Starting phenix.real_space_refine on Thu Mar 6 07:31:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8grs_34214/03_2025/8grs_34214_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8grs_34214/03_2025/8grs_34214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8grs_34214/03_2025/8grs_34214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8grs_34214/03_2025/8grs_34214.map" model { file = "/net/cci-nas-00/data/ceres_data/8grs_34214/03_2025/8grs_34214_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8grs_34214/03_2025/8grs_34214_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 3411 2.51 5 N 821 2.21 5 O 884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5148 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5096 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 22, 'TRANS': 603} Chain breaks: 4 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.99, per 1000 atoms: 0.78 Number of scatterers: 5148 At special positions: 0 Unit cell: (95.12, 82.82, 86.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 1 15.00 O 884 8.00 N 821 7.00 C 3411 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: 1.41 Conformation dependent library (CDL) restraints added in 645.2 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: 1198 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 64.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.899A pdb=" N SER A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 65 Processing helix chain 'A' and resid 136 through 167 Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 191 through 216 removed outlier: 4.231A pdb=" N LEU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 268 through 287 Processing helix chain 'A' and resid 321 through 350 removed outlier: 4.035A pdb=" N LYS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Proline residue: A 346 - end of helix removed outlier: 4.407A pdb=" N ALA A 350 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.333A pdb=" N PHE A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 414 through 446 Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.637A pdb=" N LEU A 458 " --> pdb=" O ILE A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 466 through 489 removed outlier: 3.799A pdb=" N LEU A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 494 through 534 Proline residue: A 518 - end of helix Processing helix chain 'A' and resid 553 through 574 Processing helix chain 'A' and resid 574 through 587 removed outlier: 6.160A pdb=" N LEU A 580 " --> pdb=" O PRO A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 599 Processing helix chain 'A' and resid 608 through 626 removed outlier: 4.121A pdb=" N ILE A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 removed outlier: 7.241A pdb=" N ILE A 630 " --> pdb=" O THR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.554A pdb=" N ILE A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR A 638 " --> pdb=" O PHE A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 689 removed outlier: 4.249A pdb=" N HIS A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Proline residue: A 675 - end of helix Processing helix chain 'A' and resid 694 through 717 285 hydrogen bonds defined for protein. 837 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: 1.34 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 763 1.27 - 1.41: 1434 1.41 - 1.54: 3010 1.54 - 1.67: 30 1.67 - 1.81: 46 Bond restraints: 5283 Sorted by residual: bond pdb=" CA ILE A 511 " pdb=" C ILE A 511 " ideal model delta sigma weight residual 1.524 1.399 0.126 1.16e-02 7.43e+03 1.17e+02 bond pdb=" C VAL A 153 " pdb=" O VAL A 153 " ideal model delta sigma weight residual 1.236 1.138 0.099 1.11e-02 8.12e+03 7.94e+01 bond pdb=" CA ALA A 562 " pdb=" C ALA A 562 " ideal model delta sigma weight residual 1.524 1.416 0.108 1.28e-02 6.10e+03 7.12e+01 bond pdb=" CA SER A 157 " pdb=" C SER A 157 " ideal model delta sigma weight residual 1.523 1.416 0.107 1.34e-02 5.57e+03 6.35e+01 bond pdb=" CA PHE A 512 " pdb=" C PHE A 512 " ideal model delta sigma weight residual 1.523 1.418 0.105 1.34e-02 5.57e+03 6.18e+01 ... (remaining 5278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 6711 3.67 - 7.34: 371 7.34 - 11.01: 63 11.01 - 14.68: 15 14.68 - 18.35: 3 Bond angle restraints: 7163 Sorted by residual: angle pdb=" C ILE A 511 " pdb=" CA ILE A 511 " pdb=" CB ILE A 511 " ideal model delta sigma weight residual 111.70 