Starting phenix.real_space_refine on Fri Dec 27 22:42:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hio_34824/12_2024/8hio_34824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hio_34824/12_2024/8hio_34824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hio_34824/12_2024/8hio_34824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hio_34824/12_2024/8hio_34824.map" model { file = "/net/cci-nas-00/data/ceres_data/8hio_34824/12_2024/8hio_34824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hio_34824/12_2024/8hio_34824.cif" } resolution = 3.73 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= 0.012 sd= 0.211 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 47 5.49 5 Mg 1 5.21 5 S 21 5.16 5 C 3952 2.51 5 N 1281 2.21 5 O 1378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6681 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1019 Classifications: {'RNA': 47} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 20, 'rna3p_pyr': 12} Link IDs: {'rna2p': 15, 'rna3p': 31} Chain: "A" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4436 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 543} Chain breaks: 2 Chain: "D" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1224 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5151 SG CYS A 552 106.496 33.507 50.395 1.00185.32 S ATOM 5284 SG CYS A 569 106.415 36.312 50.252 1.00190.90 S ATOM 5302 SG CYS A 572 107.743 36.523 47.525 1.00196.84 S Time building chain proxies: 4.41, per 1000 atoms: 0.66 Number of scatterers: 6681 At special positions: 0 Unit cell: (118.101, 99.603, 102.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 21 16.00 P 47 15.00 Mg 1 11.99 O 1378 8.00 N 1281 7.00 C 3952 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: 2.10 Conformation dependent library (CDL) restraints added in 943.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 549 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 552 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 572 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 569 " Number of angles added : 3 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 61.3% alpha, 12.2% beta 11 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 18 through 52 Processing helix chain 'A' and resid 53 through 85 Processing helix chain 'A' and resid 92 through 119 Processing helix chain 'A' and resid 122 through 145 Processing helix chain 'A' and resid 151 through 175 Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.501A pdb=" N ASP A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.575A pdb=" N ARG A 345 " --> pdb=" O PHE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 397 Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 417 through 428 removed outlier: 4.602A pdb=" N PHE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 479 removed outlier: 3.710A pdb=" N TRP A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ARG A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 518 through 534 removed outlier: 4.114A pdb=" N LEU A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.744A pdb=" N SER A 564 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 591 Processing helix chain 'D' and resid 19 through 52 Processing helix chain 'D' and resid 53 through 64 Processing helix chain 'D' and resid 96 through 118 removed outlier: 3.640A pdb=" N ALA D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 122 through 145 removed outlier: 3.519A pdb=" N TYR D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 176 removed outlier: 3.598A pdb=" N ALA D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY D 176 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 195 removed outlier: 6.716A pdb=" N THR A 299 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A 281 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS A 297 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU A 283 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS A 295 