Starting phenix.real_space_refine on Mon Sep 23 19:13:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/09_2024/1oed_1044.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/09_2024/1oed_1044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/09_2024/1oed_1044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/09_2024/1oed_1044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/09_2024/1oed_1044.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/1oed_1044/09_2024/1oed_1044.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3331 2.51 5 N 735 2.21 5 O 823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4926 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 978 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 982 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain breaks: 1 Chain: "D" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 978 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "E" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Time building chain proxies: 3.31, per 1000 atoms: 0.67 Number of scatterers: 4926 At special positions: 0 Unit cell: (96, 88, 67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 823 8.00 N 735 7.00 C 3331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 599.7 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 92.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 212 through 239 removed outlier: 3.584A pdb=" N VAL A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Proline residue: A 221 - end of helix Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 242 through 271 removed outlier: 3.660A pdb=" N GLU A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 275 through 302 removed outlier: 3.935A pdb=" N PHE A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 437 Processing helix chain 'B' and resid 218 through 245 removed outlier: 3.668A pdb=" N VAL B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Proline residue: B 227 - end of helix Proline residue: B 242 - end of helix Processing helix chain 'B' and resid 248 through 277 removed outlier: 3.500A pdb=" N ALA B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Proline residue: B 271 - end of helix removed outlier: 3.781A pdb=" N LEU B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 307 removed outlier: 4.130A pdb=" N ILE B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 462 Processing helix chain 'C' and resid 226 through 253 removed outlier: 4.092A pdb=" N ASN C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Proline residue: C 235 - end of helix Proline residue: C 250 - end of helix Processing helix chain 'C' and resid 256 through 285 Proline residue: C 279 - end of helix Processing helix chain 'C' and resid 289 through 316 removed outlier: 3.916A pdb=" N PHE C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 295 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 484 Proline residue: C 463 - end of helix Proline residue: C 481 - end of helix Processing helix chain 'D' and resid 212 through 239 removed outlier: 3.582A pdb=" N VAL D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 219 " --> pdb=" O VAL D 215 " (cutoff:3.500A) Proline residue: D 221 - end of helix Proline residue: D 236 - end of helix Processing helix chain 'D' and resid 242 through 271 removed outlier: 3.660A pdb=" N GLU D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Proline residue: D 265 - end of helix Processing helix chain 'D' and resid 275 through 302 removed outlier: 3.936A pdb=" N PHE D 280 " --> pdb=" O LYS D 276 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR D 281 " --> pdb=" O TYR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 437 Processing helix chain 'E' and resid 221 through 246 Proline residue: E 229 - end of helix removed outlier: 3.979A pdb=" N SER E 234 " --> pdb=" O CYS E 230 " (cutoff:3.500A) Proline residue: E 244 - end of helix Processing helix chain 'E' and resid 250 through 280 Proline residue: E 274 - end of helix Processing helix chain 'E' and resid 285 through 311 Processing helix chain 'E' and resid 445 through 478 Proline residue: E 476 - end of helix 435 hydrogen bonds defined for protein. 