Starting phenix.real_space_refine on Fri Aug 22 15:51:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8grs_34214/08_2025/8grs_34214_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8grs_34214/08_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_34214/08_2025/8grs_34214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8grs_34214/08_2025/8grs_34214.map" model { file = "/net/cci-nas-00/data/ceres_data/8grs_34214/08_2025/8grs_34214_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8grs_34214/08_2025/8grs_34214_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.12, per 1000 atoms: 0.22 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: 0.34 Conformation dependent library (CDL) restraints added in 131.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.12 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: 0.73 Time building geometry restraints manager: 0.46 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: 2.150 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.600 ------------------------------------------------------------------------------- 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= 1.204 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG A 240 TYR 0.016 0.002 TYR A 139 PHE 0.017 0.002 PHE A 565 TRP 0.014 0.002 TRP A 76 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.01619 ( 5283) covalent geometry : angle 1.94402 ( 7163) hydrogen bonds : bond 0.15014 ( 285) hydrogen bonds : angle 8.61139 ( 837) *********************** 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 : 0.201 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: 0.0909 time to fit residues: 37.4083 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 : 0.139 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.159086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115856 restraints weight = 6808.155| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.86 r_work: 0.3283 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5283 Z= 0.224 Angle : 0.874 11.212 7163 Z= 0.451 Chirality : 0.048 0.199 815 Planarity : 0.008 0.086 869 Dihedral : 18.236 80.186 910 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 1.14 % Allowed : 15.75 % Favored : 83.12 % Rotamer: Outliers : 17.29 % Allowed : 22.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.34 (0.31), residues: 616 helix: -0.79 (0.24), residues: 381 sheet: -5.15 (1.09), residues: 10 loop : -4.70 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 334 TYR 0.018 0.002 TYR A 559 PHE 0.021 0.002 PHE A 68 TRP 0.010 0.001 TRP A 10 HIS 0.009 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 5283) covalent geometry : angle 0.87396 ( 7163) hydrogen bonds : bond 0.04993 ( 285) hydrogen bonds : angle 6.08090 ( 837) *********************** 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 237 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 140 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.5202 (OUTLIER) cc_final: 0.4941 (mp) REVERT: A 76 TRP cc_start: 0.8005 (m-90) cc_final: 0.7756 (m-90) REVERT: A 78 TYR cc_start: 0.8016 (t80) cc_final: 0.7669 (t80) REVERT: A 135 ASP cc_start: 0.8310 (m-30) cc_final: 0.8010 (t0) REVERT: A 235 LEU cc_start: 0.7155 (mt) cc_final: 0.6921 (tp) REVERT: A 240 ARG cc_start: 0.6170 (ptp-110) cc_final: 0.5966 (ptp-110) REVERT: A 241 LYS cc_start: 0.7291 (ttmt) cc_final: 0.6956 (ttpt) REVERT: A 252 TYR cc_start: 0.5258 (m-80) cc_final: 0.4957 (m-80) REVERT: A 256 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 269 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7922 (tp) REVERT: A 281 LYS cc_start: 0.8569 (tmmt) cc_final: 0.8329 (tttt) REVERT: A 338 GLU cc_start: 0.8658 (tt0) cc_final: 0.8153 (tm-30) REVERT: A 342 VAL cc_start: 0.8953 (t) cc_final: 0.8603 (t) REVERT: A 364 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8502 (pp) REVERT: A 391 TYR cc_start: 0.7581 (m-80) cc_final: 0.7352 (m-10) REVERT: A 394 LYS cc_start: 0.7634 (tmtt) cc_final: 0.7416 (tmtt) REVERT: A 405 ASP cc_start: 0.8559 (m-30) cc_final: 0.8150 (t0) REVERT: A 429 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8109 (mm) REVERT: A 490 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7179 (mt-10) REVERT: A 534 ASP cc_start: 0.9135 (m-30) cc_final: 0.8752 (m-30) REVERT: A 595 ARG cc_start: 0.8753 (ptp-170) cc_final: 0.8427 (ptp-170) REVERT: A 610 MET cc_start: 0.7937 (mmt) cc_final: 0.7581 (mmm) outliers start: 97 outliers final: 53 residues processed: 207 average time/residue: 0.0723 time to fit residues: 19.4908 Evaluate side-chains 188 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 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 195 