Starting phenix.real_space_refine on Wed Sep 17 06:40:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jj6_61517/09_2025/9jj6_61517.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jj6_61517/09_2025/9jj6_61517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jj6_61517/09_2025/9jj6_61517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jj6_61517/09_2025/9jj6_61517.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jj6_61517/09_2025/9jj6_61517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jj6_61517/09_2025/9jj6_61517.map" } resolution = 2.94 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 4023 2.51 5 N 1040 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6314 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1407 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 167} Chain breaks: 2 Chain: "A" Number of atoms: 4817 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4810 Classifications: {'peptide': 590} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 563} Conformer: "B" Number of residues, atoms: 590, 4810 Classifications: {'peptide': 590} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 563} bond proxies already assigned to first conformer: 4934 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 90 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.86, per 1000 atoms: 0.45 Number of scatterers: 6314 At special positions: 0 Unit cell: (76.65, 83.95, 110.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1213 8.00 N 1040 7.00 C 4023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 418 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 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: 0.57 Conformation dependent library (CDL) restraints added in 696.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1458 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 56.7% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 388 through 392 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.726A pdb=" N LEU B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 4.798A pdb=" N SER B 447 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.324A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.806A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.594A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.532A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.585A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 193 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 250 removed outlier: 3.770A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.786A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.581A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 removed outlier: 3.549A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.887A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.620A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.432A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.989A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.764A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.773A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'B' and resid 393 through 397 removed outlier: 3.596A pdb=" N ASN B 393 " --> pdb=" O TYR B 438 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER B 433 " --> pdb=" O THR B 556 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 502 through 505 removed outlier: 3.621A pdb=" N GLY B 502 " --> pdb=" O GLY B 499 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ASN B 490 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA B 541 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE B 492 " --> pdb=" O GLN B 539 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLN B 539 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.820A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.014A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1039 1.31 - 1.43: 1807 1.43 - 1.56: 3577 1.56 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 6485 Sorted by residual: bond pdb=" C7 NAG A 701 " pdb=" N2 NAG A 701 " ideal model delta sigma weight residual 1.346 1.473 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C7 NAG A 704 " pdb=" N2 NAG A 704 " ideal model delta sigma weight residual 1.346 1.473 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C7 NAG A 705 " pdb=" N2 NAG A 705 " ideal model delta sigma weight residual 1.346 1.472 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C7 NAG A 703 " pdb=" N2 NAG A 703 " ideal model delta sigma weight residual 1.346 1.472 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C7 NAG A 702 " pdb=" N2 NAG A 702 " ideal model delta sigma weight residual 1.346 1.472 -0.126 2.00e-02 2.50e+03 3.94e+01 ... (remaining 6480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 8611 1.82 - 3.64: 146 3.64 - 5.46: 40 5.46 - 7.27: 19 7.27 - 9.09: 2 Bond angle restraints: 8818 Sorted by residual: angle pdb=" CA PRO A 346 " pdb=" N PRO A 346 " pdb=" CD PRO A 346 " ideal model delta sigma weight residual 112.00 105.67 6.33 1.40e+00 5.10e-01 2.04e+01 angle pdb=" N PRO A 346 " pdb=" CD PRO A 346 " pdb=" CG PRO A 346 " ideal model delta sigma weight residual 103.20 97.00 6.20 1.50e+00 4.44e-01 1.71e+01 