Starting phenix.real_space_refine on Fri Dec 8 03:49:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/12_2023/7drt_30827_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/12_2023/7drt_30827.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/12_2023/7drt_30827_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/12_2023/7drt_30827_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/12_2023/7drt_30827_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/12_2023/7drt_30827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/12_2023/7drt_30827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/12_2023/7drt_30827_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/12_2023/7drt_30827_updated.pdb" } resolution = 2.2 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= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 66 5.16 5 C 4438 2.51 5 N 1152 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6849 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2618 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain: "B" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4037 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 21, 'TRANS': 474} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PAM': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'CLR': 1, 'LPE': 1, 'PCW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 3.73, per 1000 atoms: 0.54 Number of scatterers: 6849 At special positions: 0 Unit cell: (123.918, 91.308, 96.1995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 3 15.00 O 1190 8.00 N 1152 7.00 C 4438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 56 " distance=2.07 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=1.79 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 155 " distance=2.15 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 217 " distance=2.07 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 312 " distance=2.07 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 307 " distance=2.09 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 351 " distance=2.09 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.04 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 339 " distance=2.01 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 335 " distance=2.34 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 71 " distance=2.02 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 179 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.3 seconds 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 6 sheets defined 43.1% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 63 through 80 removed outlier: 3.607A pdb=" N ALA A 67 " --> pdb=" O MET A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 107 through 129 Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.827A pdb=" N ASP A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 198 Processing helix chain 'A' and resid 224 through 237 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.549A pdb=" N LEU A 310 " --> pdb=" O CYS A 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 8 No H-bonds generated for 'chain 'B' and resid 5 through 8' Processing helix chain 'B' and resid 11 through 34 removed outlier: 3.507A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 228 through 257 Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 265 through 281 Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 294 through 322 removed outlier: 4.435A pdb=" N LEU B 297 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 298 " --> pdb=" O TRP B 295 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 318 " --> pdb=" O TRP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 336 through 362 Proline residue: B 341 - end of helix removed outlier: 3.704A pdb=" N THR B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 410 Processing helix chain 'B' and resid 419 through 454 Processing helix chain 'B' and resid 469 through 491 removed outlier: 3.558A pdb=" N ASN B 482 " --> pdb=" O TYR B 478 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 200 through 206 Processing sheet with id= B, first strand: chain 'A' and resid 241 through 246 Processing sheet with id= C, first strand: chain 'A' and resid 319 through 327 removed outlier: 3.761A pdb=" N GLN A 340 " --> pdb=" O CYS A 327 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 40 through 46 removed outlier: 3.995A pdb=" N GLU B 215 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP B 117 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ILE B 219 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN B 115 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 221 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 113 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY B 223 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 111 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU B 114 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 48 through 51 removed outlier: 5.712A pdb=" N TYR B 140 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU B 150 " --> pdb=" O TYR B 140 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 459 through 462 321 hydrogen bonds defined for protein. 