Starting phenix.real_space_refine on Wed Sep 17 05:03:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3l_61118/09_2025/9j3l_61118.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3l_61118/09_2025/9j3l_61118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j3l_61118/09_2025/9j3l_61118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3l_61118/09_2025/9j3l_61118.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j3l_61118/09_2025/9j3l_61118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3l_61118/09_2025/9j3l_61118.map" } resolution = 2.72 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= 0.093 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 3 5.49 5 S 28 5.16 5 C 3117 2.51 5 N 742 2.21 5 O 840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 4730 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3750 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3746 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 25, 'TRANS': 456} Conformer: "B" Number of residues, atoms: 482, 3746 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 25, 'TRANS': 456} bond proxies already assigned to first conformer: 3840 Chain: "C" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 949 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.15, per 1000 atoms: 0.45 Number of scatterers: 4730 At special positions: 0 Unit cell: (71.61, 74.4, 110.67, 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 28 16.00 P 3 15.00 O 840 8.00 N 742 7.00 C 3117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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: 0.47 Conformation dependent library (CDL) restraints added in 305.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1112 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 69.6% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 110 through 143 removed outlier: 4.182A pdb=" N LYS A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Proline residue: A 118 - end of helix removed outlier: 3.668A pdb=" N ASP A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 removed outlier: 4.381A pdb=" N PHE A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 removed outlier: 4.028A pdb=" N ASN A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 188 through 201 Processing helix chain 'A' and resid 203 through 207 removed outlier: 4.505A pdb=" N ASN A 207 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.715A pdb=" N ILE A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 removed outlier: 3.690A pdb=" N GLY A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.606A pdb=" N GLN A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 273 through 297 removed outlier: 3.503A pdb=" N LEU A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 335 removed outlier: 4.046A pdb=" N ILE A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 Processing helix chain 'A' and resid 365 through 397 removed outlier: 3.752A pdb=" N ASP A 370 " --> pdb=" O PRO A 366 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 371 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 433 removed outlier: 4.459A pdb=" N GLN A 426 " --> pdb=" O MET A 422 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASN A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 457 removed outlier: 3.632A pdb=" N LYS A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 472 through 504 removed outlier: 3.539A pdb=" N SER A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP A 497 " --> pdb=" O TYR A 493 " (cutoff:3.500A) Proline residue: A 498 - end of helix removed outlier: 3.610A pdb=" N TYR A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 543 removed outlier: 3.558A pdb=" N ALA A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Proline residue: A 525 - end of helix removed outlier: 3.843A pdb=" N ALA A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 568 removed outlier: 3.519A pdb=" N ALA A 567 " --> pdb=" O TRP A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.867A pdb=" N GLU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.031A pdb=" N GLY C 10 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER C 119 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 12 " --> pdb=" O SER C 119 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.031A pdb=" N GLY C 10 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER C 119 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 12 " --> pdb=" O SER C 119 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL C 101 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 918 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: 0.88 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1398 1.34 - 1.46: 1037 1.46 - 1.58: 2369 