93.35 18.35 1.28e+00 6.10e-01 2.06e+02 angle pdb=" N ILE A 511 " pdb=" CA ILE A 511 " pdb=" C ILE A 511 " ideal model delta sigma weight residual 110.23 96.00 14.23 1.04e+00 9.25e-01 1.87e+02 angle pdb=" N GLU A 134 " pdb=" CA GLU A 134 " pdb=" C GLU A 134 " ideal model delta sigma weight residual 114.56 97.71 16.85 1.27e+00 6.20e-01 1.76e+02 angle pdb=" C LEU A 517 " pdb=" N PRO A 518 " pdb=" CA PRO A 518 " ideal model delta sigma weight residual 119.05 105.94 13.11 1.11e+00 8.12e-01 1.40e+02 angle pdb=" C ALA A 674 " pdb=" N PRO A 675 " pdb=" CA PRO A 675 " ideal model delta sigma weight residual 119.32 106.81 12.51 1.14e+00 7.69e-01 1.21e+02 ... (remaining 7158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 2419 21.14 - 42.27: 374 42.27 - 63.41: 283 63.41 - 84.54: 15 84.54 - 105.68: 5 Dihedral angle restraints: 3096 sinusoidal: 1249 harmonic: 1847 Sorted by residual: dihedral pdb=" C ILE A 511 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " pdb=" CB ILE A 511 " ideal model delta harmonic sigma weight residual -122.00 -97.70 -24.30 0 2.50e+00 1.60e-01 9.45e+01 dihedral pdb=" C VAL A 244 " pdb=" N VAL A 244 " pdb=" CA VAL A 244 " pdb=" CB VAL A 244 " ideal model delta harmonic sigma weight residual -122.00 -134.63 12.63 0 2.50e+00 1.60e-01 2.55e+01 dihedral pdb=" C ILE A 183 " pdb=" N ILE A 183 " pdb=" CA ILE A 183 " pdb=" CB ILE A 183 " ideal model delta harmonic sigma weight residual -122.00 -133.65 11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.111: 572 0.111 - 0.222: 176 0.222 - 0.333: 44 0.333 - 0.443: 16 0.443 - 0.554: 7 Chirality restraints: 815 Sorted by residual: chirality pdb=" CG LEU A 331 " pdb=" CB LEU A 331 " pdb=" CD1 LEU A 331 " pdb=" CD2 LEU A 331 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.67e+00 chirality pdb=" CA LEU A 517 " pdb=" N LEU A 517 " pdb=" C LEU A 517 " pdb=" CB LEU A 517 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" CA ALA A 267 " pdb=" N ALA A 267 " pdb=" C ALA A 267 " pdb=" CB ALA A 267 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.47 2.00e-01 2.50e+01 5.60e+00 ... (remaining 812 not shown) Planarity restraints: 869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 517 " 0.132 5.00e-02 4.00e+02 2.01e-01 6.48e+01 pdb=" N PRO A 518 " -0.348 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " 0.101 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " 0.115 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 162 " 0.120 5.00e-02 4.00e+02 1.78e-01 5.06e+01 pdb=" N PRO A 163 " -0.307 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " 0.103 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 674 " 0.117 5.00e-02 4.00e+02 1.70e-01 4.63e+01 pdb=" N PRO A 675 " -0.293 5.00e-02 4.00e+02 pdb=" CA PRO A 675 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 675 " 0.102 5.00e-02 4.00e+02 ... (remaining 866 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 2 2.01 - 2.73: 1139 2.73 - 3.45: 7258 3.45 - 4.18: 13447 4.18 - 4.90: 21965 Nonbonded interactions: 43811 Sorted by model distance: nonbonded pdb=" NH2 ARG A 249 " pdb=" OH TYR A 264 " model vdw 1.285 3.120 nonbonded pdb=" OG1 THR A 284 " pdb=" CB LEU A 331 " model vdw 1.475 3.440 nonbonded pdb=" OG1 THR A 284 " pdb=" CA LEU A 331 " model vdw 2.012 3.470 nonbonded pdb=" O PHE A 512 " pdb=" O MET A 513 " model vdw 2.265 3.040 nonbonded pdb=" N GLU A 134 " pdb=" N ASP A 135 " model vdw 2.273 2.560 ... (remaining 43806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.040 Set scattering table: 0.060 Process input model: 17.010 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 : 0.016 0.128 5283 Z= 1.047 Angle : 1.944 18.350 7163 Z= 1.326 Chirality : 0.128 0.554 815 Planarity : 0.015 0.201 869 Dihedral : 26.307 105.676 1898 Min Nonbonded Distance : 1.285 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 5.84 % Allowed : 21.27 % Favored : 72.89 % Rotamer: Outliers : 44.03 % Allowed : 14.44 % Favored : 41.53 % Cbeta Deviations : 1.00 % 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: -5.46 (0.26), residues: 616 helix: -2.81 (0.20), residues: 384 sheet: -5.55 (0.90), residues: 15 loop : -4.85 (0.34), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 76 HIS 0.003 0.001 HIS A 145 PHE 0.017 0.002 PHE A 565 TYR 0.016 0.002 TYR A 139 ARG 0.009 0.001 ARG A 240 *********************** 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 424 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 