angle pdb=" CB MET A 190 " pdb=" CG MET A 190 " pdb=" SD MET A 190 " ideal model delta sigma weight residual 112.70 121.79 -9.09 3.00e+00 1.11e-01 9.19e+00 angle pdb=" C PRO A 492 " pdb=" N HIS A 493 " pdb=" CA HIS A 493 " ideal model delta sigma weight residual 122.99 118.86 4.13 1.41e+00 5.03e-01 8.57e+00 angle pdb=" CB PRO A 346 " pdb=" CG PRO A 346 " pdb=" CD PRO A 346 " ideal model delta sigma weight residual 106.10 97.03 9.07 3.20e+00 9.77e-02 8.03e+00 ... (remaining 8813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 3415 22.61 - 45.22: 332 45.22 - 67.83: 61 67.83 - 90.44: 14 90.44 - 113.05: 117 Dihedral angle restraints: 3939 sinusoidal: 1674 harmonic: 2265 Sorted by residual: dihedral pdb=" CA MET A 462 " pdb=" C MET A 462 " pdb=" N VAL A 463 " pdb=" CA VAL A 463 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -120.84 34.84 1 1.00e+01 1.00e-02 1.72e+01 dihedral pdb=" N2 NAG A 702 " pdb=" C1 NAG A 702 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sinusoidal sigma weight residual -178.19 -65.14 -113.05 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 3936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 654 0.035 - 0.070: 211 0.070 - 0.104: 68 0.104 - 0.139: 19 0.139 - 0.174: 2 Chirality restraints: 954 Sorted by residual: chirality pdb=" CB THR A 122 " pdb=" CA THR A 122 " pdb=" OG1 THR A 122 " pdb=" CG2 THR A 122 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA MET A 462 " pdb=" N MET A 462 " pdb=" C MET A 462 " pdb=" CB MET A 462 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA TYR A 385 " pdb=" N TYR A 385 " pdb=" C TYR A 385 " pdb=" CB TYR A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 951 not shown) Planarity restraints: 1130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 345 " 0.038 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO A 346 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 134 " 0.035 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO A 135 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 42 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" CD GLN A 42 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN A 42 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN A 42 " 0.010 2.00e-02 2.50e+03 ... (remaining 1127 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1236 2.77 - 3.30: 5951 3.30 - 3.84: 11089 3.84 - 4.37: 13152 4.37 - 4.90: 22749 Nonbonded interactions: 54177 Sorted by model distance: nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.241 3.040 nonbonded pdb=" OG SER B 433 " pdb=" OG1 THR B 556 " model vdw 2.251 3.040 nonbonded pdb=" OG SER A 170 " pdb=" OE1 GLU A 171 " model vdw 2.256 3.040 nonbonded pdb=" O GLY A 268 " pdb=" ND2 ASN A 277 " model vdw 2.262 3.120 nonbonded pdb=" OG SER A 331 " pdb=" O ILE A 358 " model vdw 2.268 3.040 ... (remaining 54172 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.29 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.007 0.127 6491 Z= 0.334 Angle : 0.662 9.092 8830 Z= 0.312 Chirality : 0.040 0.174 954 Planarity : 0.005 0.056 1130 Dihedral : 28.525 113.046 2463 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.73 % Allowed : 24.34 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.54 (0.31), residues: 764 helix: 0.94 (0.27), residues: 384 sheet: -0.77 (0.58), residues: 73 loop : 0.08 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.017 0.001 TYR A 385 PHE 0.013 0.001 PHE A 315 TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00679 ( 6485) covalent geometry : angle 0.66216 ( 8818) SS BOND : bond 0.00137 ( 6) SS BOND : angle 0.58815 ( 12) hydrogen bonds : bond 0.17227 ( 313) hydrogen bonds : angle 6.72880 ( 881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.258 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 77 average time/residue: 0.5141 time to fit residues: 42.1011 Evaluate side-chains 75 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 280 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.0270 chunk 74 optimal weight: 0.3980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 ASN B 506 GLN A 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.189374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136194 restraints weight = 8530.362| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.29 r_work: 0.3301 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6491 Z= 0.123 Angle : 0.637 9.143 8830 Z= 0.292 Chirality : 0.043 0.229 954 Planarity : 0.004 0.050 1130 Dihedral : 13.501 61.526 984 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.35 % Allowed : 21.99 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.02 (0.31), residues: 764 helix: 1.32 (0.27), residues: 388 sheet: -0.51 (0.58), residues: 72 loop : 0.31 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.016 0.001 TYR A 385 PHE 0.012 0.001 PHE A 315 TRP 0.011 0.001 TRP A 165 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6485) covalent geometry : angle 0.63709 ( 8818) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.54843 ( 12) hydrogen bonds : bond 0.04114 ( 313) hydrogen bonds : angle 4.66371 ( 881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.253 Fit side-chains REVERT: B 540 SER cc_start: 