849 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: 1.88 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1050 1.29 - 1.43: 1958 1.43 - 1.56: 3916 1.56 - 1.69: 10 1.69 - 1.82: 96 Bond restraints: 7030 Sorted by residual: bond pdb=" C TRP A 86 " pdb=" N ASN A 87 " ideal model delta sigma weight residual 1.332 1.446 -0.114 1.34e-02 5.57e+03 7.23e+01 bond pdb=" C11 PCW A 502 " pdb=" O3 PCW A 502 " ideal model delta sigma weight residual 1.326 1.458 -0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" C GLU B 205 " pdb=" N LYS B 206 " ideal model delta sigma weight residual 1.332 1.232 0.100 1.53e-02 4.27e+03 4.30e+01 bond pdb=" C31 PCW A 502 " pdb=" O2 PCW A 502 " ideal model delta sigma weight residual 1.333 1.450 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C PHE B 246 " pdb=" N ILE B 247 " ideal model delta sigma weight residual 1.334 1.261 0.073 1.26e-02 6.30e+03 3.37e+01 ... (remaining 7025 not shown) Histogram of bond angle deviations from ideal: 97.89 - 105.22: 196 105.22 - 112.55: 3432 112.55 - 119.88: 2565 119.88 - 127.22: 3195 127.22 - 134.55: 109 Bond angle restraints: 9497 Sorted by residual: angle pdb=" N SER A 301 " pdb=" CA SER A 301 " pdb=" C SER A 301 " ideal model delta sigma weight residual 113.38 102.61 10.77 1.23e+00 6.61e-01 7.67e+01 angle pdb=" N PHE A 331 " pdb=" CA PHE A 331 " pdb=" C PHE A 331 " ideal model delta sigma weight residual 111.28 122.43 -11.15 1.35e+00 5.49e-01 6.82e+01 angle pdb=" C ARG A 269 " pdb=" N ASP A 270 " pdb=" CA ASP A 270 " ideal model delta sigma weight residual 123.01 109.75 13.26 1.78e+00 3.16e-01 5.55e+01 angle pdb=" N ASN B 330 " pdb=" CA ASN B 330 " pdb=" C ASN B 330 " ideal model delta sigma weight residual 110.44 118.03 -7.59 1.20e+00 6.94e-01 4.00e+01 angle pdb=" N VAL B 455 " pdb=" CA VAL B 455 " pdb=" C VAL B 455 " ideal model delta sigma weight residual 113.43 120.31 -6.88 1.09e+00 8.42e-01 3.99e+01 ... (remaining 9492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.43: 4095 28.43 - 56.86: 124 56.86 - 85.30: 24 85.30 - 113.73: 1 113.73 - 142.16: 1 Dihedral angle restraints: 4245 sinusoidal: 1853 harmonic: 2392 Sorted by residual: dihedral pdb=" CB CYS A 327 " pdb=" SG CYS A 327 " pdb=" SG CYS A 342 " pdb=" CB CYS A 342 " ideal model delta sinusoidal sigma weight residual 93.00 170.47 -77.47 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" C PHE B 395 " pdb=" N PHE B 395 " pdb=" CA PHE B 395 " pdb=" CB PHE B 395 " ideal model delta harmonic sigma weight residual -122.60 -141.74 19.14 0 2.50e+00 1.60e-01 5.86e+01 dihedral pdb=" N PHE B 395 " pdb=" C PHE B 395 " pdb=" CA PHE B 395 " pdb=" CB PHE B 395 " ideal model delta harmonic sigma weight residual 122.80 141.75 -18.95 0 2.50e+00 1.60e-01 5.74e+01 ... (remaining 4242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 956 0.158 - 0.315: 34 0.315 - 0.473: 8 0.473 - 0.630: 3 0.630 - 0.788: 2 Chirality restraints: 1003 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.35e+02 chirality pdb=" CA PHE B 395 " pdb=" N PHE B 395 " pdb=" C PHE B 395 " pdb=" CB PHE B 395 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" CA VAL A 91 " pdb=" N VAL A 91 " pdb=" C VAL A 91 " pdb=" CB VAL A 91 " both_signs ideal model delta sigma weight residual False 2.44 1.77 0.67 2.00e-01 2.50e+01 1.12e+01 ... (remaining 1000 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.339 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG H 1 " -0.096 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.202 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.484 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM A 501 " 0.074 2.00e-02 2.50e+03 5.67e-02 3.21e+01 pdb=" C11 PAM A 501 " -0.031 2.00e-02 2.50e+03 pdb=" C8 PAM A 501 " 0.031 2.00e-02 2.50e+03 pdb=" C9 PAM A 501 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 205 " 0.024 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C GLU B 205 " -0.086 2.00e-02 2.50e+03 pdb=" O GLU B 205 " 0.031 2.00e-02 2.50e+03 pdb=" N LYS B 206 " 0.031 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 54 2.63 - 3.20: 5954 3.20 - 3.77: 9743 3.77 - 4.33: 14091 4.33 - 4.90: 22704 Nonbonded interactions: 52546 Sorted by model distance: nonbonded pdb=" ND2 ASN A 87 " pdb=" C1 NAG H 1 " model vdw 2.064 3.550 nonbonded pdb=" ND2 ASN A 87 " pdb=" O5 NAG H 1 " model vdw 2.279 2.520 nonbonded pdb=" OE2 GLU A 108 " pdb=" O HOH A 601 " model vdw 2.335 2.440 nonbonded pdb=" O HIS A 142 " pdb=" CG GLN A 143 " model vdw 2.366 3.440 nonbonded pdb=" OE2 GLU B 79 " pdb=" O HOH B 701 " model vdw 2.372 2.440 ... (remaining 52541 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: 27.710 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: 35.930 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 24.320 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5537 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 : 0.011 0.132 7030 Z= 0.724 Angle : 1.320 13.262 9497 Z= 0.841 Chirality : 0.089 0.788 1003 Planarity : 0.011 0.283 1184 Dihedral : 13.148 142.161 2663 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.45 % Favored : 94.07 % Rotamer: Outliers : 2.38 % Allowed : 1.40 % Favored : 96.22 % Cbeta Deviations : 1.17 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.27), residues: 826 helix: 0.39 (0.25), residues: 361 sheet: 0.91 (0.44), residues: 112 loop : -1.97 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 295 HIS 0.003 0.000 HIS B 327 PHE 0.015 0.001 PHE B 486 TYR 0.011 0.000 TYR A 260 ARG 0.004 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 266 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 276 average time/residue: 1.0908 time to fit residues: 317.2800 Evaluate side-chains 164 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 0.754 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 0.8193 time to fit residues: 3.7145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.0050 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 0.0470 