177 time to evaluate : 0.590 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 18 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7527 (mtm-85) REVERT: A 55 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7724 (tp) REVERT: A 212 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6715 (mtt-85) REVERT: A 224 ASN cc_start: 0.4898 (OUTLIER) cc_final: 0.4357 (m-40) REVERT: A 277 LYS cc_start: 0.6149 (OUTLIER) cc_final: 0.5314 (tmtt) REVERT: A 429 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6665 (mm) REVERT: A 583 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6740 (t80) REVERT: A 702 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7787 (tp) outliers start: 247 outliers final: 82 residues processed: 334 average time/residue: 0.2087 time to fit residues: 85.0588 Evaluate side-chains 226 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 136 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 PRO Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 675 PRO Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 0.0010 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 GLN ** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.164629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.121316 restraints weight = 6533.205| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.79 r_work: 0.3294 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5283 Z= 0.278 Angle : 0.858 11.072 7163 Z= 0.445 Chirality : 0.048 0.201 815 Planarity : 0.008 0.085 869 Dihedral : 18.185 79.076 910 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 1.14 % Allowed : 15.75 % Favored : 83.12 % Rotamer: Outliers : 17.11 % Allowed : 23.17 % Favored : 59.71 % 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: -3.33 (0.31), residues: 616 helix: -0.79 (0.24), residues: 382 sheet: -5.18 (1.10), residues: 10 loop : -4.70 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 10 HIS 0.007 0.001 HIS A 247 PHE 0.019 0.002 PHE A 68 TYR 0.017 0.002 TYR A 559 ARG 0.006 0.001 ARG A 334 *********************** 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 236 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 140 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.5184 (OUTLIER) cc_final: 0.4919 (mp) REVERT: A 76 TRP cc_start: 0.7940 (m-90) cc_final: 0.7681 (m-90) REVERT: A 78 TYR cc_start: 0.7813 (t80) cc_final: 0.7291 (t80) REVERT: A 135 ASP cc_start: 0.8152 (m-30) cc_final: 0.7835 (t0) REVERT: A 191 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.7867 (p0) REVERT: A 235 LEU cc_start: 0.7114 (mt) cc_final: 0.6866 (tp) REVERT: A 241 LYS cc_start: 0.7241 (ttmt) cc_final: 0.6861 (ttpt) REVERT: A 256 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 269 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7908 (tp) REVERT: A 281 LYS cc_start: 0.8550 (tmmt) cc_final: 0.8318 (tttt) REVERT: A 364 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8468 (pp) REVERT: A 391 TYR cc_start: 0.7605 (m-80) cc_final: 0.7387 (m-10) REVERT: A 394 LYS cc_start: 0.7625 (tmtt) cc_final: 0.7409 (tmtt) REVERT: A 405 ASP cc_start: 0.8514 (m-30) cc_final: 0.8106 (t0) REVERT: A 429 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8013 (mm) REVERT: A 490 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7110 (mt-10) REVERT: A 534 ASP cc_start: 0.9089 (m-30) cc_final: 0.8542 (m-30) REVERT: A 573 LEU cc_start: 0.8407 (tp) cc_final: 0.8203 (tp) REVERT: A 595 ARG cc_start: 0.8748 (ptp-170) cc_final: 0.8456 (ptp-170) REVERT: A 610 MET cc_start: 0.7793 (mmt) cc_final: 0.7444 (mmm) outliers start: 96 outliers final: 50 residues processed: 204 average time/residue: 0.1762 time to fit residues: 45.9760 Evaluate side-chains 184 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 PRO Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 711 CYS Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 34 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.159534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116755 restraints weight = 6871.668| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.82 r_work: 0.3314 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5283 Z= 0.242 Angle : 0.778 10.298 7163 Z= 0.392 Chirality : 0.045 0.168 815 Planarity : 0.007 0.077 869 Dihedral : 15.142 79.867 806 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.65 % Allowed : 14.29 % Favored : 85.06 % Rotamer: Outliers : 11.41 % Allowed : 28.52 % Favored : 60.07 % 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: -2.30 (0.32), residues: 616 helix: 0.12 (0.26), residues: 377 sheet: -5.09 (1.10), residues: 10 loop : -4.38 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 473 HIS 0.004 0.001 HIS A 247 PHE 0.014 0.001 PHE A 565 TYR 0.030 0.003 TYR A 507 ARG 0.007 0.001 ARG A 340 *********************** 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 204 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 140 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8093 (mt0) REVERT: A 76 TRP cc_start: 0.8019 (m-90) cc_final: 0.7197 (m100) REVERT: A 135 ASP cc_start: 0.8492 (m-30) cc_final: 0.8178 (t0) REVERT: A 174 ASP cc_start: 0.8980 (t0) cc_final: 0.8607 (t0) REVERT: A 241 LYS cc_start: 0.7216 (ttmt) cc_final: 0.6564 (ttpt) REVERT: A 269 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7992 (tp) REVERT: A 271 TYR cc_start: 0.7748 (t80) cc_final: 0.7489 (t80) REVERT: A 281 LYS cc_start: 0.8518 (tmmt) cc_final: 0.8302 (tttt) REVERT: A 364 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8546 (pp) REVERT: A 394 LYS cc_start: 0.7775 (tmtt) cc_final: 0.7572 (tmtt) REVERT: A 405 ASP cc_start: 0.8517 (m-30) cc_final: 0.8051 (t0) REVERT: A 534 ASP cc_start: 0.9156 (m-30) cc_final: 0.8633 (m-30) REVERT: A 595 ARG cc_start: 0.8774 (ptp-170) cc_final: 0.8444 (ptp-170) REVERT: A 610 MET cc_start: 0.7993 (mmt) cc_final: 0.7691 (mmm) outliers start: 64 outliers final: 47 residues processed: 176 average time/residue: 0.1684 time to fit residues: 38.3650 Evaluate side-chains 169 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 711 CYS Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 57 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 HIS A 261 GLN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.160675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117553 restraints weight = 6999.806| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.88 r_work: 0.3360 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5283 Z= 0.210 Angle : 0.710 9.441 7163 Z= 0.359 Chirality : 0.042 0.155 815 Planarity : 0.006 0.068 869 Dihedral : 13.835 78.430 784 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.66 % Favored : 87.01 % Rotamer: Outliers : 10.34 % Allowed : 29.41 % Favored : 60.25 % 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: -1.68 (0.34), residues: 616 helix: 0.57 (0.27), residues: 375 sheet: -3.55 (1.35), residues: 10 loop : -4.04 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 473 HIS 0.006 0.001 HIS A 247 PHE 0.014 0.001 PHE A 565 TYR 0.027 0.002 TYR A 264 ARG 0.009 0.001 ARG A 340 *********************** 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 186 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 128 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.8629 (m-30) cc_final: 0.8310 (t0) REVERT: A 174 ASP cc_start: 0.8987 (t0) cc_final: 0.8635 (t0) REVERT: A 237 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6255 (ttm-80) REVERT: A 241 LYS cc_start: 0.6872 (ttmt) cc_final: 0.6663 (ttmt) REVERT: A 247 HIS cc_start: 0.8185 (m90) cc_final: 0.7742 (m90) REVERT: A 249 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7735 (tpt90) REVERT: A 262 LEU cc_start: 0.8653 (mp) cc_final: 0.7864 (mt) REVERT: A 269 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8032 (tp) REVERT: A 271 TYR cc_start: 0.7717 (t80) cc_final: 0.7455 (t80) REVERT: A 340 ARG cc_start: 0.8966 (mmt-90) cc_final: 0.8569 (mmt-90) REVERT: A 364 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8551 (pp) REVERT: A 366 ASP cc_start: 0.8786 (m-30) cc_final: 0.8403 (p0) REVERT: A 394 LYS cc_start: 0.7810 (tmtt) cc_final: 0.7496 (tmtt) REVERT: A 405 ASP cc_start: 0.8334 (m-30) cc_final: 0.7888 (t0) REVERT: A 458 LEU cc_start: 0.8388 (tp) cc_final: 0.8166 (tp) REVERT: A 512 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6858 (t80) REVERT: A 534 ASP cc_start: 0.9164 (m-30) cc_final: 0.8697 (m-30) REVERT: A 595 ARG cc_start: 0.8763 (ptp-170) cc_final: 0.8411 (ptp-170) REVERT: A 610 MET cc_start: 0.7990 (mmt) cc_final: 0.7625 (mmm) REVERT: A 688 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8041 (tm) outliers start: 58 outliers final: 39 residues processed: 164 average time/residue: 0.1600 time to fit residues: 33.8533 Evaluate side-chains 165 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 0.0570 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 