Starting phenix.real_space_refine on Fri Dec 27 14:30:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8grs_34214/12_2024/8grs_34214_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8grs_34214/12_2024/8grs_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_34214/12_2024/8grs_34214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8grs_34214/12_2024/8grs_34214.map" model { file = "/net/cci-nas-00/data/ceres_data/8grs_34214/12_2024/8grs_34214_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8grs_34214/12_2024/8grs_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-5532/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: 4.18, per 1000 atoms: 0.81 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: 1.55 Conformation dependent library (CDL) restraints added in 602.1 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: 0.44 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: 1.28 Time building geometry restraints manager: 1.68 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.840 ------------------------------------------------------------------------------- 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 : 0.568 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: 0.2012 time to fit residues: 82.2308 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 : 0.570 ------------------------------------------------------------------------------- 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: 1.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 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 : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5331 (mp) REVERT: A 191 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6134 (p0) REVERT: A 442 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7807 (pt) outliers start: 96 outliers final: 50 residues processed: 204 average time/residue: 0.1749 time to fit residues: 45.3334 Evaluate side-chains 179 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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 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 436 LEU Chi-restraints excluded: chain A residue 442 ILE 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 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.0070 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5283 Z= 0.234 Angle : 0.793 10.529 7163 Z= 0.398 Chirality : 0.044 0.187 815 Planarity : 0.007 0.077 869 Dihedral : 14.941 79.564 802 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.65 % Allowed : 13.80 % Favored : 85.55 % Rotamer: Outliers : 10.70 % Allowed : 28.16 % 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: -2.32 (0.32), residues: 616 helix: 0.09 (0.26), residues: 376 sheet: -4.95 (1.17), residues: 10 loop : -4.34 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 76 HIS 0.004 0.001 HIS A 247 PHE 0.014 0.001 PHE A 565 TYR 0.029 0.003 TYR A 264 ARG 0.013 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 182 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 122 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6985 (t80) outliers start: 60 outliers final: 46 residues processed: 159 average time/residue: 0.1637 time to fit residues: 33.6280 Evaluate side-chains 157 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 110 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 352 VAL Chi-restraints excluded: chain A residue 356 GLU 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 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 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 650 LEU 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 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 16 optimal weight: 0.0050 chunk 49 optimal weight: 0.3980 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.5783 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= 0.198 Angle : 0.707 9.111 7163 Z= 0.356 Chirality : 0.042 0.171 815 Planarity : 0.006 0.068 869 Dihedral : 13.450 78.190 778 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.15 % Favored : 86.53 % Rotamer: Outliers : 10.34 % Allowed : 28.16 % Favored : 61.50 % 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: -1.62 (0.34), residues: 616 helix: 0.60 (0.26), residues: 375 sheet: -3.21 (1.62), residues: 10 loop : -4.01 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 76 HIS 0.005 0.001 HIS A 247 PHE 0.013 0.001 PHE A 565 TYR 0.028 0.002 TYR A 264 ARG 0.008 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 173 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 115 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.7014 (t80) REVERT: A 458 LEU cc_start: 0.7771 (tp) cc_final: 0.7508 (tp) REVERT: A 605 TYR cc_start: 0.8153 (t80) cc_final: 0.7534 (t80) REVERT: A 650 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7702 (mp) outliers start: 58 outliers final: 39 residues processed: 151 average time/residue: 0.1714 time to fit residues: 33.5364 Evaluate side-chains 147 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 75 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 135 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 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 266 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 THR 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 517 LEU 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 650 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 672 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 34 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5283 Z= 0.317 Angle : 0.777 9.015 7163 Z= 0.389 Chirality : 0.046 0.179 815 Planarity : 0.007 0.073 869 Dihedral : 12.289 77.603 758 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.15 % Favored : 86.53 % Rotamer: Outliers : 9.45 % Allowed : 27.09 % Favored : 63.46 % 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: -1.57 (0.34), residues: 616 helix: 0.58 (0.27), residues: 379 sheet: -4.07 (1.20), residues: 15 loop : -3.88 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.008 0.001 HIS A 247 PHE 0.022 0.002 PHE A 512 TYR 0.038 0.003 TYR A 78 ARG 0.010 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 163 