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL A 285 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 293 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG A 287 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA A 294 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 11 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 10 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE A 262 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ARG A 251 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 264 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ARG A 249 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 266 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR A 247 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 323 removed outlier: 5.947A pdb=" N ALA A 328 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 361 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 323 removed outlier: 4.142A pdb=" N ASP A 485 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU A 318 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 568 374 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1691 1.33 - 1.45: 1571 1.45 - 1.57: 3522 1.57 - 1.69: 93 1.69 - 1.81: 33 Bond restraints: 6910 Sorted by residual: bond pdb=" C TRP A 261 " pdb=" N ILE A 262 " ideal model delta sigma weight residual 1.333 1.303 0.030 1.34e-02 5.57e+03 4.96e+00 bond pdb=" C ASP A 477 " pdb=" N GLN A 478 " ideal model delta sigma weight residual 1.332 1.311 0.022 1.40e-02 5.10e+03 2.40e+00 bond pdb=" CG LEU A 221 " pdb=" CD1 LEU A 221 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CB VAL A 194 " pdb=" CG1 VAL A 194 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB PHE A 443 " pdb=" CG PHE A 443 " ideal model delta sigma weight residual 1.502 1.477 0.025 2.30e-02 1.89e+03 1.22e+00 ... (remaining 6905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 9367 1.82 - 3.64: 205 3.64 - 5.46: 23 5.46 - 7.28: 4 7.28 - 9.10: 2 Bond angle restraints: 9601 Sorted by residual: angle pdb=" N TRP A 440 " pdb=" CA TRP A 440 " pdb=" C TRP A 440 " ideal model delta sigma weight residual 113.12 108.77 4.35 1.25e+00 6.40e-01 1.21e+01 angle pdb=" CA LEU A 369 " pdb=" CB LEU A 369 " pdb=" CG LEU A 369 " ideal model delta sigma weight residual 116.30 107.20 9.10 3.50e+00 8.16e-02 6.75e+00 angle pdb=" C LEU A 318 " pdb=" N GLY A 319 " pdb=" CA GLY A 319 " ideal model delta sigma weight residual 120.51 124.36 -3.85 1.63e+00 3.76e-01 5.57e+00 angle pdb=" C GLN A 453 " pdb=" N GLU A 454 " pdb=" CA GLU A 454 " ideal model delta sigma weight residual 122.42 118.79 3.63 1.55e+00 4.16e-01 5.48e+00 angle pdb=" C ALA A 281 " pdb=" N GLU A 282 " pdb=" CA GLU A 282 " ideal model delta sigma weight residual 122.99 119.73 3.26 1.41e+00 5.03e-01 5.34e+00 ... (remaining 9596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.19: 3719 19.19 - 38.38: 318 38.38 - 57.58: 133 57.58 - 76.77: 68 76.77 - 95.96: 4 Dihedral angle restraints: 4242 sinusoidal: 2150 harmonic: 2092 Sorted by residual: dihedral pdb=" O4' U B 6 " pdb=" C1' U B 6 " pdb=" N1 U B 6 " pdb=" C2 U B 6 " ideal model delta sinusoidal sigma weight residual -160.00 -83.79 -76.21 1 1.50e+01 4.44e-03 3.25e+01 dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual -106.00 -171.33 65.33 1 1.70e+01 3.46e-03 1.94e+01 dihedral pdb=" O4' C B 15 " pdb=" C1' C B 15 " pdb=" N1 C B 15 " pdb=" C2 C B 15 " ideal model delta sinusoidal sigma weight residual -160.00 -104.45 -55.55 1 1.50e+01 4.44e-03 1.85e+01 ... (remaining 4239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 688 0.029 - 0.058: 282 0.058 - 0.087: 86 0.087 - 0.115: 30 0.115 - 0.144: 10 Chirality restraints: 1096 Sorted by residual: chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA VAL A 268 " pdb=" N VAL A 268 " pdb=" C VAL A 268 " pdb=" CB VAL A 268 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA VAL A 361 " pdb=" N VAL A 361 " pdb=" C VAL A 361 " pdb=" CB VAL A 361 