Starting phenix.real_space_refine (version: dev) on Sat Feb 18 02:46:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/02_2023/7drt_30827_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/02_2023/7drt_30827.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/02_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_30827/02_2023/7drt_30827_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/02_2023/7drt_30827_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/02_2023/7drt_30827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/02_2023/7drt_30827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/02_2023/7drt_30827_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/02_2023/7drt_30827_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-dev-4877/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 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: 6 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: 4.19, per 1000 atoms: 0.61 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: 3.03 Conformation dependent library (CDL) restraints added in 1.0 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: 1.04 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: 1.83 Time building geometry restraints manager: 2.87 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=" C2 NAG H 1 " pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 109.64 97.89 11.75 5.38e-01 3.45e+00 4.77e+02 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=" C3 NAG H 1 " pdb=" C2 NAG H 1 " pdb=" N2 NAG H 1 " ideal model delta sigma weight residual 110.58 118.51 -7.93 9.20e-01 1.18e+00 7.44e+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=" C1 NAG H 1 " pdb=" C2 NAG H 1 " pdb=" C3 NAG H 1 " ideal model delta sigma weight residual 110.19 102.68 7.51 9.25e-01 1.17e+00 6.59e+01 ... (remaining 9492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.43: 3999 28.43 - 56.86: 117 56.86 - 85.30: 23 85.30 - 113.73: 1 113.73 - 142.16: 1 Dihedral angle restraints: 4141 sinusoidal: 1749 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 4138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 954 0.158 - 0.315: 36 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 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. 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: 7.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 28.530 Check model and map are aligned: 0.090 Process input model: 20.920 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 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= 0.723 Angle : 1.319 13.262 9497 Z= 0.880 Chirality : 0.089 0.788 1003 Planarity : 0.011 0.283 1184 Dihedral : 13.070 142.161 2559 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 % 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 *********************** 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 : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 276 average time/residue: 1.0969 time to fit residues: 319.6178 Evaluate side-chains 164 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 0.8071 time to fit residues: 3.6877 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7030 Z= 0.166 Angle : 0.542 6.511 9497 Z= 0.299 Chirality : 0.042 0.132 1003 Planarity : 0.005 0.043 1184 Dihedral : 9.457 113.539 999 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.75 % Favored : 96.00 % Rotamer Outliers : 6.29 % 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: 0.64 (0.30), residues: 826 helix: 2.19 (0.28), residues: 352 sheet: 0.75 (0.43), residues: 134 loop : -1.72 (0.33), residues: 340 *********************** 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 211 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 166 time to evaluate : 0.842 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 19 residues processed: 191 average time/residue: 1.0946 time to fit residues: 221.1812 Evaluate side-chains 168 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 6 average time/residue: 0.0802 time to fit residues: 1.9280 ------------------------------------------------------------------------------- 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: 0.0570 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 A 298 ASN B 411 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7030 Z= 0.190 Angle : 0.551 6.876 9497 Z= 0.304 Chirality : 0.043 0.127 1003 Planarity : 0.005 0.066 1184 Dihedral : 8.567 92.060 999 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.45 % Favored : 94.43 % Rotamer Outliers : 6.99 % 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: 0.29 (0.30), residues: 826 helix: 1.98 (0.28), residues: 351 sheet: 0.62 (0.44), residues: 135 loop : -2.04 (0.31), residues: 340 *********************** 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 210 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 160 time to evaluate : 0.779 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 21 residues processed: 191 average time/residue: 1.0491 time to fit residues: 212.3385 Evaluate side-chains 171 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 0.7183 time to fit residues: 4.1850 ------------------------------------------------------------------------------- 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: 0.6980 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.0000 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.0170 chunk 79 optimal weight: 0.7980 chunk 39 optimal weight: 0.0050 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.3036 ------------------------------------------------------------------------------- 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 A 193 GLN B 108 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 7030 Z= 0.153 Angle : 0.511 7.972 9497 Z= 0.275 Chirality : 0.041 0.133 1003 Planarity : 0.005 0.062 1184 Dihedral : 7.958 76.203 999 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.36 % Favored : 95.52 % Rotamer Outliers : 6.85 % 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: 0.40 (0.30), residues: 826 helix: 2.10 (0.28), residues: 352 sheet: 0.59 (0.45), residues: 135 loop : -1.99 (0.31), residues: 339 *********************** 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 202 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 153 time to evaluate : 0.751 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 28 residues processed: 182 average time/residue: 1.0403 time to fit residues: 200.9086 Evaluate side-chains 171 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 18 residues processed: 10 average time/residue: 0.5164 time to fit residues: 6.6964 ------------------------------------------------------------------------------- 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: 0.5980 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 225 HIS B 322 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7030 Z= 0.213 Angle : 0.571 8.875 9497 Z= 0.313 Chirality : 0.044 0.130 1003 Planarity : 0.006 0.062 1184 Dihedral : 7.693 58.552 999 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.57 % Favored : 94.31 % Rotamer Outliers : 7.13 % 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 (0.30), residues: 826 helix: 1.79 (0.28), residues: 351 sheet: 0.28 (0.47), residues: 134 loop : -2.26 (0.30), residues: 341 *********************** 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 204 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 153 time