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 110 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.7079 (t80) REVERT: A 237 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6335 (ttm-80) REVERT: A 264 TYR cc_start: 0.5289 (p90) cc_final: 0.4805 (p90) REVERT: A 364 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6284 (pp) REVERT: A 398 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8102 (p) REVERT: A 650 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7894 (mp) outliers start: 53 outliers final: 38 residues processed: 145 average time/residue: 0.1917 time to fit residues: 35.8830 Evaluate side-chains 145 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 75 PHE 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 244 VAL Chi-restraints excluded: chain A residue 268 LYS 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 386 HIS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 511 ILE 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 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 645 VAL Chi-restraints excluded: chain A residue 650 LEU 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 690 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 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 HIS A 345 GLN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5283 Z= 0.239 Angle : 0.739 9.196 7163 Z= 0.366 Chirality : 0.044 0.169 815 Planarity : 0.006 0.071 869 Dihedral : 12.028 71.819 757 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.18 % Favored : 87.50 % Rotamer: Outliers : 9.98 % Allowed : 26.92 % Favored : 63.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.34), residues: 616 helix: 0.79 (0.27), residues: 376 sheet: -3.06 (1.72), residues: 10 loop : -3.87 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 76 HIS 0.003 0.001 HIS A 648 PHE 0.018 0.001 PHE A 512 TYR 0.027 0.002 TYR A 78 ARG 0.004 0.000 ARG A 340 *********************** 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 161 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 105 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.7061 (t80) REVERT: A 237 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6281 (ttm-80) REVERT: A 264 TYR cc_start: 0.5151 (p90) cc_final: 0.4708 (p90) REVERT: A 364 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6278 (pp) REVERT: A 605 TYR cc_start: 0.7969 (t80) cc_final: 0.7628 (t80) REVERT: A 650 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7793 (mp) outliers start: 56 outliers final: 41 residues processed: 139 average time/residue: 0.1661 time to fit residues: 30.1004 Evaluate side-chains 146 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 101 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 75 PHE 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 237 ARG Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 396 THR 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 504 THR 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 616 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 692 MET 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 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** A 648 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.6320 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= 0.247 Angle : 0.751 8.173 7163 Z= 0.369 Chirality : 0.044 0.164 815 Planarity : 0.006 0.070 869 Dihedral : 11.485 68.235 754 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.18 % Favored : 87.50 % Rotamer: Outliers : 8.91 % Allowed : 28.16 % Favored : 62.92 % 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: -1.25 (0.35), residues: 616 helix: 0.84 (0.27), residues: 377 sheet: -3.04 (1.73), residues: 10 loop : -3.78 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 76 HIS 0.005 0.001 HIS A 247 PHE 0.018 0.001 PHE A 512 TYR 0.043 0.003 TYR A 78 ARG 0.013 0.001 ARG A 340 *********************** 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 159 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.7013 (t80) REVERT: A 186 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7188 (mm) REVERT: A 237 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6227 (ttm-80) REVERT: A 264 TYR cc_start: 0.5233 (p90) cc_final: 0.4710 (p90) REVERT: A 364 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6292 (pp) REVERT: A 423 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7147 (tt) REVERT: A 503 MET cc_start: 0.7314 (tmm) cc_final: 0.7032 (ttp) REVERT: A 605 TYR cc_start: 0.7907 (t80) cc_final: 0.7655 (t80) REVERT: A 650 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7826 (mp) outliers start: 50 outliers final: 39 residues processed: 141 average time/residue: 0.1668 time to fit residues: 30.8609 Evaluate side-chains 148 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 103 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 75 PHE 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 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 356 GLU Chi-restraints excluded: chain A residue 364 LEU 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 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 616 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 708 ILE 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 11 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 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 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5283 Z= 0.227 Angle : 0.745 10.059 7163 Z= 0.368 Chirality : 0.043 0.165 815 Planarity : 0.007 0.069 869 Dihedral : 11.044 62.523 754 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.18 % Favored : 87.50 % Rotamer: Outliers : 9.45 % Allowed : 27.99 % Favored : 62.