1305 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: 1.25 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 751 1.31 - 1.43: 1242 1.43 - 1.56: 2970 1.56 - 1.69: 6 1.69 - 1.82: 61 Bond restraints: 5030 Sorted by residual: bond pdb=" N PRO B 271 " pdb=" CD PRO B 271 " ideal model delta sigma weight residual 1.473 1.221 0.252 1.40e-02 5.10e+03 3.23e+02 bond pdb=" C ALA A 403 " pdb=" O ALA A 403 " ideal model delta sigma weight residual 1.231 1.384 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C ALA D 403 " pdb=" O ALA D 403 " ideal model delta sigma weight residual 1.231 1.384 -0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" CB VAL B 445 " pdb=" CG1 VAL B 445 " ideal model delta sigma weight residual 1.521 1.721 -0.200 3.30e-02 9.18e+02 3.69e+01 bond pdb=" N PRO B 464 " pdb=" CD PRO B 464 " ideal model delta sigma weight residual 1.473 1.549 -0.076 1.40e-02 5.10e+03 2.92e+01 ... (remaining 5025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 5620 2.74 - 5.47: 1040 5.47 - 8.21: 136 8.21 - 10.95: 50 10.95 - 13.68: 9 Bond angle restraints: 6855 Sorted by residual: angle pdb=" OE1 GLN E 474 " pdb=" CD GLN E 474 " pdb=" NE2 GLN E 474 " ideal model delta sigma weight residual 122.60 112.76 9.84 1.00e+00 1.00e+00 9.69e+01 angle pdb=" OE1 GLN A 435 " pdb=" CD GLN A 435 " pdb=" NE2 GLN A 435 " ideal model delta sigma weight residual 122.60 112.77 9.83 1.00e+00 1.00e+00 9.67e+01 angle pdb=" OE1 GLN E 262 " pdb=" CD GLN E 262 " pdb=" NE2 GLN E 262 " ideal model delta sigma weight residual 122.60 112.81 9.79 1.00e+00 1.00e+00 9.59e+01 angle pdb=" OE1 GLN E 246 " pdb=" CD GLN E 246 " pdb=" NE2 GLN E 246 " ideal model delta sigma weight residual 122.60 112.84 9.76 1.00e+00 1.00e+00 9.52e+01 angle pdb=" CA THR C 462 " pdb=" C THR C 462 " pdb=" N PRO C 463 " ideal model delta sigma weight residual 120.77 111.31 9.46 9.70e-01 1.06e+00 9.51e+01 ... (remaining 6850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 2582 17.92 - 35.83: 266 35.83 - 53.75: 111 53.75 - 71.67: 12 71.67 - 89.59: 4 Dihedral angle restraints: 2975 sinusoidal: 1114 harmonic: 1861 Sorted by residual: dihedral pdb=" C PRO E 476 " pdb=" N PRO E 476 " pdb=" CA PRO E 476 " pdb=" CB PRO E 476 " ideal model delta harmonic sigma weight residual -120.70 -109.72 -10.98 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" C PRO D 236 " pdb=" N PRO D 236 " pdb=" CA PRO D 236 " pdb=" CB PRO D 236 " ideal model delta harmonic sigma weight residual -120.70 -109.89 -10.81 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" C PRO A 236 " pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" CB PRO A 236 " ideal model delta harmonic sigma weight residual -120.70 -109.91 -10.79 0 2.50e+00 1.60e-01 1.86e+01 ... (remaining 2972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 898 0.276 - 0.552: 5 0.552 - 0.827: 0 0.827 - 1.103: 0 1.103 - 1.379: 1 Chirality restraints: 904 Sorted by residual: chirality pdb=" CB VAL B 445 " pdb=" CA VAL B 445 " pdb=" CG1 VAL B 445 " pdb=" CG2 VAL B 445 " both_signs ideal model delta sigma weight residual False -2.63 -4.01 1.38 2.00e-01 2.50e+01 4.75e+01 chirality pdb=" CB ILE B 446 " pdb=" CA ILE B 446 " pdb=" CG1 ILE B 446 " pdb=" CG2 ILE B 446 " both_signs ideal model delta sigma weight residual False 2.64 3.17 -0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" CA HIS E 471 " pdb=" N HIS E 471 " pdb=" C HIS E 471 " pdb=" CB HIS E 471 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 901 not shown) Planarity restraints: 798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO E 476 " -0.039 2.00e-02 2.50e+03 8.13e-02 6.62e+01 pdb=" C PRO E 476 " 0.141 2.00e-02 2.50e+03 pdb=" O PRO E 476 " -0.054 2.00e-02 2.50e+03 pdb=" N GLU E 477 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 275 " 0.026 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C LEU B 275 " -0.086 2.00e-02 2.50e+03 pdb=" O LEU B 275 " 0.031 2.00e-02 2.50e+03 pdb=" N SER B 276 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 445 " 0.019 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C LYS E 445 " -0.072 2.00e-02 2.50e+03 pdb=" O LYS E 445 " 0.029 2.00e-02 2.50e+03 pdb=" N VAL E 446 " 0.024 2.00e-02 2.50e+03 ... (remaining 795 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.93: 21 1.93 - 2.67: 595 2.67 - 3.41: 8998 3.41 - 4.16: 13035 4.16 - 4.90: 21585 Nonbonded interactions: 44234 Sorted by model distance: nonbonded pdb=" O TYR E 241 " pdb=" CG PRO E 244 " model vdw 1.183 3.440 nonbonded pdb=" O HIS B 460 " pdb=" CD PRO B 464 " model vdw 1.352 3.440 nonbonded pdb=" O TYR E 241 " pdb=" CD PRO E 244 " model vdw 1.447 3.440 nonbonded pdb=" O PHE B 239 " pdb=" CD PRO B 242 " model vdw 1.624 3.440 nonbonded pdb=" O PHE C 459 " pdb=" CD PRO C 463 " model vdw 1.640 3.440 ... (remaining 44229 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } 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 group one per residue 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: 0.040 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.070 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1921 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 : 0.014 0.252 5030 Z= 0.934 Angle : 2.288 13.685 6855 Z= 1.670 Chirality : 0.097 1.379 904 Planarity : 0.009 0.081 798 Dihedral : 17.230 89.585 1757 Min Nonbonded Distance : 1.183 Molprobity Statistics. All-atom Clashscore : 224.94 Ramachandran Plot: Outliers : 2.11 % Allowed : 5.19 % Favored : 92.69 % Rotamer: Outliers : 19.76 % Allowed : 14.04 % Favored : 66.20 % Cbeta Deviations : 0.49 % 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: -3.67 (0.27), residues: 616 helix: -2.15 (0.18), residues: 512 sheet: None (None), residues: 0 loop : -2.61 (0.54), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.005 TRP E 453 HIS 0.006 0.001 HIS B 460 PHE 0.021 0.002 PHE C 247 TYR 0.014 0.001 TYR B 220 ARG 0.001 0.000 ARG E 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 111 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 PHE cc_start: 0.4349 (OUTLIER) cc_final: 0.4004 (m-80) REVERT: A 284 PHE cc_start: 0.2953 (OUTLIER) cc_final: 0.2420 (t80) REVERT: A 411 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.4758 (mm) REVERT: C 457 SER cc_start: -0.6578 (OUTLIER) cc_final: -0.7210 (m) REVERT: C 462 THR cc_start: 0.6349 (m) cc_final: 0.5915 (m) REVERT: C 475 MET cc_start: 0.0883 (OUTLIER) cc_final: -0.0572 (mtt) REVERT: C 479 ASN cc_start: -0.2803 (OUTLIER) cc_final: -0.3292 (t0) REVERT: D 243 MET cc_start: 0.3821 (mtt) cc_final: 0.2367 (pmm) REVERT: D 298 THR cc_start: 0.5185 (OUTLIER) cc_final: 0.4842 (m) REVERT: D 302 SER cc_start: 0.6645 (OUTLIER) cc_final: 0.5667 (t) REVERT: E 272 LYS cc_start: 0.5415 (OUTLIER) cc_final: 0.4499 (tttt) REVERT: E 297 ILE cc_start: 0.1827 (OUTLIER) cc_final: 0.1572 (tp) outliers start: 114 outliers final: 46 residues processed: 198 average time/residue: 0.1403 time to fit residues: 35.9919 Evaluate side-chains 128 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 72 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 453 TRP Chi-restraints excluded: chain E residue 463 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 25 optimal weight: 50.0000 chunk 15 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 50.0000 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 0.0980 overall best weight: 7.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN C 479 ASN D 217 ASN ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2077 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 5030 Z= 0.436 Angle : 1.144 11.708 6855 Z= 0.582 Chirality : 0.055 0.316 904 Planarity : 0.009 0.068 798 Dihedral : 13.847 84.525 764 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 39.