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1093 not shown) Planarity restraints: 1072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 452 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C GLN A 452 " 0.045 2.00e-02 2.50e+03 pdb=" O GLN A 452 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 453 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 472 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C ALA A 472 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA A 472 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 473 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 459 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C LYS A 459 " -0.032 2.00e-02 2.50e+03 pdb=" O LYS A 459 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA A 460 " 0.011 2.00e-02 2.50e+03 ... (remaining 1069 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 30 2.38 - 3.01: 3883 3.01 - 3.64: 10567 3.64 - 4.27: 15151 4.27 - 4.90: 24433 Nonbonded interactions: 54064 Sorted by model distance: nonbonded pdb=" OP1 G B -22 " pdb="MG MG B 101 " model vdw 1.744 2.170 nonbonded pdb=" OP2 C B -21 " pdb="MG MG B 101 " model vdw 1.992 2.170 nonbonded pdb=" OP1 G B -7 " pdb=" NZ LYS A 14 " model vdw 2.111 3.120 nonbonded pdb=" OD2 ASP A 466 " pdb=" NE2 GLN A 470 " model vdw 2.147 3.120 nonbonded pdb=" O TRP A 428 " pdb=" OG SER A 436 " model vdw 2.153 3.040 ... (remaining 54059 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.050 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.260 Find NCS groups from input model: 0.060 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 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 : 0.005 0.042 6910 Z= 0.352 Angle : 0.664 9.097 9601 Z= 0.363 Chirality : 0.037 0.144 1096 Planarity : 0.004 0.031 1072 Dihedral : 18.515 95.962 2880 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.32), residues: 707 helix: 2.70 (0.25), residues: 421 sheet: -0.24 (0.58), residues: 75 loop : -0.43 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 320 HIS 0.009 0.002 HIS A 7 PHE 0.008 0.001 PHE A 443 TYR 0.019 0.002 TYR A 217 ARG 0.005 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.711 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6616 (mm-30) REVERT: A 138 LYS cc_start: 0.8899 (tttt) cc_final: 0.8609 (tmtt) REVERT: A 169 ILE cc_start: 0.8917 (mm) cc_final: 0.8404 (tp) REVERT: A 333 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7792 (tpp80) REVERT: A 356 SER cc_start: 0.7773 (t) cc_final: 0.7543 (p) REVERT: A 420 ARG cc_start: 0.7515 (mmm-85) cc_final: 0.5416 (mpp-170) REVERT: A 530 MET cc_start: 0.8057 (mmt) cc_final: 0.7515 (mmm) REVERT: D 27 LEU cc_start: 0.9226 (mt) cc_final: 0.8976 (mt) REVERT: D 32 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8005 (ttp-170) REVERT: D 42 TYR cc_start: 0.8057 (t80) cc_final: 0.7857 (t80) REVERT: D 46 LEU cc_start: 0.9019 (mt) cc_final: 0.8653 (mt) REVERT: D 50 TRP cc_start: 0.8448 (m100) cc_final: 0.8030 (m100) REVERT: D 98 ARG cc_start: 0.4191 (mtt180) cc_final: 0.3519 (tpm170) REVERT: D 115 ILE cc_start: 0.4875 (mt) cc_final: 0.4406 (mt) REVERT: D 127 LYS cc_start: 0.9577 (tppt) cc_final: 0.9344 (tptp) REVERT: D 163 LYS cc_start: 0.8615 (mttt) cc_final: 0.8395 (mmtt) REVERT: D 185 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7354 (mtp180) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3100 time to fit residues: 69.4820 Evaluate side-chains 121 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 449 GLN A 516 HIS D 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6910 Z= 0.316 Angle : 0.674 7.692 9601 Z= 0.353 Chirality : 0.040 0.172 1096 Planarity : 0.005 0.054 1072 Dihedral : 18.740 98.257 1546 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.44 % Allowed : 19.10 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.33), residues: 707 helix: 2.67 (0.24), residues: 426 sheet: -0.06 (0.62), residues: 73 loop : -0.37 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 450 HIS 0.012 0.002 