LEU 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 476 SER 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 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 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 36 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.157896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115331 restraints weight = 6895.239| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.82 r_work: 0.3300 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5283 Z= 0.189 Angle : 0.773 9.943 7163 Z= 0.390 Chirality : 0.044 0.169 815 Planarity : 0.007 0.077 869 Dihedral : 15.160 79.428 807 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.65 % Allowed : 14.61 % Favored : 84.74 % Rotamer: Outliers : 11.41 % Allowed : 26.74 % Favored : 61.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.32), residues: 616 helix: 0.01 (0.25), residues: 378 sheet: -5.18 (1.06), residues: 10 loop : -4.35 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 340 TYR 0.030 0.002 TYR A 264 PHE 0.015 0.001 PHE A 565 TRP 0.007 0.001 TRP A 473 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 5283) covalent geometry : angle 0.77319 ( 7163) hydrogen bonds : bond 0.04582 ( 285) hydrogen bonds : angle 5.70893 ( 837) *********************** 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 202 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 138 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: A 76 TRP cc_start: 0.7991 (m-90) cc_final: 0.7189 (m100) REVERT: A 78 TYR cc_start: 0.8175 (t80) cc_final: 0.7719 (t80) REVERT: A 135 ASP cc_start: 0.8614 (m-30) cc_final: 0.8265 (t0) REVERT: A 174 ASP cc_start: 0.8985 (t0) cc_final: 0.8616 (t0) REVERT: A 241 LYS cc_start: 0.7227 (ttmt) cc_final: 0.6869 (ttpt) REVERT: A 262 LEU cc_start: 0.8645 (mp) cc_final: 0.8186 (mp) REVERT: A 263 CYS cc_start: 0.7856 (m) cc_final: 0.6567 (t) REVERT: A 269 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7986 (tp) REVERT: A 271 TYR cc_start: 0.7751 (t80) cc_final: 0.7500 (t80) REVERT: A 338 GLU cc_start: 0.8612 (tt0) cc_final: 0.8393 (tm-30) REVERT: A 364 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8536 (pp) REVERT: A 405 ASP cc_start: 0.8525 (m-30) cc_final: 0.8061 (t0) REVERT: A 507 TYR cc_start: 0.8493 (t80) cc_final: 0.8250 (t80) REVERT: A 534 ASP cc_start: 0.9203 (m-30) cc_final: 0.8611 (m-30) REVERT: A 595 ARG cc_start: 0.8782 (ptp-170) cc_final: 0.8465 (ptp-170) REVERT: A 610 MET cc_start: 0.7989 (mmt) cc_final: 0.7659 (mmm) REVERT: A 670 GLN cc_start: 0.8977 (mt0) cc_final: 0.8421 (mt0) outliers start: 64 outliers final: 44 residues processed: 175 average time/residue: 0.0603 time to fit residues: 13.9153 Evaluate side-chains 167 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 120 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 55 LEU 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 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 189 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TYR 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 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 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 496 SER 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 603 PHE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 17 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 HIS ** 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 = 0.3966 r_free = 0.3966 target = 0.159016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.116794 restraints weight = 6871.498| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.68 r_work: 0.3352 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5637 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= 0.170 Angle : 0.741 9.331 7163 Z= 0.373 Chirality : 0.043 0.156 815 Planarity : 0.006 0.070 869 Dihedral : 13.600 77.305 776 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.99 % Favored : 86.69 % Rotamer: Outliers : 10.16 % Allowed : 27.