0.8153 (t) cc_final: 0.7868 (p) REVERT: A 24 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7294 (mt0) REVERT: A 70 SER cc_start: 0.8153 (m) cc_final: 0.7731 (p) REVERT: A 171 GLU cc_start: 0.7167 (mp0) cc_final: 0.6837 (mp0) REVERT: A 480 MET cc_start: 0.7786 (mtt) cc_final: 0.7517 (mtt) outliers start: 16 outliers final: 5 residues processed: 89 average time/residue: 0.4865 time to fit residues: 46.1712 Evaluate side-chains 72 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 485 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 ASN A 42 GLN A 64 ASN A 194 ASN A 586 ASN A 599 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.183621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127146 restraints weight = 9653.143| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.48 r_work: 0.3192 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 6491 Z= 0.271 Angle : 0.653 8.428 8830 Z= 0.326 Chirality : 0.046 0.165 954 Planarity : 0.005 0.048 1130 Dihedral : 7.526 56.092 981 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.81 % Allowed : 20.67 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.47 (0.30), residues: 764 helix: 0.83 (0.26), residues: 389 sheet: -0.75 (0.59), residues: 73 loop : 0.11 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 169 TYR 0.015 0.002 TYR A 183 PHE 0.016 0.002 PHE A 315 TRP 0.011 0.002 TRP A 165 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00663 ( 6485) covalent geometry : angle 0.65243 ( 8818) SS BOND : bond 0.00339 ( 6) SS BOND : angle 0.97347 ( 12) hydrogen bonds : bond 0.05242 ( 313) hydrogen bonds : angle 4.73053 ( 881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.272 Fit side-chains REVERT: B 540 SER cc_start: 0.8331 (t) cc_final: 0.8123 (p) REVERT: B 543 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6403 (ttp) REVERT: A 24 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7253 (mt0) REVERT: A 171 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6897 (mp0) outliers start: 26 outliers final: 10 residues processed: 98 average time/residue: 0.4754 time to fit residues: 49.7003 Evaluate side-chains 79 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 485 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 ASN A 42 GLN A 194 ASN A 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.187025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.132780 restraints weight = 8182.862| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.67 r_work: 0.3214 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6491 Z= 0.135 Angle : 0.536 8.060 8830 Z= 0.272 Chirality : 0.041 0.160 954 Planarity : 0.004 0.047 1130 Dihedral : 5.959 57.500 981 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.35 % Allowed : 20.82 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.79 (0.31), residues: 764 helix: 1.09 (0.26), residues: 389 sheet: -0.62 (0.61), residues: 73 loop : 0.25 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.016 0.001 TYR A 385 PHE 0.014 0.001 PHE A 315 TRP 0.010 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6485) covalent geometry : angle 0.53611 ( 8818) SS BOND : bond 0.00148 ( 6) SS BOND : angle 0.50554 ( 12) hydrogen bonds : bond 0.04114 ( 313) hydrogen bonds : angle 4.49542 ( 881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.324 Fit side-chains REVERT: B 540 SER cc_start: 0.8215 (t) cc_final: 0.8003 (p) REVERT: B 543 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6325 (ttp) REVERT: A 24 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7262 (mt0) REVERT: A 171 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6765 (mp0) outliers start: 16 outliers final: 7 residues processed: 83 average time/residue: 0.5052 time to fit residues: 44.5907 Evaluate side-chains 75 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 485 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 ASN A 42 GLN A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.189068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135558 restraints weight = 8260.505| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.27 r_work: 0.3315 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6491 Z= 0.110 Angle : 0.497 8.341 8830 Z= 0.253 Chirality : 0.039 0.164 954 Planarity : 0.004 0.047 1130 Dihedral : 5.240 58.876 981 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.23 % Allowed : 19.94 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.06 (0.31), residues: 764 helix: 1.35 (0.27), residues: 389 sheet: -0.39 (0.63), residues: 72 loop : 0.28 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 518 TYR 0.016 0.001 TYR A 385 PHE 0.014 0.001 PHE A 315 TRP 0.010 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6485) covalent geometry : angle 0.49711 ( 8818) SS BOND : bond 0.00126 ( 6) SS BOND : angle 0.44469 ( 12) hydrogen bonds : bond 0.03744 ( 313) hydrogen bonds : angle 4.29263 ( 881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.244 Fit side-chains REVERT: B 540 SER cc_start: 0.8109 (t) cc_final: 0.7824 (p) REVERT: B 543 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6302 (ttp) REVERT: A 24 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: A 171 