to evaluate : 0.767 Fit side-chains outliers start: 51 outliers final: 24 residues processed: 186 average time/residue: 1.0350 time to fit residues: 204.1076 Evaluate side-chains 174 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 0.764 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.4121 time to fit residues: 2.4087 ------------------------------------------------------------------------------- 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: 0.9980 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 B 411 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.4533 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= 0.225 Angle : 0.583 9.814 9497 Z= 0.317 Chirality : 0.043 0.133 1003 Planarity : 0.006 0.060 1184 Dihedral : 7.523 58.412 999 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Rotamer Outliers : 6.57 % 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: -0.29 (0.29), residues: 826 helix: 1.72 (0.28), residues: 352 sheet: -0.01 (0.47), residues: 134 loop : -2.48 (0.30), residues: 340 *********************** 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 198 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 151 time to evaluate : 0.819 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 30 residues processed: 182 average time/residue: 1.0045 time to fit residues: 194.3121 Evaluate side-chains 174 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 25 residues processed: 5 average time/residue: 0.7318 time to fit residues: 5.1263 ------------------------------------------------------------------------------- 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: 0.0980 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 A 193 GLN B 331 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 7030 Z= 0.203 Angle : 0.564 10.608 9497 Z= 0.307 Chirality : 0.043 0.134 1003 Planarity : 0.005 0.062 1184 Dihedral : 7.324 58.472 999 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.81 % Favored : 94.07 % Rotamer Outliers : 6.43 % 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: -0.35 (0.29), residues: 826 helix: 1.77 (0.28), residues: 353 sheet: -0.20 (0.46), residues: 134 loop : -2.56 (0.30), residues: 339 *********************** 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 194 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 148 time to evaluate : 0.816 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 32 residues processed: 181 average time/residue: 0.9126 time to fit residues: 176.2724 Evaluate side-chains 178 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 0.722 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 28 residues processed: 4 average time/residue: 0.9839 time to fit residues: 5.2254 ------------------------------------------------------------------------------- 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: 1.9990 chunk 15 optimal weight: 0.0570 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 331 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.4754 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= 0.214 Angle : 0.585 11.337 9497 Z= 0.315 Chirality : 0.043 0.136 1003 Planarity : 0.005 0.061 1184 Dihedral : 7.366 59.575 999 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer Outliers : 6.29 % 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 (0.30), residues: 826 helix: 1.73 (0.28), residues: 353 sheet: -0.28 (0.46), residues: 134 loop : -2.58 (0.30), residues: 339 *********************** 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 193 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 148 time to evaluate : 0.789 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 35 residues processed: 181 average time/residue: 1.0239 time to fit residues: 196.8757 Evaluate side-chains 190 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 155 time to evaluate : 0.753 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 28 residues processed: 7 average time/residue: 0.8062 time to fit residues: 7.1270 ------------------------------------------------------------------------------- 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: 0.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 7030 Z= 0.251 Angle : 0.630 11.923 9497 Z= 0.343 Chirality : 0.045 0.148 1003 Planarity : 0.006 0.061 1184 Dihedral : 7.385 56.236 999 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.14 % Favored : 92.74 % Rotamer Outliers : 5.45 % 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: -0.59 (0.29), residues: 826 helix: 1.56 (0.28), residues: 352 sheet: -0.20 (0.48), residues: 131 loop : -2.71 (0.29), residues: 343 *********************** 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 195 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 156 time to evaluate : 0.807 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 34 residues processed: 185 average time/residue: 1.0392 time to fit residues: 203.5162 Evaluate side-chains 181 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 29 residues processed: 5 average time/residue: 0.8247 time to fit residues: 5.4698 ------------------------------------------------------------------------------- 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: 0.1980 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 0.0010 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 331 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 7030 Z= 0.207 Angle : 0.598 12.351 9497 Z= 0.323 Chirality : 0.044 0.155 1003 Planarity : 0.005 0.061 1184 Dihedral : 7.251 56.570 999 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.05 % Favored : 93.83 % Rotamer Outliers : 4.62 % 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: -0.38 (0.30), residues: 826 helix: 1.88 (0.28), residues: 345 sheet: -0.25 (0.47), residues: 133 loop : -2.62 (0.30), residues: 348 ********************** 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 180 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 0.712 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 29 residues processed: 175 average time/residue: 0.9446 time to fit residues: 176.8391 Evaluate side-chains 174 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 0.1761 time to fit residues: 1.7194 ------------------------------------------------------------------------------- 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: 0.9980 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.0570 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 331 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.234730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.215282 restraints weight = 5907.026| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 1.07 r_work: 0.4261 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.4158 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 7030 Z= 0.203 Angle : 0.609 12.339 9497 Z= 0.323 Chirality : 0.043 0.141 1003 Planarity : 0.005 0.060 1184 Dihedral : 7.154 56.216 999 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.30 % Favored : 93.58 % Rotamer Outliers : 5.31 % 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: -0.39 (0.30), residues: 826 helix: 1.88 (0.28), residues: 345 sheet: -0.37 (0.46), residues: 134 loop : -2.59 (0.30), residues: 347 =============================================================================== Job complete usr+sys time: 4072.52 seconds wall clock time: 72 minutes 44.95 seconds (4364.95 seconds total)