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.33), residues: 616 helix: 0.35 (0.26), residues: 383 sheet: -5.36 (0.96), residues: 10 loop : -4.10 (0.34), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 340 TYR 0.030 0.002 TYR A 264 PHE 0.014 0.001 PHE A 565 TRP 0.010 0.001 TRP A 473 HIS 0.015 0.002 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 5283) covalent geometry : angle 0.74109 ( 7163) hydrogen bonds : bond 0.04303 ( 285) hydrogen bonds : angle 5.44939 ( 837) *********************** 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: 57 poor density : 129 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: A 76 TRP cc_start: 0.8023 (m-90) cc_final: 0.7555 (m100) REVERT: A 78 TYR cc_start: 0.8219 (t80) cc_final: 0.7605 (t80) REVERT: A 135 ASP cc_start: 0.8603 (m-30) cc_final: 0.8313 (t0) REVERT: A 174 ASP cc_start: 0.9000 (t0) cc_final: 0.8659 (t0) REVERT: A 241 LYS cc_start: 0.7070 (ttmt) cc_final: 0.6598 (ttmt) REVERT: A 247 HIS cc_start: 0.8142 (m-70) cc_final: 0.7729 (m-70) REVERT: A 249 ARG cc_start: 0.8052 (mtt90) cc_final: 0.7458 (tpt90) REVERT: A 263 CYS cc_start: 0.7925 (m) cc_final: 0.6558 (t) REVERT: A 264 TYR cc_start: 0.6574 (p90) cc_final: 0.5914 (p90) REVERT: A 269 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8044 (tp) REVERT: A 271 TYR cc_start: 0.7711 (t80) cc_final: 0.7079 (t80) REVERT: A 338 GLU cc_start: 0.8602 (tt0) cc_final: 0.8400 (tm-30) REVERT: A 340 ARG cc_start: 0.8905 (mmt-90) cc_final: 0.8627 (mmt-90) REVERT: A 366 ASP cc_start: 0.8800 (m-30) cc_final: 0.8400 (p0) REVERT: A 405 ASP cc_start: 0.8420 (m-30) cc_final: 0.7953 (t0) REVERT: A 534 ASP cc_start: 0.9188 (m-30) cc_final: 0.8671 (m-30) REVERT: A 595 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8543 (ptp-170) REVERT: A 610 MET cc_start: 0.8079 (mmt) cc_final: 0.7713 (mmm) REVERT: A 646 ASP cc_start: 0.8543 (m-30) cc_final: 0.8265 (m-30) REVERT: A 650 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8599 (mp) outliers start: 57 outliers final: 44 residues processed: 161 average time/residue: 0.0666 time to fit residues: 14.0870 Evaluate side-chains 164 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 116 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 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 141 SER 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 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 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 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 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 566 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 595 ARG 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 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 143 GLN A 185 ASN A 190 ASN A 247 HIS ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS A 670 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.161692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119370 restraints weight = 7028.186| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.75 r_work: 0.3394 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.6002 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= 0.153 Angle : 0.703 8.663 7163 Z= 0.354 Chirality : 0.043 0.149 815 Planarity : 0.006 0.062 869 Dihedral : 12.952 71.627 767 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.15 % Favored : 86.69 % Rotamer: Outliers : 9.80 % Allowed : 27.81 % Favored : 62.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.34), residues: 616 helix: 0.79 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -3.90 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 340 TYR 0.027 0.002 TYR A 264 PHE 0.014 0.001 PHE A 565 TRP 0.009 0.001 TRP A 473 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5283) covalent geometry : angle 0.70251 ( 7163) hydrogen bonds : bond 0.04126 ( 285) hydrogen bonds : angle 5.27492 ( 837) *********************** 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 180 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 125 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 TRP cc_start: 0.7970 (m-90) cc_final: 0.7461 (m100) REVERT: A 78 TYR cc_start: 0.8315 (t80) cc_final: 0.7701 (t80) REVERT: A 135 ASP cc_start: 0.8618 (m-30) cc_final: 0.8381 (t0) REVERT: A 174 ASP cc_start: 0.9019 (t0) cc_final: 0.8708 (t0) REVERT: A 237 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6090 (ttm-80) REVERT: A 247 HIS cc_start: 0.7850 (m90) cc_final: 0.7633 (m-70) REVERT: A 249 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7805 (tpt90) REVERT: A 262 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8212 (mt) REVERT: A 269 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8000 (tp) REVERT: A 338 GLU cc_start: 0.8580 (tt0) cc_final: 0.8365 (tm-30) REVERT: A 340 ARG cc_start: 0.9006 (mmt-90) cc_final: 0.8577 (mmt-90) REVERT: A 363 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8805 (mp) REVERT: A 366 ASP cc_start: 0.8762 (m-30) cc_final: 0.8335 (p0) REVERT: A 398 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8729 (p) REVERT: A 405 ASP cc_start: 0.8355 (m-30) cc_final: 0.7869 (t0) REVERT: A 406 ILE cc_start: 0.8979 (tt) cc_final: 0.8627 (tt) REVERT: A 499 ASN cc_start: 0.7741 (t0) cc_final: 0.7384 (t0) REVERT: A 595 ARG cc_start: 0.8768 (ptp-170) cc_final: 0.8549 (ptp-170) REVERT: A 605 TYR cc_start: 