HIS D 161 PHE 0.008 0.001 PHE A 155 TYR 0.020 0.002 TYR A 217 ARG 0.013 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.679 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 9 MET cc_start: 0.8313 (mtt) cc_final: 0.7975 (mtm) REVERT: A 29 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.7260 (t-90) REVERT: A 53 TYR cc_start: 0.7589 (m-10) cc_final: 0.7161 (m-10) REVERT: A 127 LYS cc_start: 0.9348 (tmmt) cc_final: 0.9147 (tmmt) REVERT: A 138 LYS cc_start: 0.8888 (tttt) cc_final: 0.8566 (tmtt) REVERT: A 169 ILE cc_start: 0.8655 (mm) cc_final: 0.7994 (tp) REVERT: A 356 SER cc_start: 0.7815 (t) cc_final: 0.7477 (p) REVERT: A 420 ARG cc_start: 0.7601 (mmm-85) cc_final: 0.5221 (mpp-170) REVERT: D 23 GLN cc_start: 0.8858 (tp40) cc_final: 0.8572 (mt0) REVERT: D 32 ARG cc_start: 0.8529 (ttp80) cc_final: 0.7977 (ttp-170) REVERT: D 42 TYR cc_start: 0.8074 (t80) cc_final: 0.7755 (t80) REVERT: D 46 LEU cc_start: 0.9135 (mt) cc_final: 0.8667 (mm) REVERT: D 138 LYS cc_start: 0.9445 (mttt) cc_final: 0.9153 (mttp) REVERT: D 167 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8175 (mmmt) REVERT: D 185 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7390 (mtm180) outliers start: 20 outliers final: 9 residues processed: 138 average time/residue: 0.2596 time to fit residues: 44.5493 Evaluate side-chains 116 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 68 optimal weight: 30.0000 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 23 optimal weight: 0.0070 chunk 54 optimal weight: 0.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 516 HIS D 29 HIS D 143 GLN D 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6910 Z= 0.235 Angle : 0.601 6.778 9601 Z= 0.314 Chirality : 0.038 0.274 1096 Planarity : 0.004 0.040 1072 Dihedral : 18.615 99.195 1546 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.93 % Allowed : 19.97 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.33), residues: 707 helix: 2.81 (0.25), residues: 426 sheet: 0.09 (0.62), residues: 77 loop : -0.24 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 450 HIS 0.011 0.002 HIS D 29 PHE 0.006 0.001 PHE A 155 TYR 0.017 0.002 TYR A 217 ARG 0.004 0.001 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.841 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: symmetry clash REVERT: A 9 MET cc_start: 0.8269 (mtt) cc_final: 0.7932 (mtm) REVERT: A 26 TRP cc_start: 0.8343 (t60) cc_final: 0.7010 (t60) REVERT: A 29 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7265 (t-90) REVERT: A 63 MET cc_start: 0.9038 (ptp) cc_final: 0.8362 (ptp) REVERT: A 93 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6682 (tp) REVERT: A 119 LYS cc_start: 0.9185 (ttpp) cc_final: 0.8951 (tptp) REVERT: A 127 LYS cc_start: 0.9329 (tmmt) cc_final: 0.9070 (tmmt) REVERT: A 138 LYS cc_start: 0.8848 (tttt) cc_final: 0.8526 (tmtt) REVERT: A 260 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8396 (mm110) REVERT: A 356 SER cc_start: 0.7798 (t) cc_final: 0.7449 (p) REVERT: D 42 TYR cc_start: 0.7971 (t80) cc_final: 0.7712 (t80) REVERT: D 127 LYS cc_start: 0.9427 (tppt) cc_final: 0.9067 (tppt) REVERT: D 167 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8163 (mmmt) REVERT: D 185 ARG cc_start: 0.8284 (mmm160) cc_final: 0.7386 (mtm180) outliers start: 17 outliers final: 10 residues processed: 121 average time/residue: 0.2223 time to fit residues: 34.9117 Evaluate side-chains 110 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain D residue 43 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 452 GLN D 29 HIS D 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 6910 Z= 0.328 Angle : 0.649 11.398 9601 Z= 0.332 Chirality : 0.039 0.161 1096 Planarity : 0.005 0.047 1072 Dihedral : 18.647 100.063 1546 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.16 % Allowed : 21.34 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.33), residues: 707 helix: 2.62 (0.25), residues: 425 sheet: -0.08 (0.63), residues: 75 loop : -0.46 