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 overall best weight: 0.2692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS A 188 ASN A 193 GLN A 279 ASN A 298 ASN B 8 ASN B 70 HIS B 95 HIS B 108 GLN B 406 ASN B 482 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5608 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7030 Z= 0.164 Angle : 0.551 6.600 9497 Z= 0.298 Chirality : 0.042 0.130 1003 Planarity : 0.005 0.044 1184 Dihedral : 9.775 115.321 1103 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.63 % Favored : 96.13 % Rotamer: Outliers : 6.29 % Allowed : 15.94 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.30), residues: 826 helix: 2.23 (0.28), residues: 350 sheet: 0.72 (0.42), residues: 137 loop : -1.72 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 481 HIS 0.006 0.001 HIS B 424 PHE 0.016 0.001 PHE B 395 TYR 0.014 0.001 TYR A 274 ARG 0.002 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 164 time to evaluate : 0.676 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 19 residues processed: 189 average time/residue: 1.1330 time to fit residues: 226.7222 Evaluate side-chains 163 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 7 average time/residue: 0.2864 time to fit residues: 3.5413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 0.0270 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN B 411 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7030 Z= 0.191 Angle : 0.562 6.836 9497 Z= 0.305 Chirality : 0.043 0.123 1003 Planarity : 0.006 0.066 1184 Dihedral : 8.936 103.525 1103 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Rotamer: Outliers : 7.13 % Allowed : 16.64 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.30), residues: 826 helix: 1.98 (0.28), residues: 351 sheet: 0.63 (0.44), residues: 135 loop : -2.06 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 336 HIS 0.008 0.001 HIS B 424 PHE 0.030 0.002 PHE B 401 TYR 0.017 0.002 TYR A 274 ARG 0.004 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 161 time to evaluate : 0.781 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 22 residues processed: 193 average time/residue: 1.0535 time to fit residues: 214.9111 Evaluate side-chains 173 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 17 residues processed: 6 average time/residue: 0.3401 time to fit residues: 3.4147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.0010 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 74 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN B 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7030 Z= 0.170 Angle : 0.537 7.818 9497 Z= 0.287 Chirality : 0.042 0.131 1003 Planarity : 0.005 0.063 1184 Dihedral : 8.435 92.523 1103 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.36 % Favored : 95.52 % Rotamer: Outliers : 6.85 % Allowed : 18.32 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.30), residues: 826 helix: 2.02 (0.28), residues: 352 sheet: 0.40 (0.45), residues: 137 loop : -2.11 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 336 HIS 0.006 0.001 HIS B 424 PHE 0.020 0.001 PHE B 401 TYR 0.018 0.001 TYR A 274 ARG 0.002 0.000 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 158 time to evaluate : 0.775 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 27 residues processed: 189 average time/residue: 1.0539 time to fit residues: 210.7425 Evaluate side-chains 173 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 6 average time/residue: 0.4366 time to fit residues: 4.0282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN B 225 HIS B 322 HIS B 411 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7030 Z= 0.213 Angle : 0.571 9.441 9497 Z= 0.310 Chirality : 0.043 0.127 1003 Planarity : 0.005 0.062 1184 Dihedral : 8.275 83.822 1103 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Rotamer: Outliers : 7.13 % Allowed : 20.00 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.29), residues: 826 helix: 1.83 (0.28), residues: 351 sheet: 0.22 (0.47), residues: 134 loop : -2.27 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 336 HIS 0.007 0.001 HIS B 424 PHE 0.027 0.002 PHE B 401 TYR 0.021 0.002 TYR A 274 ARG 0.004 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 146 time to evaluate : 0.796 Fit side-chains outliers start: 51 outliers final: 32 residues processed: 178 average time/residue: 1.0054 time to fit residues: 190.3690 Evaluate side-chains 183 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 25 residues processed: 7 average time/residue: 0.6797 time to fit residues: 6.2397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.0270 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5758 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7030 Z= 0.200 Angle : 0.569 9.671 9497 Z= 0.306 Chirality : 0.043 0.132 1003 Planarity : 0.005 0.060 1184 Dihedral : 8.025 73.469 1103 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.33 % Favored : 94.55 % Rotamer: Outliers : 6.71 % Allowed : 21.54 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.30), residues: 826 helix: 1.81 (0.28), residues: 352 sheet: -0.03 (0.46), residues: 134 loop : -2.34 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 336 HIS 0.007 0.001 HIS B 424 PHE 0.024 0.002 PHE B 401 TYR 0.019 0.002 TYR A 274 ARG 0.006 0.000 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 155 time to evaluate : 0.867 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 28 residues processed: 183 average time/residue: 1.0202 time to fit residues: 198.2927 Evaluate side-chains 171 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 