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 10.05 % Allowed : 17.33 % Favored : 72.62 % 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: -1.65 (0.32), residues: 616 helix: -0.77 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -2.70 (0.83), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP E 453 HIS 0.007 0.002 HIS D 300 PHE 0.036 0.004 PHE B 286 TYR 0.033 0.003 TYR C 248 ARG 0.004 0.001 ARG D 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 73 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 THR cc_start: 0.6568 (OUTLIER) cc_final: 0.6366 (m) REVERT: B 433 MET cc_start: 0.4038 (mpp) cc_final: 0.1572 (mpp) REVERT: B 440 LEU cc_start: 0.5372 (OUTLIER) cc_final: 0.5130 (tp) REVERT: C 257 MET cc_start: -0.0543 (mtt) cc_final: -0.1230 (mtt) REVERT: D 232 VAL cc_start: 0.0309 (OUTLIER) cc_final: -0.0026 (t) REVERT: E 454 ILE cc_start: -0.0582 (OUTLIER) cc_final: -0.0798 (pp) outliers start: 58 outliers final: 21 residues processed: 115 average time/residue: 0.1363 time to fit residues: 20.9005 Evaluate side-chains 86 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 61 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 453 TRP Chi-restraints excluded: chain E residue 454 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 54 optimal weight: 50.0000 chunk 58 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN C 267 GLN C 305 ASN C 313 HIS D 300 HIS ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2152 moved from start: 0.8444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 5030 Z= 0.326 Angle : 0.972 11.462 6855 Z= 0.477 Chirality : 0.047 0.275 904 Planarity : 0.007 0.068 798 Dihedral : 10.071 82.314 689 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.03 % Allowed : 19.41 % Favored : 75.56 % 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: -0.76 (0.32), residues: 616 helix: -0.22 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -1.74 (0.70), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 453 HIS 0.009 0.002 HIS B 306 PHE 0.026 0.003 PHE D 256 TYR 0.010 0.002 TYR B 223 ARG 0.005 0.001 ARG B 437 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 69 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 257 MET cc_start: -0.1260 (mtt) cc_final: -0.2934 (mmt) REVERT: C 475 MET cc_start: -0.1284 (ptt) cc_final: -0.4026 (mmt) REVERT: D 435 GLN cc_start: -0.2305 (OUTLIER) cc_final: -0.2801 (mt0) outliers start: 29 outliers final: 13 residues processed: 93 average time/residue: 0.1272 time to fit residues: 16.1880 Evaluate side-chains 70 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 54 optimal weight: 0.1980 chunk 57 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2196 moved from start: 0.9407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5030 Z= 0.296 Angle : 0.888 11.534 6855 Z= 0.433 Chirality : 0.045 0.178 904 Planarity : 0.007 0.065 798 Dihedral : 8.217 79.899 672 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.68 % Allowed : 20.45 % Favored : 74.87 % 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 (0.33), residues: 616 helix: 0.26 (0.21), residues: 555 sheet: None (None), residues: 0 loop : -1.62 (0.73), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP E 453 HIS 0.005 0.001 HIS D 299 PHE 0.023 0.002 PHE C 314 TYR 0.008 0.001 TYR C 248 ARG 0.003 0.001 ARG C 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 67 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 MET cc_start: 0.0714 (mtt) cc_final: 0.0430 (mtp) REVERT: B 302 LEU cc_start: 0.3870 (OUTLIER) cc_final: 0.3533 (tt) REVERT: C 257 MET cc_start: -0.1891 (mtt) cc_final: -0.2986 (mmt) REVERT: C 475 MET cc_start: -0.0965 (ptt) cc_final: -0.3540 (mmt) REVERT: D 435 GLN cc_start: -0.2873 (OUTLIER) cc_final: -0.3091 (mt0) outliers start: 27 outliers final: 14 residues processed: 90 average time/residue: 0.1137 time to fit residues: 14.4246 Evaluate side-chains 77 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 29 optimal weight: 0.0970 chunk 52 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 50.0000 chunk 34 optimal weight: 3.9990 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN C 479 ASN E 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2335 moved from start: 1.0544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5030 Z= 0.293 Angle : 0.885 11.185 6855 Z= 0.429 Chirality : 0.045 0.249 904 Planarity : 0.007 0.063 798 Dihedral : 7.006 69.983 666 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.33 % Allowed : 21.84 % Favored : 73.83 % 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: 0.60 (0.33), residues: 616 helix: 0.72 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.84 (0.74), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 453 HIS 0.003 0.001 HIS B 460 PHE 0.022 0.002 