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 450 HIS 0.015 0.002 HIS D 29 PHE 0.006 0.001 PHE A 582 TYR 0.019 0.002 TYR A 217 ARG 0.006 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.706 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 9 MET cc_start: 0.8400 (mtt) cc_final: 0.8023 (mtm) REVERT: A 29 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.7280 (t-90) REVERT: A 63 MET cc_start: 0.9231 (ptp) cc_final: 0.8580 (ptp) REVERT: A 127 LYS cc_start: 0.9411 (tmmt) cc_final: 0.9088 (tmmt) REVERT: A 138 LYS cc_start: 0.8845 (tttt) cc_final: 0.8566 (tmtt) REVERT: A 185 ARG cc_start: 0.6799 (mtm180) cc_final: 0.6475 (mtt180) REVERT: A 187 ASP cc_start: 0.8861 (p0) cc_final: 0.8609 (p0) REVERT: A 356 SER cc_start: 0.7828 (t) cc_final: 0.7467 (p) REVERT: A 478 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8386 (mt0) REVERT: A 535 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8543 (m) REVERT: A 568 ARG cc_start: 0.7455 (tpp80) cc_final: 0.7251 (tpp80) REVERT: D 23 GLN cc_start: 0.9041 (tp40) cc_final: 0.8677 (mt0) REVERT: D 24 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8155 (mm110) REVERT: D 32 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8032 (ttm-80) REVERT: D 40 LEU cc_start: 0.8512 (mm) cc_final: 0.8056 (mm) REVERT: D 42 TYR cc_start: 0.8092 (t80) cc_final: 0.7887 (t80) REVERT: D 44 ASP cc_start: 0.9431 (m-30) cc_final: 0.9163 (p0) REVERT: D 50 TRP cc_start: 0.8726 (m100) cc_final: 0.7883 (m100) REVERT: D 115 ILE cc_start: 0.4821 (mt) cc_final: 0.4286 (mt) REVERT: D 127 LYS cc_start: 0.9433 (tppt) cc_final: 0.9077 (tppt) REVERT: D 137 GLN cc_start: 0.9108 (mt0) cc_final: 0.8829 (mm110) REVERT: D 167 LYS cc_start: 0.8483 (mtpt) cc_final: 0.8271 (mmmt) REVERT: D 184 HIS cc_start: 0.6195 (m-70) cc_final: 0.5753 (m90) REVERT: D 185 ARG cc_start: 0.8435 (mmm160) cc_final: 0.7444 (mtm180) outliers start: 30 outliers final: 19 residues processed: 127 average time/residue: 0.2234 time to fit residues: 36.3136 Evaluate side-chains 120 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 24 optimal weight: 0.1980 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 30 ASN D 95 GLN D 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6910 Z= 0.225 Angle : 0.572 9.363 9601 Z= 0.295 Chirality : 0.037 0.164 1096 Planarity : 0.004 0.041 1072 Dihedral : 18.495 101.057 1546 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.61 % Allowed : 22.72 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.33), residues: 707 helix: 2.75 (0.24), residues: 426 sheet: -0.09 (0.64), residues: 75 loop : -0.24 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 450 HIS 0.014 0.001 HIS D 29 PHE 0.008 0.001 PHE A 582 TYR 0.013 0.001 TYR A 217 ARG 0.004 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.696 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: symmetry clash REVERT: A 9 MET cc_start: 0.8329 (mtt) cc_final: 0.7946 (mtm) REVERT: A 29 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.7140 (t-90) REVERT: A 63 MET cc_start: 0.9153 (ptp) cc_final: 0.8709 (ptt) REVERT: A 119 LYS cc_start: 0.9085 (tptp) cc_final: 0.8871 (tppt) REVERT: A 127 LYS cc_start: 0.9381 (tmmt) cc_final: 0.9086 (tmmt) REVERT: A 138 LYS cc_start: 0.8940 (tttt) cc_final: 0.8604 (tmtt) REVERT: A 185 ARG cc_start: 0.6544 (mtm180) cc_final: 0.6136 (mtm180) REVERT: A 356 SER cc_start: 0.7733 (t) cc_final: 0.7382 (p) REVERT: A 475 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6757 (mm) REVERT: D 32 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8054 (ttm-80) REVERT: D 40 LEU cc_start: 0.8593 (mm) cc_final: 0.8358 (mm) REVERT: D 42 TYR cc_start: 0.7981 (t80) cc_final: 0.7764 (t80) REVERT: D 50 TRP cc_start: 0.8704 (m100) cc_final: 0.8201 (m100) REVERT: D 127 LYS cc_start: 0.9398 (tppt) cc_final: 0.9018 (tppt) REVERT: D 138 LYS cc_start: 0.9257 (ptpt) cc_final: 0.9020 (ptpp) REVERT: D 184 HIS cc_start: 0.6213 (m-70) cc_final: 0.5927 (m-70) REVERT: D 185 ARG cc_start: 0.8468 (mmm160) cc_final: 