 905 Dihedral : 7.807 91.357 723 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 3.07 % Allowed : 13.54 % 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: 1.87 (0.34), residues: 618 helix: 1.90 (0.28), residues: 345 sheet: 2.75 (1.29), residues: 15 loop : 0.34 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.005 0.001 HIS I 281 PHE 0.014 0.002 PHE J 295 TYR 0.021 0.002 TYR I 91 ARG 0.005 0.001 ARG H 268 *********************** 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 119 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.651 Fit side-chains REVERT: I 268 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.6128 (pm20) REVERT: J 42 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5032 (mmmt) REVERT: J 92 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7210 (m-30) outliers start: 17 outliers final: 7 residues processed: 112 average time/residue: 1.3591 time to fit residues: 158.3471 Evaluate side-chains 112 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 268 GLU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5261 Z= 0.158 Angle : 0.508 5.981 7121 Z= 0.261 Chirality : 0.040 0.140 779 Planarity : 0.004 0.034 905 Dihedral : 7.639 91.508 723 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.99 % Allowed : 14.62 % 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: 2.24 (0.34), residues: 618 helix: 2.21 (0.28), residues: 339 sheet: 2.81 (1.31), residues: 15 loop : 0.54 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.003 0.001 HIS I 161 PHE 0.013 0.002 PHE J 295 TYR 0.018 0.002 TYR I 91 ARG 0.006 0.000 ARG H 268 *********************** 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 115 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.630 Fit side-chains REVERT: I 141 GLU cc_start: 0.7196 (tp30) cc_final: 0.6933 (tp30) REVERT: J 42 LYS cc_start: 0.5782 (OUTLIER) cc_final: 0.5001 (mmmt) REVERT: J 92 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7125 (m-30) outliers start: 11 outliers final: 7 residues processed: 110 average time/residue: 1.3283 time to fit residues: 151.8783 Evaluate side-chains 111 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 124 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5261 Z= 0.319 Angle : 0.652 6.505 7121 Z= 0.337 Chirality : 0.045 0.154 779 Planarity : 0.005 0.039 905 Dihedral : 7.961 89.623 723 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.89 % Allowed : 14.08 % 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: 1.52 (0.34), residues: 618 helix: 1.56 (0.28), residues: 345 sheet: 2.58 (1.27), residues: 15 loop : 0.26 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP I 11 HIS 0.008 0.002 HIS I 281 PHE 0.019 0.003 PHE J 156 TYR 0.025 0.003 TYR I 91 ARG 0.005 0.001 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 119 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.529 Fit side-chains REVERT: I 268 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5736 (pm20) REVERT: J 92 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7269 (m-30) outliers start: 16 outliers final: 7 residues processed: 113 average time/residue: 1.4076 time to fit residues: 164.7314 Evaluate side-chains 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 268 GLU Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 124 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5261 Z= 0.296 Angle : 0.640 6.397 7121 Z= 0.330 Chirality : 0.044 0.150 779 Planarity : 0.005 0.039 905 Dihedral : 7.984 89.392 723 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.62 % Allowed : 16.25 % 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: 1.36 (0.34), residues: 618 helix: 1.44 (0.28), residues: 345 sheet: 2.40 (1.25), residues: 15 loop : 0.20 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP I 11 HIS 0.007 0.002 HIS I 281 PHE 0.019 0.003 PHE J 23 TYR 0.024 0.003 TYR I 91 ARG 0.005 0.001 ARG H 268 *********************** 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 111 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.637 Fit side-chains REVERT: I 268 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5696 (pm20) REVERT: J 92 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7267 (m-30) outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 1.4651 time to fit residues: 162.8787 Evaluate side-chains 107 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 268 GLU Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 124 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5261 Z= 0.149 Angle : 0.516 6.434 7121 Z= 0.263 Chirality : 0.040 0.145 779 Planarity : 0.004 0.034 905 Dihedral : 7.634 90.671 723 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.26 % Allowed : 16.61 % 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: 2.19 (0.35), residues: 618 helix: 2.15 (0.28), residues: 340 sheet: 2.81 (1.32), residues: 15 loop : 0.53 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.004 0.001 HIS I 161 PHE 0.013 0.002 PHE I 110 TYR 0.016 0.002 TYR I 60 ARG 0.007 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 115 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.652 Fit side-chains REVERT: I 124 GLN cc_start: 0.6850 (pt0) cc_final: 0.6035 (tp-100) REVERT: I 141 GLU cc_start: 0.7193 (tp30) cc_final: 0.6948 (tp30) REVERT: I 268 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5663 (pm20) REVERT: J 92 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7094 (m-30) outliers start: 7 outliers final: 4 residues processed: 111 average time/residue: 1.3724 time to fit residues: 158.0322 Evaluate side-chains 110 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 268 GLU Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 7.9990 chunk 56 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5261 Z= 0.195 Angle : 0.568 6.150 7121 Z= 0.290 Chirality : 0.041 0.143 779 Planarity : 0.005 0.038 905 Dihedral : 7.696 91.471 723 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.08 % Allowed : 16.79 % 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: 2.07 (0.34), residues: 618 helix: 2.04 (0.28), residues: 340 sheet: 2.71 (1.32), residues: 15 loop : 0.50 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 11 HIS 0.004 0.001 HIS I 281 PHE 0.015 0.002 PHE J 295 TYR 0.019 0.002 TYR I 91 ARG 0.006 0.001 ARG I 28 ********************** 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 110 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.667 Fit side-chains REVERT: I 141 GLU cc_start: 0.7220 (tp30) cc_final: 0.6934 (tp30) REVERT: I 268 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.5730 (pm20) REVERT: J 92 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7174 (m-30) outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 1.3598 time to fit residues: 151.0910 Evaluate side-chains 111 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 268 GLU Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 302 THR 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: 0.9990 chunk 20 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 124 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.170127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.143008 restraints weight = 18219.487| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.02 r_work: 0.3654 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5261 Z= 0.303 Angle : 0.662 7.001 7121 Z= 0.340 Chirality : 0.044 0.152 779 Planarity : 0.005 0.043 905 Dihedral : 7.949 89.854 723 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 17.15 % 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: 1.65 (0.34), residues: 618 helix: 1.66 (0.28), residues: 339 sheet: 2.63 (1.27), residues: 15 loop : 0.38 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP I 11 HIS 0.007 0.002 HIS I 281 PHE 0.019 0.003 PHE J 156 TYR 0.025 0.003 TYR I 91 ARG 0.005 0.001 ARG H 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3186.54 seconds wall clock time: 56 minutes 2.87 seconds (3362.87 seconds total)