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.35), residues: 616 helix: 0.88 (0.27), residues: 377 sheet: -3.01 (1.69), residues: 10 loop : -3.66 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 76 HIS 0.003 0.001 HIS A 247 PHE 0.017 0.001 PHE A 512 TYR 0.040 0.002 TYR A 78 ARG 0.012 0.001 ARG A 340 *********************** 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 163 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 110 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6954 (t80) REVERT: A 237 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6165 (ttm-80) REVERT: A 264 TYR cc_start: 0.5183 (p90) cc_final: 0.4671 (p90) REVERT: A 364 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6307 (pp) REVERT: A 423 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7079 (tt) REVERT: A 499 ASN cc_start: 0.6340 (t0) cc_final: 0.6120 (t0) REVERT: A 503 MET cc_start: 0.7284 (tmm) cc_final: 0.6973 (ttp) REVERT: A 531 TRP cc_start: 0.7569 (OUTLIER) cc_final: 0.7324 (t60) REVERT: A 605 TYR cc_start: 0.7707 (t80) cc_final: 0.7481 (t80) REVERT: A 650 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7803 (mp) outliers start: 53 outliers final: 38 residues processed: 144 average time/residue: 0.1493 time to fit residues: 28.2058 Evaluate side-chains 143 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 75 PHE 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 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 356 GLU Chi-restraints excluded: chain A residue 364 LEU 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 504 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 650 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 690 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 24 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 0.0570 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.6690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5283 Z= 0.238 Angle : 0.761 9.583 7163 Z= 0.376 Chirality : 0.044 0.157 815 Planarity : 0.006 0.068 869 Dihedral : 10.380 59.393 746 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.50 % Favored : 87.18 % Rotamer: Outliers : 8.38 % Allowed : 29.41 % Favored : 62.21 % 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 (0.35), residues: 616 helix: 0.93 (0.27), residues: 372 sheet: -3.02 (1.70), residues: 10 loop : -3.77 (0.38), residues: 234 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 0.016 0.001 PHE A 512 TYR 0.039 0.002 TYR A 78 ARG 0.015 0.001 ARG A 340 *********************** 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 152 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6167 (ttm-80) REVERT: A 264 TYR cc_start: 0.5143 (p90) cc_final: 0.4673 (p90) REVERT: A 364 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6266 (pp) REVERT: A 423 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7052 (tt) REVERT: A 503 MET cc_start: 0.7263 (tmm) cc_final: 0.6915 (ttp) REVERT: A 531 TRP cc_start: 0.7558 (OUTLIER) cc_final: 0.7208 (t60) REVERT: A 605 TYR cc_start: 0.7670 (t80) cc_final: 0.7464 (t80) outliers start: 47 outliers final: 39 residues processed: 134 average time/residue: 0.1740 time to fit residues: 30.6270 Evaluate side-chains 145 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 75 PHE 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 364 LEU 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 504 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 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 690 LEU Chi-restraints excluded: chain A residue 692 MET 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 61 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5283 Z= 0.247 Angle : 0.783 9.885 7163 Z= 0.384 Chirality : 0.045 0.227 815 Planarity : 0.006 0.069 869 Dihedral : 10.056 59.286 743 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.50 % Favored : 87.18 % Rotamer: Outliers : 7.49 % Allowed : 29.59 % Favored : 62.92 % 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: -1.16 (0.35), residues: 616 helix: 0.88 (0.27), residues: 378 sheet: -2.90 (1.74), residues: 10 loop : -3.73 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 473 HIS 0.004 0.001 HIS A 386 PHE 0.018 0.001 PHE A 68 TYR 0.039 0.002 TYR A 78 ARG 0.010 0.001 ARG A 340 ********************** 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 148 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 75 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.7035 (t80) REVERT: A 237 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6096 (ttm-80) REVERT: A 264 TYR cc_start: 0.5036 (p90) cc_final: 0.4605 (p90) REVERT: A 364 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6270 (pp) REVERT: A 423 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7034 (tt) REVERT: A 503 MET cc_start: 0.7264 (tmm) cc_final: 0.6919 (ttp) REVERT: A 531 TRP cc_start: 0.7551 (OUTLIER) cc_final: 0.7192 (t60) outliers start: 42 outliers final: 35 residues processed: 132 average time/residue: 0.1642 time to fit residues: 28.2735 Evaluate side-chains 144 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 75 PHE 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 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 364 LEU 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 504 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 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 690 LEU Chi-restraints excluded: chain A residue 692 MET 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 13 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** 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 = 0.4188 r_free = 0.4188 target = 0.173972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129995 restraints weight = 7175.590| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.94 r_work: 0.3511 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.6955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5283 Z= 0.237 Angle : 0.780 9.330 7163 Z= 0.382 Chirality : 0.045 0.176 815 Planarity : 0.006 0.067 869 Dihedral : 9.650 57.779 739 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.34 % Favored : 87.34 % Rotamer: Outliers : 7.13 % Allowed : 30.84 % 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: -1.05 (0.36), residues: 616 helix: 0.95 (0.27), residues: 379 sheet: -2.81 (1.76), residues: 10 loop : -3.65 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 473 HIS 0.003 0.001 HIS A 247 PHE 0.019 0.001 PHE A 68 TYR 0.037 0.002 TYR A 78 ARG 0.008 0.001 ARG A 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1671.92 seconds wall clock time: 31 minutes 3.83 seconds (1863.83 seconds total)