0.7410 (mtm180) outliers start: 21 outliers final: 14 residues processed: 118 average time/residue: 0.2389 time to fit residues: 35.6778 Evaluate side-chains 115 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 69 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: A 449 GLN D 29 HIS D 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6910 Z= 0.286 Angle : 0.631 9.095 9601 Z= 0.326 Chirality : 0.038 0.199 1096 Planarity : 0.004 0.040 1072 Dihedral : 18.539 100.729 1546 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.65 % Allowed : 23.06 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.33), residues: 707 helix: 2.53 (0.24), residues: 426 sheet: -0.33 (0.64), residues: 75 loop : -0.24 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 450 HIS 0.014 0.002 HIS D 29 PHE 0.006 0.001 PHE A 155 TYR 0.017 0.002 TYR A 217 ARG 0.005 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.660 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8325 (mtt) cc_final: 0.7882 (mtm) REVERT: A 11 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8291 (t) REVERT: A 29 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7297 (t-90) REVERT: A 63 MET cc_start: 0.9100 (ptp) cc_final: 0.8371 (ptp) REVERT: A 127 LYS cc_start: 0.9408 (tmmt) cc_final: 0.9090 (tmmt) REVERT: A 138 LYS cc_start: 0.8975 (tttt) cc_final: 0.8610 (tmtt) REVERT: A 185 ARG cc_start: 0.6450 (mtm180) cc_final: 0.6076 (mtm180) REVERT: A 208 MET cc_start: 0.8574 (mpp) cc_final: 0.8323 (mmp) REVERT: A 431 ASN cc_start: 0.7166 (p0) cc_final: 0.6919 (p0) REVERT: A 446 ASP cc_start: 0.8293 (t0) cc_final: 0.8014 (t70) REVERT: A 475 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6828 (mm) REVERT: A 556 ASN cc_start: 0.8859 (m-40) cc_final: 0.8403 (m110) REVERT: A 575 MET cc_start: 0.8743 (tpp) cc_final: 0.8500 (tpp) REVERT: D 32 ARG cc_start: 0.8422 (ttp80) cc_final: 0.7854 (ttm-80) REVERT: D 42 TYR cc_start: 0.7951 (t80) cc_final: 0.7340 (t80) REVERT: D 50 TRP cc_start: 0.8662 (m100) cc_final: 0.8094 (m100) REVERT: D 127 LYS cc_start: 0.9397 (tppt) cc_final: 0.9000 (tppt) REVERT: D 185 ARG cc_start: 0.8520 (mmm160) cc_final: 0.7429 (mtm180) outliers start: 27 outliers final: 17 residues processed: 118 average time/residue: 0.2205 time to fit residues: 33.7361 Evaluate side-chains 114 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 45 optimal weight: 0.1980 chunk 44 optimal weight: 0.0980 chunk 33 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 HIS D 30 ASN D 132 GLN D 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6910 Z= 0.164 Angle : 0.574 16.957 9601 Z= 0.291 Chirality : 0.036 0.177 1096 Planarity : 0.004 0.040 1072 Dihedral : 18.373 101.367 1546 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.10 % Allowed : 24.44 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.33), residues: 707 helix: 2.59 (0.24), residues: 432 sheet: -0.10 (0.70), residues: 65 loop : -0.31 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 320 HIS 0.013 0.001 HIS D 29 PHE 0.012 0.001 PHE A 582 TYR 0.020 0.002 TYR A 576 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.631 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8256 (mtt) cc_final: 0.7889 (mtm) REVERT: A 29 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.6954 (t-90) REVERT: A 63 MET cc_start: 0.9115 (ptp) cc_final: 0.8471 (ptp) REVERT: A 127 LYS cc_start: 0.9425 (tmmt) cc_final: 0.9097 (tmmt) REVERT: A 138 LYS cc_start: 0.8953 (tttt) cc_final: 0.8552 (tmtt) REVERT: A 185 ARG cc_start: 0.6610 (mtm180) cc_final: 0.6177 (mtm180) REVERT: A 194 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7614 (p) REVERT: A 208 MET cc_start: 0.8623 (mpp) cc_final: 0.8351 (mmp) REVERT: A 556 ASN cc_start: 0.8830 (m-40) cc_final: 0.8341 (m110) REVERT: A 562 TYR cc_start: 0.7315 (m-80) cc_final: 0.7113 (m-80) REVERT: D 24 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8386 (mm-40) REVERT: D 42 TYR cc_start: 0.8002 (t80) cc_final: 0.7331 (t80) REVERT: D 50 TRP cc_start: 0.8616 (m100) cc_final: 0.8061 (m100) REVERT: D 53 TYR cc_start: 0.6066 (m-80) cc_final: 0.4990 (m-80) REVERT: D 159 LEU cc_start: 0.9391 (tp) cc_final: 0.9039 (pp) REVERT: D 185 ARG cc_start: 0.8418 (mmm160) cc_final: 0.7393 (mtm180) outliers start: 18 outliers final: 11 residues processed: 110 average time/residue: 0.2269 time to fit residues: 32.0667 Evaluate side-chains 101 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 43 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 63 optimal weight: 50.0000 chunk 67 optimal weight: 6.