0.0870 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN ** A 568 ASN ** 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 = 0.3980 r_free = 0.3980 target = 0.161874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119597 restraints weight = 6942.206| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.78 r_work: 0.3373 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5283 Z= 0.200 Angle : 0.693 7.687 7163 Z= 0.349 Chirality : 0.043 0.191 815 Planarity : 0.006 0.068 869 Dihedral : 12.729 75.797 766 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.15 % Favored : 86.69 % Rotamer: Outliers : 9.45 % Allowed : 28.52 % Favored : 62.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.34), residues: 616 helix: 0.86 (0.27), residues: 374 sheet: -5.17 (1.08), residues: 10 loop : -3.94 (0.35), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 473 HIS 0.002 0.001 HIS A 456 PHE 0.014 0.001 PHE A 565 TYR 0.031 0.002 TYR A 507 ARG 0.007 0.001 ARG A 388 *********************** 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 178 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.8649 (m-30) cc_final: 0.8361 (t0) REVERT: A 174 ASP cc_start: 0.8949 (t0) cc_final: 0.8652 (t0) REVERT: A 249 ARG cc_start: 0.8290 (mtt90) cc_final: 0.7711 (tpt90) REVERT: A 262 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.7732 (mt) REVERT: A 264 TYR cc_start: 0.6371 (p90) cc_final: 0.6151 (p90) REVERT: A 269 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8091 (tp) REVERT: A 271 TYR cc_start: 0.7621 (t80) cc_final: 0.7388 (t80) REVERT: A 340 ARG cc_start: 0.9039 (mmt-90) cc_final: 0.8635 (mmt-90) REVERT: A 363 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8826 (mp) REVERT: A 366 ASP cc_start: 0.8730 (m-30) cc_final: 0.8295 (p0) REVERT: A 394 LYS cc_start: 0.7845 (tmtt) cc_final: 0.7529 (tmtt) REVERT: A 398 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8593 (p) REVERT: A 419 TRP cc_start: 0.7747 (OUTLIER) cc_final: 0.7525 (m100) REVERT: A 499 ASN cc_start: 0.7618 (t0) cc_final: 0.7255 (t0) REVERT: A 512 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6785 (t80) REVERT: A 534 ASP cc_start: 0.9083 (m-30) cc_final: 0.8720 (m-30) REVERT: A 595 ARG cc_start: 0.8773 (ptp-170) cc_final: 0.8549 (ptp-170) REVERT: A 605 TYR cc_start: 0.8553 (t80) cc_final: 0.8083 (t80) REVERT: A 610 MET cc_start: 0.7974 (mmt) cc_final: 0.7672 (mmt) REVERT: A 688 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8058 (tm) REVERT: A 705 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8762 (tt) outliers start: 53 outliers final: 35 residues processed: 157 average time/residue: 0.1720 time to fit residues: 34.7423 Evaluate side-chains 159 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.161250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114866 restraints weight = 7097.440| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.98 r_work: 0.3334 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5283 Z= 0.216 Angle : 0.693 8.261 7163 Z= 0.346 Chirality : 0.042 0.164 815 Planarity : 0.006 0.068 869 Dihedral : 12.206 70.750 761 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.50 % Favored : 87.34 % Rotamer: Outliers : 9.45 % Allowed : 28.88 % Favored : 61.68 % 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: 0.99 (0.27), residues: 373 sheet: -5.20 (1.07), residues: 10 loop : -3.80 (0.35), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 473 HIS 0.006 0.001 HIS A 247 PHE 0.014 0.001 PHE A 565 TYR 0.016 0.002 TYR A 264 ARG 0.003 0.000 ARG A 388 *********************** 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 174 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8000 (t80) cc_final: 0.7519 (t80) REVERT: A 135 ASP cc_start: 0.8718 (m-30) cc_final: 0.8438 (t0) REVERT: A 186 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7742 (mm) REVERT: A 237 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6106 (ttm-80) REVERT: A 262 LEU cc_start: 0.8602 (mp) cc_final: 0.7852 (mt) REVERT: A 264 TYR cc_start: 0.6404 (p90) cc_final: 0.6066 (p90) REVERT: A 269 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8055 (tp) REVERT: A 271 TYR cc_start: 0.7715 (t80) cc_final: 0.7474 (t80) REVERT: A 340 ARG cc_start: 0.9077 (mmt-90) cc_final: 0.8676 (mmt-90) REVERT: A 363 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8755 (mp) REVERT: A 366 ASP cc_start: 0.8738 (m-30) cc_final: 