0.7989 time to fit residues: 4.5085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN B 331 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5783 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7030 Z= 0.225 Angle : 0.584 10.547 9497 Z= 0.317 Chirality : 0.044 0.138 1003 Planarity : 0.006 0.061 1184 Dihedral : 7.992 66.577 1103 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.30 % Favored : 93.58 % Rotamer: Outliers : 6.99 % Allowed : 21.26 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.29), residues: 826 helix: 1.68 (0.28), residues: 353 sheet: -0.20 (0.46), residues: 134 loop : -2.55 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 336 HIS 0.007 0.001 HIS B 322 PHE 0.026 0.002 PHE B 401 TYR 0.023 0.002 TYR A 274 ARG 0.003 0.000 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 148 time to evaluate : 0.766 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 31 residues processed: 181 average time/residue: 0.9974 time to fit residues: 192.7063 Evaluate side-chains 177 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 28 residues processed: 3 average time/residue: 1.0460 time to fit residues: 4.9069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 75 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN B 331 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7030 Z= 0.198 Angle : 0.576 11.326 9497 Z= 0.308 Chirality : 0.043 0.138 1003 Planarity : 0.005 0.060 1184 Dihedral : 7.786 59.890 1103 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.95 % Rotamer: Outliers : 5.59 % Allowed : 22.38 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.30), residues: 826 helix: 1.76 (0.28), residues: 353 sheet: -0.25 (0.46), residues: 134 loop : -2.52 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 336 HIS 0.008 0.001 HIS B 322 PHE 0.021 0.001 PHE B 401 TYR 0.021 0.001 TYR A 274 ARG 0.003 0.000 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 0.740 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 31 residues processed: 178 average time/residue: 0.9603 time to fit residues: 182.0133 Evaluate side-chains 185 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 5 average time/residue: 0.6930 time to fit residues: 4.8043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN B 331 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5783 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7030 Z= 0.236 Angle : 0.620 11.999 9497 Z= 0.332 Chirality : 0.044 0.142 1003 Planarity : 0.006 0.060 1184 Dihedral : 7.731 56.461 1103 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.78 % Favored : 93.10 % Rotamer: Outliers : 5.45 % Allowed : 23.36 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.29), residues: 826 helix: 1.61 (0.28), residues: 353 sheet: -0.32 (0.46), residues: 134 loop : -2.70 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 336 HIS 0.008 0.001 HIS B 322 PHE 0.026 0.002 PHE B 401 TYR 0.023 0.002 TYR A 274 ARG 0.003 0.000 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 158 time to evaluate : 0.923 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 31 residues processed: 187 average time/residue: 0.9367 time to fit residues: 187.1309 Evaluate side-chains 183 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 25 residues processed: 6 average time/residue: 0.8819 time to fit residues: 6.6194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN B 70 HIS ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5767 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7030 Z= 0.204 Angle : 0.601 12.349 9497 Z= 0.320 Chirality : 0.043 0.152 1003 Planarity : 0.005 0.060 1184 Dihedral : 7.560 56.753 1103 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.95 % Rotamer: Outliers : 4.76 % Allowed : 24.76 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.30), residues: 826 helix: 1.73 (0.28), residues: 353 sheet: -0.25 (0.47), residues: 131 loop : -2.60 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 336 HIS 0.008 0.001 HIS B 322 PHE 0.021 0.001 PHE B 401 TYR 0.021 0.002 TYR A 274 ARG 0.005 0.000 ARG A 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 0.816 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 31 residues processed: 175 average time/residue: 0.9115 time to fit residues: 170.9963 Evaluate side-chains 179 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 25 residues processed: 6 average time/residue: 0.3139 time to fit residues: 3.3155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN A 184 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN B 331 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.233535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.214123 restraints weight = 5882.235| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 1.04 r_work: 0.4246 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.4151 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7030 Z= 0.221 Angle : 0.628 12.383 9497 Z= 0.330 Chirality : 0.044 0.145 1003 Planarity : 0.005 0.060 1184 Dihedral : 7.618 55.655 1103 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.66 % Favored : 93.22 % Rotamer: Outliers : 5.31 % Allowed : 24.20 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.29), residues: 826 helix: 1.84 (0.28), residues: 345 sheet: -0.30 (0.47), residues: 131 loop : -2.59 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 336 HIS 0.009 0.001 HIS B 331 PHE 0.024 0.002 PHE B 401 TYR 0.024 0.002 TYR A 274 ARG 0.005 0.000 ARG A 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4212.62 seconds wall clock time: 76 minutes 52.26 seconds (4612.26 seconds total)