0.8649 (t80) cc_final: 0.8231 (t80) REVERT: A 610 MET cc_start: 0.8095 (mmt) cc_final: 0.7605 (mmm) REVERT: A 624 TYR cc_start: 0.8175 (m-80) cc_final: 0.7909 (m-80) REVERT: A 650 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8573 (mp) REVERT: A 688 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8152 (tm) outliers start: 55 outliers final: 36 residues processed: 159 average time/residue: 0.0707 time to fit residues: 14.6661 Evaluate side-chains 157 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 156 LEU 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 185 ASN 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 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 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 455 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 645 VAL 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 711 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 2 optimal weight: 0.0570 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.161925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119013 restraints weight = 7016.004| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.82 r_work: 0.3352 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.6235 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= 0.149 Angle : 0.697 8.104 7163 Z= 0.348 Chirality : 0.042 0.179 815 Planarity : 0.006 0.059 869 Dihedral : 12.017 65.286 759 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.82 % Favored : 87.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.34), residues: 616 helix: 0.93 (0.27), residues: 376 sheet: -4.21 (1.10), residues: 15 loop : -3.80 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 388 TYR 0.059 0.002 TYR A 507 PHE 0.016 0.001 PHE A 701 TRP 0.009 0.001 TRP A 422 HIS 0.003 0.001 HIS A 648 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5283) covalent geometry : angle 0.69746 ( 7163) hydrogen bonds : bond 0.04024 ( 285) hydrogen bonds : angle 5.22031 ( 837) *********************** 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 176 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 120 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8297 (t80) cc_final: 0.7578 (t80) REVERT: A 135 ASP cc_start: 0.8671 (m-30) cc_final: 0.8417 (t0) REVERT: A 174 ASP cc_start: 0.8948 (t0) cc_final: 0.8685 (t0) REVERT: A 237 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.5844 (ttm-80) REVERT: A 249 ARG cc_start: 0.8221 (mtt90) cc_final: 0.7712 (tpt90) REVERT: A 269 LEU cc_start: 0.8453 (tp) cc_final: 0.8088 (tp) REVERT: A 340 ARG cc_start: 0.9055 (mmt-90) cc_final: 0.8647 (mmt-90) REVERT: A 363 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8759 (mp) REVERT: A 366 ASP cc_start: 0.8751 (m-30) cc_final: 0.8323 (p0) REVERT: A 405 ASP cc_start: 0.8285 (m-30) cc_final: 0.7943 (t70) REVERT: A 406 ILE cc_start: 0.8917 (tt) cc_final: 0.8588 (tt) REVERT: A 499 ASN cc_start: 0.7684 (t0) cc_final: 0.7321 (t0) REVERT: A 507 TYR cc_start: 0.8648 (t80) cc_final: 0.8259 (t80) REVERT: A 534 ASP cc_start: 0.9094 (m-30) cc_final: 0.8722 (m-30) REVERT: A 593 ASP cc_start: 0.8436 (t0) cc_final: 0.8068 (t70) REVERT: A 595 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8540 (ptp-170) REVERT: A 605 TYR cc_start: 0.8501 (t80) cc_final: 0.8177 (t80) REVERT: A 610 MET cc_start: 0.8034 (mmt) cc_final: 0.7639 (mmm) REVERT: A 650 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8592 (mp) REVERT: A 684 PHE cc_start: 0.8036 (t80) cc_final: 0.7774 (t80) outliers start: 56 outliers final: 40 residues processed: 153 average time/residue: 0.0714 time to fit residues: 14.3066 Evaluate side-chains 152 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 156 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 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 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 501 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 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 645 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 655 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 705 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 26 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 670 GLN ** 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 = 0.3968 r_free = 0.3968 target = 0.160871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117776 restraints weight = 6996.176| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.83 r_work: 0.3298 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5283 Z= 0.158 Angle : 0.709 8.314 7163 Z= 0.355 Chirality : 0.043 0.169 815 Planarity : 0.005 0.057 869 Dihedral : 11.401 62.720 758 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.34 % Favored : 87.34 % Rotamer: Outliers : 9.63 % Allowed : 28.