PHE C 314 TYR 0.010 0.001 TYR B 220 ARG 0.003 0.001 ARG D 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 61 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: -0.2336 (OUTLIER) cc_final: -0.2610 (pttt) REVERT: B 249 MET cc_start: 0.4974 (pmm) cc_final: 0.4764 (pmm) REVERT: B 302 LEU cc_start: 0.3718 (OUTLIER) cc_final: 0.3237 (tt) REVERT: C 257 MET cc_start: -0.2213 (mtt) cc_final: -0.2717 (mmt) REVERT: C 296 MET cc_start: 0.2737 (mtt) cc_final: 0.2508 (mtt) REVERT: C 475 MET cc_start: -0.0528 (ptt) cc_final: -0.3257 (mmt) outliers start: 25 outliers final: 12 residues processed: 81 average time/residue: 0.1255 time to fit residues: 14.0839 Evaluate side-chains 73 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 268 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 0.1980 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2367 moved from start: 1.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5030 Z= 0.264 Angle : 0.860 11.731 6855 Z= 0.411 Chirality : 0.044 0.218 904 Planarity : 0.007 0.062 798 Dihedral : 6.219 58.216 662 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.29 % Allowed : 21.32 % Favored : 75.39 % 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: 1.13 (0.34), residues: 616 helix: 1.12 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -1.90 (0.71), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 453 HIS 0.024 0.002 HIS B 306 PHE 0.022 0.002 PHE C 314 TYR 0.007 0.001 TYR B 220 ARG 0.002 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 257 MET cc_start: -0.1881 (mtt) cc_final: -0.2797 (mmt) REVERT: C 475 MET cc_start: -0.0584 (ptt) cc_final: -0.3452 (mmt) outliers start: 19 outliers final: 12 residues processed: 80 average time/residue: 0.1149 time to fit residues: 12.8688 Evaluate side-chains 71 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 268 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 30.0000 chunk 57 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 17 optimal weight: 40.0000 chunk 11 optimal weight: 50.0000 chunk 39 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN E 225 ASN E 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2549 moved from start: 1.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5030 Z= 0.292 Angle : 0.877 10.677 6855 Z= 0.424 Chirality : 0.044 0.193 904 Planarity : 0.007 0.063 798 Dihedral : 5.924 58.032 660 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.99 % Allowed : 20.28 % Favored : 75.74 % 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: 1.20 (0.34), residues: 616 helix: 1.21 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -2.33 (0.66), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 453 HIS 0.012 0.002 HIS B 306 PHE 0.025 0.002 PHE B 262 TYR 0.014 0.002 TYR B 220 ARG 0.004 0.001 ARG D 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 0.557 Fit side-chains REVERT: C 257 MET cc_start: -0.1950 (mtt) cc_final: -0.2742 (mmt) REVERT: C 296 MET cc_start: 0.2002 (mtt) cc_final: 0.1767 (mmp) outliers start: 23 outliers final: 14 residues processed: 80 average time/residue: 0.1434 time to fit residues: 15.3120 Evaluate side-chains 70 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 268 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 42 optimal weight: 0.2980 chunk 16 optimal weight: 20.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2571 moved from start: 1.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5030 Z= 0.275 Angle : 0.900 11.367 6855 Z= 0.429 Chirality : 0.045 0.261 904 Planarity : 0.007 0.067 798 Dihedral : 5.904 58.427 660 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.08 % Allowed : 23.22 % Favored : 74.70 % 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: 1.34 (0.34), residues: 616 helix: 1.32 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -2.21 (0.67), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 453 HIS 0.006 0.001 HIS B 306 PHE 0.033 0.002 PHE B 262 TYR 0.011 0.001 TYR B 220 ARG 0.002 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.605 Fit side-chains REVERT: C 257 MET cc_start: -0.2140 (mtt) cc_final: -0.2894 (mmt) REVERT: D 278 MET cc_start: 0.4887 (ppp) cc_final: 0.4582 (ppp) REVERT: E 225 ASN cc_start: 0.5812 (m110) cc_final: 0.5442 (t0) outliers start: 12 outliers final: 11 residues processed: 76 average time/residue: 0.1218 time to fit residues: 13.3007 Evaluate side-chains 71 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 264 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 30.0000 chunk 50 optimal weight: 50.0000 chunk 53 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 50.0000 chunk 39 optimal weight: 40.0000 chunk 59 optimal weight: 40.0000 chunk 55 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2773 moved from start: 1.