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: A 376 MET cc_start: 0.8579 (mmt) cc_final: 0.8199 (tpt) outliers start: 22 outliers final: 8 residues processed: 92 average time/residue: 0.4300 time to fit residues: 42.3899 Evaluate side-chains 81 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 485 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 ASN A 42 GLN A 194 ASN A 195 HIS A 599 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.186065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133566 restraints weight = 8216.803| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.51 r_work: 0.3188 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6491 Z= 0.171 Angle : 0.549 8.736 8830 Z= 0.278 Chirality : 0.042 0.174 954 Planarity : 0.004 0.046 1130 Dihedral : 5.315 58.760 981 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.49 % Allowed : 21.26 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.93 (0.31), residues: 764 helix: 1.24 (0.26), residues: 388 sheet: -0.45 (0.62), residues: 72 loop : 0.25 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 518 TYR 0.015 0.001 TYR A 385 PHE 0.016 0.001 PHE A 315 TRP 0.011 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 6485) covalent geometry : angle 0.54896 ( 8818) SS BOND : bond 0.00196 ( 6) SS BOND : angle 0.66507 ( 12) hydrogen bonds : bond 0.04330 ( 313) hydrogen bonds : angle 4.35535 ( 881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.272 Fit side-chains REVERT: B 540 SER cc_start: 0.8208 (t) cc_final: 0.7973 (p) REVERT: B 543 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6361 (ttp) REVERT: A 24 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7291 (mt0) REVERT: A 171 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6776 (mp0) outliers start: 17 outliers final: 8 residues processed: 77 average time/residue: 0.4604 time to fit residues: 38.0480 Evaluate side-chains 78 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 485 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 ASN A 42 GLN A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.186999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130232 restraints weight = 13185.656| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.86 r_work: 0.3235 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6491 Z= 0.134 Angle : 0.523 8.664 8830 Z= 0.265 Chirality : 0.041 0.197 954 Planarity : 0.004 0.047 1130 Dihedral : 4.730 36.430 980 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.49 % Allowed : 20.97 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.04 (0.31), residues: 764 helix: 1.28 (0.26), residues: 390 sheet: -0.37 (0.62), residues: 72 loop : 0.37 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 518 TYR 0.016 0.001 TYR A 385 PHE 0.015 0.001 PHE A 315 TRP 0.010 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6485) covalent geometry : angle 0.52255 ( 8818) SS BOND : bond 0.00224 ( 6) SS BOND : angle 0.60375 ( 12) hydrogen bonds : bond 0.04007 ( 313) hydrogen bonds : angle 4.28530 ( 881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 540 SER cc_start: 0.8173 (t) cc_final: 0.7909 (p) REVERT: B 543 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6369 (ttp) REVERT: A 24 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: A 89 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7008 (mp-120) REVERT: A 171 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6848 (mp0) outliers start: 17 outliers final: 9 residues processed: 77 average time/residue: 0.4448 time to fit residues: 36.5401 Evaluate side-chains 79 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 485 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.187519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131295 restraints weight = 12110.849| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.74 r_work: 0.3252 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6491 Z= 0.130 Angle : 0.519 8.694 8830 Z= 0.263 Chirality : 0.040 0.183 954 Planarity : 0.004 0.044 1130 Dihedral : 4.574 35.380 980 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.49 % Allowed : 21.26 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.31), residues: 764 helix: 1.34 (0.26), residues: 389 sheet: -0.34 (0.63), residues: 72 loop : 0.41 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 518 TYR 0.016 0.001 TYR A 385 PHE 0.017 0.001 PHE A 315 TRP 0.010 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6485) covalent geometry : angle 0.51889 ( 8818) SS BOND : bond 0.00182 ( 6) SS BOND : angle 0.53940 ( 12) hydrogen bonds : bond 0.03940 ( 313) hydrogen bonds : angle 4.24942 ( 881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: B 540 SER cc_start: 0.8175 (t) cc_final: 0.7896 (p) REVERT: B 543 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6338 (ttp) REVERT: A 24 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7350 (mt0) REVERT: A 89 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6846 (mp-120) REVERT: A 171 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: A 376 MET cc_start: 0.8547 (mmm) cc_final: 0.8194 (tpt) outliers start: 17 outliers final: 10 residues processed: 78 average time/residue: 0.4571 time to fit residues: 