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.35), residues: 616 helix: 1.00 (0.27), residues: 377 sheet: -4.16 (1.13), residues: 15 loop : -3.75 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 330 TYR 0.028 0.002 TYR A 507 PHE 0.013 0.001 PHE A 701 TRP 0.009 0.001 TRP A 473 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5283) covalent geometry : angle 0.70918 ( 7163) hydrogen bonds : bond 0.04099 ( 285) hydrogen bonds : angle 5.19646 ( 837) *********************** 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 171 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 117 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8323 (t80) cc_final: 0.7607 (t80) REVERT: A 135 ASP cc_start: 0.8706 (m-30) cc_final: 0.8267 (t0) REVERT: A 237 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.5745 (ttm-80) REVERT: A 264 TYR cc_start: 0.6372 (p90) cc_final: 0.6069 (p90) REVERT: A 269 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8044 (tp) REVERT: A 275 GLU cc_start: 0.8585 (tt0) cc_final: 0.7961 (mt-10) REVERT: A 340 ARG cc_start: 0.9068 (mmt-90) cc_final: 0.8630 (mmt-90) REVERT: A 363 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 366 ASP cc_start: 0.8739 (m-30) cc_final: 0.8322 (p0) REVERT: A 405 ASP cc_start: 0.8200 (m-30) cc_final: 0.7829 (t70) REVERT: A 499 ASN cc_start: 0.7673 (t0) cc_final: 0.7322 (t0) REVERT: A 531 TRP cc_start: 0.8178 (OUTLIER) cc_final: 0.7151 (t60) REVERT: A 534 ASP cc_start: 0.9088 (m-30) cc_final: 0.8699 (m-30) REVERT: A 593 ASP cc_start: 0.8481 (t0) cc_final: 0.8086 (t70) REVERT: A 595 ARG cc_start: 0.8775 (ptp-170) cc_final: 0.8571 (ptp-170) REVERT: A 610 MET cc_start: 0.8024 (mmt) cc_final: 0.7591 (mmm) REVERT: A 650 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8547 (mp) REVERT: A 660 GLU cc_start: 0.8045 (mp0) cc_final: 0.7710 (mp0) REVERT: A 670 GLN cc_start: 0.8641 (mt0) cc_final: 0.8417 (mm-40) REVERT: A 684 PHE cc_start: 0.7983 (t80) cc_final: 0.7733 (t80) REVERT: A 688 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8220 (tm) outliers start: 54 outliers final: 39 residues processed: 147 average time/residue: 0.0634 time to fit residues: 12.4414 Evaluate side-chains 159 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 141 SER Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 156 LEU 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 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 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 501 ILE Chi-restraints excluded: chain A residue 514 VAL 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 645 VAL Chi-restraints excluded: chain A residue 650 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 0.0050 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.0570 chunk 29 optimal weight: 0.0570 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 0.0170 chunk 21 optimal weight: 0.8980 overall best weight: 0.1468 ------------------------------------------------------------------------------- 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 247 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.166775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.125288 restraints weight = 6836.483| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.81 r_work: 0.3405 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.6877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5283 Z= 0.133 Angle : 0.699 7.215 7163 Z= 0.348 Chirality : 0.041 0.163 815 Planarity : 0.005 0.055 869 Dihedral : 10.442 64.621 754 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.66 % Favored : 87.01 % Rotamer: Outliers : 8.02 % Allowed : 30.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.35), residues: 616 helix: 1.32 (0.27), residues: 375 sheet: -3.86 (1.23), residues: 15 loop : -3.59 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 249 TYR 0.026 0.002 TYR A 507 PHE 0.015 0.001 PHE A 701 TRP 0.010 0.001 TRP A 613 HIS 0.006 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 5283) covalent geometry : angle 0.69883 ( 7163) hydrogen bonds : bond 0.03752 ( 285) hydrogen bonds : angle 5.03032 ( 837) *********************** 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 169 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.7953 (mm) cc_final: 0.7670 (mm) REVERT: A 78 TYR cc_start: 0.8161 (t80) cc_final: 0.7371 (t80) REVERT: A 135 ASP cc_start: 0.8497 (m-30) cc_final: 0.8232 (t0) REVERT: A 191 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8206 (p0) REVERT: A 237 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.5690 (ttm-80) REVERT: A 264 TYR cc_start: 0.6188 (p90) cc_final: 0.5599 (p90) REVERT: A 269 LEU cc_start: 0.8466 (tp) cc_final: 0.8128 (tp) REVERT: A 275 GLU cc_start: 0.8565 (tt0) cc_final: 0.7979 (mt-10) REVERT: A 340 ARG cc_start: 0.9064 (mmt-90) cc_final: 0.8602 (mmt-90) REVERT: A 363 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8695 (mp) REVERT: A 366 ASP cc_start: 0.8671 (m-30) cc_final: 0.8276 (p0) REVERT: A 388 ARG cc_start: 0.8434 (mmm160) cc_final: 0.8131 (mmm160) REVERT: A 423 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7566 (tt) REVERT: A 499 ASN cc_start: 0.7614 (t0) cc_final: 0.7246 (t0) REVERT: A 503 MET cc_start: 0.8673 (tmm) cc_final: 0.8458 (ttp) REVERT: A 531 TRP cc_start: 0.8088 (OUTLIER) cc_final: 0.7357 (t60) REVERT: A 534 ASP cc_start: 0.9031 (m-30) cc_final: 0.8664 (m-30) REVERT: A 543 ARG cc_start: 0.8651 (mtp180) cc_final: 0.8194 (mtp85) REVERT: A 593 ASP cc_start: 0.8477 (t0) cc_final: 0.8099 (t70) REVERT: A 595 ARG cc_start: 0.8765 (ptp-170) cc_final: 0.8563 (ptp-170) REVERT: A 610 MET cc_start: 0.7865 (mmt) cc_final: 0.7461 (mmm) REVERT: A 650 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8384 (mp) REVERT: A 670 GLN cc_start: 0.8466 (mt0) cc_final: 0.8207 (mm-40) REVERT: A 684 PHE cc_start: 0.7978 (t80) cc_final: 0.7749 (t80) REVERT: A 688 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8144 (tm) outliers start: 45 outliers final: 27 residues processed: 151 average time/residue: 0.0634 time to fit residues: 12.5699 Evaluate side-chains 154 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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 71 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 237 ARG Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 433 LEU 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 514 VAL 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 648 HIS ** A 670 GLN ** 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 = 0.3941 r_free = 0.3941 target = 0.158006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115003 restraints weight = 7022.393| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.86 r_work: 0.3265 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.6689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5283 Z= 0.200 Angle : 0.749 8.122 7163 Z= 0.375 Chirality : 0.044 0.162 815 Planarity : 0.005 0.053 869 Dihedral : 10.138 68.097 747 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.99 % Favored : 86.69 % Rotamer: Outliers : 6.77 % Allowed : 31.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.35), residues: 616 helix: 1.12 (0.27), residues: 380 sheet: -3.87 (1.24), residues: 15 loop : -3.54 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 388 TYR 0.020 0.002 TYR A 507 PHE 0.015 0.001 PHE A 565 TRP 0.010 0.001 TRP A 473 HIS 0.004 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 5283) covalent geometry : angle 0.74908 ( 7163) hydrogen bonds : bond 0.04189 ( 285) hydrogen bonds : angle 5.10862 ( 837) *********************** 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 150 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8456 (t80) cc_final: 0.7588 (t80) REVERT: A 135 ASP cc_start: 0.8895 (m-30) cc_final: 0.8298 (t0) REVERT: A 138 HIS cc_start: 0.8008 (m-70) cc_final: 0.7788 (m-70) REVERT: A 237 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.5696 (ttm-80) REVERT: A 264 TYR cc_start: 0.6167 (p90) cc_final: 0.5759 (p90) REVERT: A 269 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8072 (tp) REVERT: A 275 GLU cc_start: 0.8560 (tt0) cc_final: 0.7990 (mt-10) REVERT: A 340 ARG cc_start: 0.9101 (mmt-90) cc_final: 0.8642 (mmt-90) REVERT: A 363 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8730 (mp) REVERT: A 366 ASP cc_start: 0.8697 (m-30) cc_final: 0.8306 (p0) REVERT: A 423 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7576 (tt) REVERT: A 499 ASN cc_start: 0.7716 (t0) cc_final: 0.7337 (t0) REVERT: A 531 TRP cc_start: 0.8244 (OUTLIER) cc_final: 0.7279 (t60) REVERT: A 543 ARG cc_start: 0.8682 (mtp180) cc_final: 0.8333 (mtp85) REVERT: A 595 ARG cc_start: 0.8782 (ptp-170) cc_final: 0.8553 (ptp-170) REVERT: A 606 GLU cc_start: 0.8270 (pm20) cc_final: 0.7962 (pm20) REVERT: A 610 MET cc_start: 0.8030 (mmt) cc_final: 0.7687 (mmm) outliers start: 38 outliers final: 28 residues processed: 132 average time/residue: 0.0739 time to fit residues: 12.7236 Evaluate side-chains 142 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 71 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 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 396 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 430 