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 HIS D 30 ASN D 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6910 Z= 0.231 Angle : 0.623 14.794 9601 Z= 0.312 Chirality : 0.037 0.158 1096 Planarity : 0.004 0.040 1072 Dihedral : 18.381 100.835 1546 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.27 % Allowed : 24.10 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.33), residues: 707 helix: 2.51 (0.25), residues: 426 sheet: -0.06 (0.70), residues: 65 loop : -0.32 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.014 0.002 HIS D 29 PHE 0.009 0.001 PHE A 582 TYR 0.018 0.002 TYR A 576 ARG 0.011 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.700 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: symmetry clash REVERT: A 9 MET cc_start: 0.8297 (mtt) cc_final: 0.7873 (mtm) REVERT: A 29 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7070 (t-90) REVERT: A 63 MET cc_start: 0.9168 (ptp) cc_final: 0.8448 (ptp) REVERT: A 127 LYS cc_start: 0.9445 (tmmt) cc_final: 0.9112 (tmmt) REVERT: A 138 LYS cc_start: 0.8970 (tttt) cc_final: 0.8667 (tmtt) REVERT: A 185 ARG cc_start: 0.6521 (mtm180) cc_final: 0.6144 (mtm180) REVERT: A 208 MET cc_start: 0.8706 (mpp) cc_final: 0.8446 (mmp) REVERT: A 309 THR cc_start: 0.8681 (p) cc_final: 0.8422 (t) REVERT: A 556 ASN cc_start: 0.8850 (m-40) cc_final: 0.8384 (m110) REVERT: D 23 GLN cc_start: 0.9071 (tp40) cc_final: 0.8729 (mp10) REVERT: D 32 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8138 (ttm170) REVERT: D 42 TYR cc_start: 0.7901 (t80) cc_final: 0.7306 (t80) REVERT: D 50 TRP cc_start: 0.8575 (m100) cc_final: 0.8129 (m100) REVERT: D 185 ARG cc_start: 0.8442 (mmm160) cc_final: 0.7424 (mtm180) outliers start: 19 outliers final: 13 residues processed: 107 average time/residue: 0.2273 time to fit residues: 31.0824 Evaluate side-chains 108 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 32 ARG Chi-restraints excluded: chain D residue 43 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 63 optimal weight: 40.0000 chunk 67 optimal weight: 0.0970 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 HIS D 30 ASN D 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6910 Z= 0.173 Angle : 0.616 17.465 9601 Z= 0.301 Chirality : 0.036 0.162 1096 Planarity : 0.004 0.039 1072 Dihedral : 18.294 101.050 1546 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.58 % Allowed : 25.30 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.33), residues: 707 helix: 2.51 (0.24), residues: 432 sheet: 0.02 (0.65), residues: 75 loop : -0.44 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 320 HIS 0.013 0.001 HIS D 29 PHE 0.011 0.001 PHE A 582 TYR 0.016 0.002 TYR D 141 ARG 0.007 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.660 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: symmetry clash REVERT: A 9 MET cc_start: 0.7967 (mtt) cc_final: 0.7583 (mtm) REVERT: A 29 HIS cc_start: 0.7525 (OUTLIER) cc_final: 0.7001 (t-90) REVERT: A 63 MET cc_start: 0.9102 (ptp) cc_final: 0.8455 (ptp) REVERT: A 127 LYS cc_start: 0.9432 (tmmt) cc_final: 0.9103 (tmmt) REVERT: A 138 LYS cc_start: 0.8959 (tttt) cc_final: 0.8604 (tmtt) REVERT: A 185 ARG cc_start: 0.6713 (mtm180) cc_final: 0.5930 (mtm-85) REVERT: A 208 MET cc_start: 0.8668 (mpp) cc_final: 0.8396 (mmp) REVERT: A 309 THR cc_start: 0.8612 (p) cc_final: 0.8339 (t) REVERT: A 556 ASN cc_start: 0.8838 (m-40) cc_final: 0.8284 (m110) REVERT: A 562 