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 5030 Z= 0.319 Angle : 0.958 11.396 6855 Z= 0.463 Chirality : 0.048 0.406 904 Planarity : 0.008 0.066 798 Dihedral : 6.108 58.432 660 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.43 % Allowed : 23.74 % Favored : 73.83 % 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: 1.15 (0.34), residues: 616 helix: 1.20 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -2.39 (0.65), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 453 HIS 0.010 0.001 HIS B 306 PHE 0.027 0.002 PHE B 262 TYR 0.024 0.002 TYR A 213 ARG 0.002 0.000 ARG C 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 248 TYR cc_start: 0.3432 (OUTLIER) cc_final: 0.1517 (t80) REVERT: C 257 MET cc_start: -0.2305 (mtt) cc_final: -0.2875 (mmt) outliers start: 14 outliers final: 12 residues processed: 75 average time/residue: 0.1211 time to fit residues: 12.8326 Evaluate side-chains 74 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 50 optimal weight: 40.0000 chunk 14 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 47 optimal weight: 50.0000 chunk 19 optimal weight: 30.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2917 moved from start: 1.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5030 Z= 0.309 Angle : 0.992 11.206 6855 Z= 0.480 Chirality : 0.051 0.350 904 Planarity : 0.008 0.068 798 Dihedral : 6.257 59.120 660 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.43 % Allowed : 24.78 % Favored : 72.79 % 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: 1.20 (0.33), residues: 616 helix: 1.24 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.56 (0.68), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 453 HIS 0.015 0.002 HIS B 306 PHE 0.033 0.002 PHE B 262 TYR 0.033 0.003 TYR A 234 ARG 0.016 0.001 ARG B 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 248 TYR cc_start: 0.3626 (OUTLIER) cc_final: 0.1665 (t80) REVERT: C 257 MET cc_start: -0.2695 (mtt) cc_final: -0.3283 (mmt) REVERT: D 296 ILE cc_start: 0.5710 (pp) cc_final: 0.5499 (pp) outliers start: 14 outliers final: 11 residues processed: 72 average time/residue: 0.1214 time to fit residues: 12.3002 Evaluate side-chains 68 residues out of total 577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 7.9990 chunk 6 optimal weight: 0.0980 chunk 8 optimal weight: 30.0000 chunk 41 optimal weight: 0.0020 chunk 2 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.099881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.087365 restraints weight = 38301.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.085647 restraints weight = 58852.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.085647 restraints weight = 79703.120| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4100 moved from start: 1.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5030 Z= 0.277 Angle : 0.982 12.406 6855 Z= 0.463 Chirality : 0.048 0.267 904 Planarity : 0.007 0.060 798 Dihedral : 6.087 57.184 660 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.91 % Allowed : 25.82 % Favored : 72.27 % 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: 1.35 (0.34), residues: 616 helix: 1.33 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -2.51 (0.70), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 453 HIS 0.009 0.001 HIS B 306 PHE 0.039 0.002 PHE B 262 TYR 0.010 0.001 TYR C 248 ARG 0.001 0.000 ARG A 301 =============================================================================== Job complete usr+sys time: 1045.92 seconds wall clock time: 19 minutes 34.23 seconds (1174.23 seconds total)