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 514 VAL Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS 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 655 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 692 MET Chi-restraints excluded: chain A residue 698 LEU 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 40 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 247 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.158748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115736 restraints weight = 7015.361| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.83 r_work: 0.3321 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.6835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5283 Z= 0.186 Angle : 0.765 7.587 7163 Z= 0.383 Chirality : 0.045 0.178 815 Planarity : 0.005 0.053 869 Dihedral : 9.934 71.762 745 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.18 % Favored : 87.50 % Rotamer: Outliers : 6.42 % Allowed : 32.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.35), residues: 616 helix: 1.14 (0.26), residues: 378 sheet: -3.87 (1.25), residues: 15 loop : -3.52 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 334 TYR 0.021 0.002 TYR A 507 PHE 0.014 0.001 PHE A 701 TRP 0.011 0.001 TRP A 473 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 5283) covalent geometry : angle 0.76478 ( 7163) hydrogen bonds : bond 0.04107 ( 285) hydrogen bonds : angle 5.13051 ( 837) ********************** 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 145 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8476 (t80) cc_final: 0.7551 (t80) REVERT: A 135 ASP cc_start: 0.8919 (m-30) cc_final: 0.8360 (t0) REVERT: A 237 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.5740 (ttm-80) REVERT: A 269 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8105 (tp) REVERT: A 275 GLU cc_start: 0.8542 (tt0) cc_final: 0.7964 (mt-10) REVERT: A 327 MET cc_start: 0.5650 (ptm) cc_final: 0.4128 (mtt) REVERT: A 363 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8743 (mp) REVERT: A 366 ASP cc_start: 0.8700 (m-30) cc_final: 0.8255 (p0) REVERT: A 389 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7460 (mm-30) REVERT: A 423 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7615 (tt) REVERT: A 499 ASN cc_start: 0.7726 (t0) cc_final: 0.7324 (t0) REVERT: A 531 TRP cc_start: 0.8323 (OUTLIER) cc_final: 0.7284 (t60) REVERT: A 593 ASP cc_start: 0.8551 (t0) cc_final: 0.8243 (t70) REVERT: A 595 ARG cc_start: 0.8785 (ptp-170) cc_final: 0.8555 (ptp-170) REVERT: A 606 GLU cc_start: 0.8335 (pm20) cc_final: 0.8060 (pm20) REVERT: A 670 GLN cc_start: 0.8754 (mt0) cc_final: 0.8303 (mm-40) REVERT: A 684 PHE cc_start: 0.8113 (t80) cc_final: 0.7841 (t80) outliers start: 36 outliers final: 30 residues processed: 126 average time/residue: 0.0721 time to fit residues: 12.0257 Evaluate side-chains 144 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 71 ILE Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU 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 396 THR Chi-restraints excluded: chain A residue 407 CYS 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 443 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS 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 655 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 692 MET Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 708 ILE 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 48 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.158882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.115817 restraints weight = 7078.197| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.84 r_work: 0.3320 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.6823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 5283 Z= 0.254 Angle : 1.223 59.190 7163 Z= 0.686 Chirality : 0.045 0.322 815 Planarity : 0.005 0.053 869 Dihedral : 9.936 71.798 745 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.34 % Favored : 87.50 % Rotamer: Outliers : 7.49 % Allowed : 31.19 % Favored : 61.32 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.35), residues: 616 helix: 1.15 (0.26), residues: 378 sheet: -3.88 (1.25), residues: 15 loop : -3.53 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 334 TYR 0.017 0.002 TYR A 507 PHE 0.014 0.001 PHE A 565 TRP 0.011 0.001 TRP A 473 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 5283) covalent geometry : angle 1.22295 ( 7163) hydrogen bonds : bond 0.04111 ( 285) hydrogen bonds : angle 5.13288 ( 837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1427.39 seconds wall clock time: 25 minutes 10.82 seconds (1510.82 seconds total)