38.1387 Evaluate side-chains 81 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 485 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 41 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 ASN A 42 GLN A 586 ASN A 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.189137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136752 restraints weight = 8258.881| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.56 r_work: 0.3239 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6491 Z= 0.117 Angle : 0.512 8.796 8830 Z= 0.259 Chirality : 0.040 0.180 954 Planarity : 0.004 0.043 1130 Dihedral : 4.382 33.973 980 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.05 % Allowed : 21.85 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.20 (0.31), residues: 764 helix: 1.41 (0.26), residues: 391 sheet: -0.33 (0.63), residues: 72 loop : 0.44 (0.39), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 518 TYR 0.016 0.001 TYR A 385 PHE 0.016 0.001 PHE A 315 TRP 0.011 0.001 TRP A 478 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6485) covalent geometry : angle 0.51184 ( 8818) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.46404 ( 12) hydrogen bonds : bond 0.03778 ( 313) hydrogen bonds : angle 4.19709 ( 881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 540 SER cc_start: 0.8120 (t) cc_final: 0.7825 (p) REVERT: B 543 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6346 (ttp) REVERT: A 24 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7364 (mt0) REVERT: A 171 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: A 376 MET cc_start: 0.8575 (mmm) cc_final: 0.8255 (tpt) outliers start: 14 outliers final: 10 residues processed: 78 average time/residue: 0.4756 time to fit residues: 39.6305 Evaluate side-chains 81 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 51 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 0.2980 chunk 48 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 56 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 ASN A 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.190420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136267 restraints weight = 9728.390| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.42 r_work: 0.3121 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6491 Z= 0.107 Angle : 0.506 9.127 8830 Z= 0.257 Chirality : 0.039 0.177 954 Planarity : 0.004 0.043 1130 Dihedral : 4.227 32.317 980 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.05 % Allowed : 22.14 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.36 (0.32), residues: 764 helix: 1.54 (0.27), residues: 390 sheet: -0.30 (0.64), residues: 72 loop : 0.54 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 518 TYR 0.017 0.001 TYR A 385 PHE 0.016 0.001 PHE A 315 TRP 0.014 0.001 TRP A 478 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6485) covalent geometry : angle 0.50604 ( 8818) SS BOND : bond 0.00120 ( 6) SS BOND : angle 0.48156 ( 12) hydrogen bonds : bond 0.03608 ( 313) hydrogen bonds : angle 4.16203 ( 881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 540 SER cc_start: 0.8131 (t) cc_final: 0.7864 (p) REVERT: B 543 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.6143 (ttp) REVERT: A 24 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7120 (mt0) REVERT: A 35 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8312 (mt-10) REVERT: A 157 ASP cc_start: 0.7472 (m-30) cc_final: 0.7233 (t0) REVERT: A 171 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: A 376 MET cc_start: 0.8704 (mmm) cc_final: 0.8398 (tpt) REVERT: A 462 MET cc_start: 0.7745 (ptt) cc_final: 0.6903 (ppp) REVERT: A 534 LYS cc_start: 0.8454 (mmtt) cc_final: 0.7707 (mttt) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.4391 time to fit residues: 36.4054 Evaluate side-chains 77 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 61 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 0.0370 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 0.0050 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 154 ASN A 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.190650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136690 restraints weight = 9751.227| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.47 r_work: 0.3126 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6491 Z= 0.108 Angle : 0.506 9.036 8830 Z= 0.256 Chirality : 0.039 0.175 954 Planarity : 0.004 0.043 1130 Dihedral : 4.136 31.026 980 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.05 % Allowed : 22.43 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.43 (0.32), residues: 764 helix: 1.59 (0.27), residues: 390 sheet: -0.27 (0.63), residues: 72 loop : 0.58 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 518 TYR 0.017 0.001 TYR A 385 PHE 0.015 0.001 PHE A 315 TRP 0.020 0.001 TRP A 478 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6485) covalent geometry : angle 0.50572 ( 8818) SS BOND : bond 0.00131 ( 6) SS BOND : angle 0.44852 ( 12) hydrogen bonds : bond 0.03627 ( 313) hydrogen bonds : angle 4.15166 ( 881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.83 seconds wall clock time: 43 minutes 12.66 seconds (2592.66 seconds total)