TYR cc_start: 0.7303 (m-80) cc_final: 0.7085 (m-80) REVERT: D 23 GLN cc_start: 0.9089 (tp40) cc_final: 0.8741 (mp10) REVERT: D 32 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8262 (ttm-80) REVERT: D 42 TYR cc_start: 0.8020 (t80) cc_final: 0.7314 (t80) REVERT: D 44 ASP cc_start: 0.9385 (m-30) cc_final: 0.9074 (p0) REVERT: D 50 TRP cc_start: 0.8327 (m100) cc_final: 0.7760 (m100) REVERT: D 159 LEU cc_start: 0.9400 (tp) cc_final: 0.9044 (pp) REVERT: D 185 ARG cc_start: 0.8399 (mmm160) cc_final: 0.7396 (mtm180) outliers start: 15 outliers final: 10 residues processed: 100 average time/residue: 0.2282 time to fit residues: 29.3421 Evaluate side-chains 95 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 32 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 50.0000 chunk 18 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 HIS D 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6910 Z= 0.191 Angle : 0.622 17.049 9601 Z= 0.306 Chirality : 0.036 0.175 1096 Planarity : 0.004 0.040 1072 Dihedral : 18.284 100.916 1546 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.41 % Allowed : 25.82 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.33), residues: 707 helix: 2.45 (0.24), residues: 431 sheet: -0.03 (0.65), residues: 75 loop : -0.47 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.013 0.001 HIS D 29 PHE 0.010 0.001 PHE A 582 TYR 0.016 0.001 TYR D 141 ARG 0.008 0.000 ARG A 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.700 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: symmetry clash REVERT: A 9 MET cc_start: 0.8017 (mtt) cc_final: 0.7611 (mtm) REVERT: A 29 HIS cc_start: 0.7585 (OUTLIER) cc_final: 0.7111 (t-90) REVERT: A 63 MET cc_start: 0.9115 (ptp) cc_final: 0.8516 (ptp) REVERT: A 104 LEU cc_start: 0.9703 (tt) cc_final: 0.9326 (mt) REVERT: A 127 LYS cc_start: 0.9450 (tmmt) cc_final: 0.9123 (tmmt) REVERT: A 138 LYS cc_start: 0.8965 (tttt) cc_final: 0.8666 (tmtt) REVERT: A 185 ARG cc_start: 0.6573 (mtm180) cc_final: 0.6192 (mtm180) REVERT: A 208 MET cc_start: 0.8706 (mpp) cc_final: 0.8437 (mmp) REVERT: A 309 THR cc_start: 0.8610 (p) cc_final: 0.8336 (t) REVERT: A 356 SER cc_start: 0.7667 (t) cc_final: 0.7393 (p) REVERT: A 556 ASN cc_start: 0.8897 (m-40) cc_final: 0.8394 (m110) REVERT: D 32 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8366 (ttm-80) REVERT: D 42 TYR cc_start: 0.8040 (t80) cc_final: 0.7339 (t80) REVERT: D 44 ASP cc_start: 0.9379 (m-30) cc_final: 0.9069 (p0) REVERT: D 50 TRP cc_start: 0.8424 (m100) cc_final: 0.7812 (m100) REVERT: D 185 ARG cc_start: 0.8399 (mmm160) cc_final: 0.7360 (mtm180) outliers start: 14 outliers final: 10 residues processed: 98 average time/residue: 0.2319 time to fit residues: 29.2484 Evaluate side-chains 96 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain D residue 32 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 HIS D 30 ASN D 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.168794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.128884 restraints weight = 13731.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.133086 restraints weight = 7243.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.135866 restraints weight = 4913.919| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6910 Z= 0.265 Angle : 0.674 16.152 9601 Z= 0.334 Chirality : 0.038 0.178 1096 Planarity : 0.004 0.039 1072 Dihedral : 18.352 100.875 1546 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.75 % Allowed : 26.51 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.89 (0.33), residues: 707 helix: 2.31 (0.25), residues: 425 sheet: -0.21 (0.65), residues: 75 loop : -0.40 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 50 HIS 0.013 0.001 HIS D 29 PHE 0.006 0.001 PHE A 582 TYR 0.015 0.002 TYR A 141 ARG 0.009 0.000 ARG A 249 =============================================================================== Job complete usr+sys time: 1499.46 seconds wall clock time: 28 minutes 2.75 seconds (1682.75 seconds total)