0.8317 (p0) REVERT: A 405 ASP cc_start: 0.8288 (m-30) cc_final: 0.7732 (t0) REVERT: A 423 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7560 (tt) REVERT: A 499 ASN cc_start: 0.7700 (t0) cc_final: 0.7343 (t0) REVERT: A 507 TYR cc_start: 0.8653 (t80) cc_final: 0.8279 (t80) REVERT: A 512 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6791 (t80) REVERT: A 534 ASP cc_start: 0.9088 (m-30) cc_final: 0.8708 (m-30) REVERT: A 595 ARG cc_start: 0.8761 (ptp-170) cc_final: 0.8539 (ptp-170) REVERT: A 610 MET cc_start: 0.8011 (mmt) cc_final: 0.7568 (mmm) REVERT: A 684 PHE cc_start: 0.7994 (t80) cc_final: 0.7714 (t80) outliers start: 53 outliers final: 37 residues processed: 155 average time/residue: 0.1670 time to fit residues: 33.6028 Evaluate side-chains 162 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 430 PHE Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 190 ASN ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.160077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117130 restraints weight = 6875.355| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.80 r_work: 0.3311 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5283 Z= 0.216 Angle : 0.687 8.134 7163 Z= 0.343 Chirality : 0.042 0.157 815 Planarity : 0.006 0.064 869 Dihedral : 11.677 63.943 760 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.01 % Favored : 87.66 % Rotamer: Outliers : 9.98 % Allowed : 29.59 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.35), residues: 616 helix: 1.09 (0.27), residues: 377 sheet: -5.25 (1.06), residues: 10 loop : -3.70 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 473 HIS 0.002 0.001 HIS A 456 PHE 0.013 0.001 PHE A 565 TYR 0.016 0.002 TYR A 264 ARG 0.005 0.000 ARG A 388 *********************** 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 180 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 124 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7979 (t80) cc_final: 0.7420 (t80) REVERT: A 135 ASP cc_start: 0.8705 (m-30) cc_final: 0.8424 (t0) REVERT: A 186 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.8012 (mm) REVERT: A 237 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6037 (ttm-80) REVERT: A 238 ASP cc_start: 0.7961 (m-30) cc_final: 0.7734 (m-30) REVERT: A 262 LEU cc_start: 0.8452 (mp) cc_final: 0.8173 (mp) REVERT: A 264 TYR cc_start: 0.6395 (p90) cc_final: 0.5777 (p90) REVERT: A 269 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8039 (tp) REVERT: A 271 TYR cc_start: 0.7687 (t80) cc_final: 0.7449 (t80) REVERT: A 340 ARG cc_start: 0.9107 (mmt-90) cc_final: 0.8681 (mmt-90) REVERT: A 363 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8723 (mp) REVERT: A 366 ASP cc_start: 0.8728 (m-30) cc_final: 0.8324 (p0) REVERT: A 405 ASP cc_start: 0.8192 (m-30) cc_final: 0.7778 (t70) REVERT: A 423 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7533 (tt) REVERT: A 499 ASN cc_start: 0.7689 (t0) cc_final: 0.7356 (t0) REVERT: A 507 TYR cc_start: 0.8604 (t80) cc_final: 0.7665 (t80) REVERT: A 512 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.6799 (t80) REVERT: A 531 TRP cc_start: 0.8155 (OUTLIER) cc_final: 0.7187 (t60) REVERT: A 534 ASP cc_start: 0.9082 (m-30) cc_final: 0.8701 (m-30) REVERT: A 593 ASP cc_start: 0.8460 (t0) cc_final: 0.8062 (t70) REVERT: A 595 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8539 (ptp-170) REVERT: A 670 GLN cc_start: 0.8848 (mt0) cc_final: 0.8002 (mt0) REVERT: A 684 PHE cc_start: 0.7954 (t80) cc_final: 0.7709 (t80) REVERT: A 688 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8203 (tm) REVERT: A 705 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8761 (tt) outliers start: 56 outliers final: 35 residues processed: 159 average time/residue: 0.1537 time to fit residues: 32.2610 Evaluate side-chains 160 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 430 PHE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN A 648 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.158071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115600 restraints weight = 6963.233| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.78 r_work: 0.3316 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5283 Z= 0.256 Angle : 0.722 7.857 7163 Z= 0.362 Chirality : 0.043 0.153 815 Planarity : 0.006 0.063 869 Dihedral : 10.920 59.588 757 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.99 % Favored : 86.85 % Rotamer: Outliers : 9.09 % Allowed : 29.77 % Favored : 61.14 % 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: -0.97 (0.35), residues: 616 helix: 1.10 (0.27), residues: 377 sheet: -5.32 (1.11), residues: 10 loop : -3.61 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.003 0.001 HIS A 247 PHE 0.014 0.001 PHE A 565 TYR 0.015 0.002 TYR A 264 ARG 0.005 0.000 ARG A 388 *********************** 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 164 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 113 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 TRP cc_start: 0.7869 (m-90) cc_final: 0.7331 (m100) REVERT: A 78 TYR cc_start: 0.8176 (t80) cc_final: 0.7545 (t80) REVERT: A 135 ASP cc_start: 0.8784 (m-30) cc_final: 0.8459 (t0) REVERT: A 237 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6019 (ttm-80) REVERT: A 262 LEU cc_start: 0.8555 (mp) cc_final: 0.8272 (mt) REVERT: A 264 TYR cc_start: 0.6141 (p90) cc_final: 0.5788 (p90) REVERT: A 269 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8043 (tp) REVERT: A 271 TYR cc_start: 0.7662 (t80) cc_final: 0.7429 (t80) REVERT: A 287 THR cc_start: 0.7264 (OUTLIER) cc_final: 0.7015 (p) REVERT: A 340 ARG cc_start: 0.9133 (mmt-90) cc_final: 0.8658 (mmt-90) REVERT: A 363 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8726 (mp) REVERT: A 366 ASP cc_start: 0.8708 (m-30) cc_final: 0.8311 (p0) REVERT: A 423 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7637 (tt) REVERT: A 499 ASN cc_start: 0.7725 (t0) cc_final: 0.7361 (t0) REVERT: A 512 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6775 (t80) REVERT: A 531 TRP cc_start: 0.8241 (OUTLIER) cc_final: 0.7234 (t60) REVERT: A 593 ASP cc_start: 0.8482 (t0) cc_final: 0.8096 (t70) REVERT: A 610 MET cc_start: 0.8096 (mmt) cc_final: 0.7815 (mmm) REVERT: A 624 TYR cc_start: 0.8163 (m-80) cc_final: 0.7962 (m-10) REVERT: A 670 GLN cc_start: 0.8918 (mt0) cc_final: 0.8532 (mt0) outliers start: 51 outliers final: 37 residues processed: 142 average time/residue: 0.1602 time to fit residues: 29.7470 Evaluate side-chains 153 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 430 PHE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.162220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117087 restraints weight = 7002.746| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.94 r_work: 0.3328 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.6613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5283 Z= 0.212 Angle : 0.706 9.080 7163 Z= 0.350 Chirality : 0.042 0.154 815 Planarity : 0.005 0.061 869 Dihedral : 10.348 59.349 749 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.50 % Favored : 87.34 % Rotamer: Outliers : 7.84 % Allowed : 31.19 % Favored : 60.96 % 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: -0.84 (0.35), residues: 616 helix: 1.18 (0.27), residues: 379 sheet: -5.18 (1.20), residues: 10 loop : -3.55 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.002 0.001 HIS A 386 PHE 0.013 0.001 PHE A 565 TYR 0.022 0.002 TYR A 683 ARG 0.006 0.000 ARG A 388 *********************** 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 155 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8026 (t80) cc_final: 0.7279 (t80) REVERT: A 135 ASP cc_start: 0.8733 (m-30) cc_final: 0.8269 (t0) REVERT: A 191 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8139 (p0) REVERT: A 237 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6046 (ttm-80) REVERT: A 262 LEU cc_start: 0.8544 (mp) cc_final: 0.8261 (mp) REVERT: A 264 TYR cc_start: 0.6147 (p90) cc_final: 0.5789 (p90) REVERT: A 269 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8024 (tp) REVERT: A 271 TYR cc_start: 0.7676 (t80) cc_final: 0.7430 (t80) REVERT: A 327 MET cc_start: 0.6150 (ptm) cc_final: 0.5109 (mtt) REVERT: A 340 ARG cc_start: 0.9110 (mmt-90) cc_final: 0.8628 (mmt-90) REVERT: A 363 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8731 (mp) REVERT: A 366 ASP cc_start: 0.8694 (m-30) cc_final: 0.8295 (p0) REVERT: A 405 ASP cc_start: 0.8346 (t0) cc_final: 0.7907 (t70) REVERT: A 423 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7588 (tt) REVERT: A 499 ASN cc_start: 0.7713 (t0) cc_final: 0.7345 (t0) REVERT: A 512 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6825 (t80) REVERT: A 531 TRP cc_start: 0.8253 (OUTLIER) cc_final: 0.7245 (t60) REVERT: A 610 MET cc_start: 0.7993 (mmt) cc_final: 0.7738 (mmm) REVERT: A 670 GLN cc_start: 0.8847 (mt0) cc_final: 0.8466 (mt0) REVERT: A 684 PHE cc_start: 0.8084 (t80) cc_final: 0.7836 (t80) REVERT: A 705 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8763 (tt) outliers start: 44 outliers final: 34 residues processed: 135 average time/residue: 0.1703 time to fit residues: 29.7129 Evaluate side-chains 149 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 430 PHE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 43 optimal weight: 0.0980 chunk 32 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.161726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.118651 restraints weight = 6910.202| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.81 r_work: 0.3317 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5283 Z= 0.203 Angle : 0.701 8.853 7163 Z= 0.346 Chirality : 0.042 0.153 815 Planarity : 0.006 0.059 869 Dihedral : 10.163 63.052 749 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.82 % Favored : 87.01 % Rotamer: Outliers : 7.84 % Allowed : 31.73 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.36), residues: 616 helix: 1.29 (0.27), residues: 379 sheet: -5.13 (1.25), residues: 10 loop : -3.49 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.002 0.001 HIS A 247 PHE 0.013 0.001 PHE A 565 TYR 0.021 0.002 TYR A 683 ARG 0.009 0.001 ARG A 388 ********************** 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 157 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7956 (t80) cc_final: 0.7168 (t80) REVERT: A 135 ASP cc_start: 0.8727 (m-30) cc_final: 0.8408 (t0) REVERT: A 187 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: A 191 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8293 (p0) REVERT: A 237 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6026 (ttm-80) REVERT: A 252 TYR cc_start: 0.5733 (m-80) cc_final: 0.5410 (m-80) REVERT: A 262 LEU cc_start: 0.8489 (mp) cc_final: 0.7820 (mt) REVERT: A 264 TYR cc_start: 0.6112 (p90) cc_final: 0.5757 (p90) REVERT: A 269 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8009 (tp) REVERT: A 271 TYR cc_start: 0.7670 (t80) cc_final: 0.7420 (t80) REVERT: A 327 MET cc_start: 0.6103 (ptm) cc_final: 0.5087 (mtt) REVERT: A 340 ARG cc_start: 0.9106 (mmt-90) cc_final: 0.8675 (mmt-90) REVERT: A 343 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8682 (mm-40) REVERT: A 363 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8716 (mp) REVERT: A 366 ASP cc_start: 0.8669 (m-30) cc_final: 0.8266 (p0) REVERT: A 405 ASP cc_start: 0.8122 (t0) cc_final: 0.7874 (t70) REVERT: A 423 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7564 (tt) REVERT: A 499 ASN cc_start: 0.7654 (t0) cc_final: 0.7290 (t0) REVERT: A 512 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6742 (t80) REVERT: A 531 TRP cc_start: 0.8197 (OUTLIER) cc_final: 0.7255 (t60) REVERT: A 610 MET cc_start: 0.7863 (mmt) cc_final: 0.7608 (mmm) REVERT: A 670 GLN cc_start: 0.8813 (mt0) cc_final: 0.8361 (mt0) REVERT: A 684 PHE cc_start: 0.7945 (t80) cc_final: 0.7701 (t80) REVERT: A 688 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8238 (tm) outliers start: 44 outliers final: 29 residues processed: 138 average time/residue: 0.1880 time to fit residues: 34.1561 Evaluate side-chains 144 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 430 PHE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.0470 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 0.0370 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 247 HIS ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.162446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119553 restraints weight = 6981.426| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.84 r_work: 0.3333 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5283 Z= 0.200 Angle : 0.696 7.833 7163 Z= 0.346 Chirality : 0.042 0.151 815 Planarity : 0.005 0.059 869 Dihedral : 9.880 67.697 747 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.01 % Favored : 87.82 % Rotamer: Outliers : 7.49 % Allowed : 31.91 % Favored : 60.61 % 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 (0.36), residues: 616 helix: 1.38 (0.27), residues: 379 sheet: -4.06 (1.24), residues: 15 loop : -3.49 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.002 0.001 HIS A 386 PHE 0.012 0.001 PHE A 565 TYR 0.021 0.002 TYR A 683 ARG 0.008 0.001 ARG A 595 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2957.47 seconds wall clock time: 51 minutes 31.08 seconds (3091.08 seconds total)