1.58 - 1.69: 5 1.69 - 1.81: 48 Bond restraints: 4857 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" N9 ATP A 701 " ideal model delta sigma weight residual 1.374 1.303 0.071 1.00e-02 1.00e+04 5.02e+01 bond pdb=" C5 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.387 1.318 0.069 1.00e-02 1.00e+04 4.82e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.450 -0.062 1.00e-02 1.00e+04 3.84e+01 bond pdb=" O5' ATP A 701 " pdb=" PA ATP A 701 " ideal model delta sigma weight residual 1.579 1.633 -0.054 1.10e-02 8.26e+03 2.38e+01 bond pdb=" C8 ATP A 701 " pdb=" N9 ATP A 701 " ideal model delta sigma weight residual 1.370 1.312 0.058 1.20e-02 6.94e+03 2.33e+01 ... (remaining 4852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 6541 3.31 - 6.62: 58 6.62 - 9.93: 7 9.93 - 13.25: 2 13.25 - 16.56: 1 Bond angle restraints: 6609 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 123.31 16.56 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 127.81 9.02 1.00e+00 1.00e+00 8.13e+01 angle pdb=" C5 ATP A 701 " pdb=" C4 ATP A 701 " pdb=" N3 ATP A 701 " ideal model delta sigma weight residual 126.80 118.78 8.02 1.00e+00 1.00e+00 6.43e+01 angle pdb=" N3 ATP A 701 " pdb=" C4 ATP A 701 " pdb=" N9 ATP A 701 " ideal model delta sigma weight residual 127.04 134.83 -7.79 1.15e+00 7.59e-01 4.60e+01 angle pdb=" N TYR A 208 " pdb=" CA TYR A 208 " pdb=" C TYR A 208 " ideal model delta sigma weight residual 114.56 106.39 8.17 1.27e+00 6.20e-01 4.14e+01 ... (remaining 6604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 2624 17.42 - 34.84: 184 34.84 - 52.26: 42 52.26 - 69.68: 10 69.68 - 87.10: 1 Dihedral angle restraints: 2861 sinusoidal: 1114 harmonic: 1747 Sorted by residual: dihedral pdb=" CA GLU A 349 " pdb=" C GLU A 349 " pdb=" N LYS A 350 " pdb=" CA LYS A 350 " ideal model delta harmonic sigma weight residual -180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA GLN A 426 " pdb=" C GLN A 426 " pdb=" N TYR A 427 " pdb=" CA TYR A 427 " ideal model delta harmonic sigma weight residual 180.00 153.56 26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA LYS A 352 " pdb=" C LYS A 352 " pdb=" N MET A 353 " pdb=" CA MET A 353 " ideal model delta harmonic sigma weight residual 180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 2858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 442 0.029 - 0.058: 194 0.058 - 0.088: 83 0.088 - 0.117: 23 0.117 - 0.146: 9 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA TYR A 208 " pdb=" N TYR A 208 " pdb=" C TYR A 208 " pdb=" CB TYR A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CG LEU A 446 " pdb=" CB LEU A 446 " pdb=" CD1 LEU A 446 " pdb=" CD2 LEU A 446 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ASN A 160 " pdb=" N ASN A 160 " pdb=" C ASN A 160 " pdb=" CB ASN A 160 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 748 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 492 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C LYS A 492 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 492 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 493 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 203 " 0.038 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO A 204 " -0.098 5.00e-02 4.00e+02 pdb=" CA APRO A 204 " 0.028 5.00e-02 4.00e+02 pdb=" CD APRO A 204 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 203 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.99e+00 pdb=" N PRO A 204 " -0.097 5.00e-02 4.00e+02 pdb=" CA BPRO A 204 " 0.028 5.00e-02 4.00e+02 pdb=" CD BPRO A 204 " 0.031 5.00e-02 4.00e+02 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 889 2.77 - 3.30: 4719 3.30 - 3.83: 8299 3.83 - 4.37: 10174 4.37 - 4.90: 16780 Nonbonded interactions: 40861 Sorted by model distance: nonbonded pdb=" NE2 HIS A 210 " pdb=" OG SER A 237 " model vdw 2.234 3.120 nonbonded pdb=" O THR A 388 " pdb=" OG SER A 391 " model vdw 2.253 3.040 nonbonded pdb=" O MET A 168 " pdb=" OG1 THR A 172 " model vdw 2.269 3.040 nonbonded pdb=" O ALA A 567 " pdb=" N GLU A 571 " model vdw 2.270 3.120 nonbonded pdb=" O LYS A 314 " pdb=" OG SER A 318 " model vdw 2.280 3.040 ... (remaining 40856 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.840 Find NCS groups from input model: 0.020 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:8.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.004 0.071 4858 Z= 0.268 Angle : 0.787 16.558 6611 Z= 0.480 Chirality : 0.041 0.146 751 Planarity : 0.006 0.057 803 Dihedral : 13.033 87.096 1746 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.40 % Allowed : 0.00 % Favored : 99.60 % 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: -1.92 (0.33), residues: 599 helix: -1.10 (0.24), residues: 402 sheet: -1.46 (0.75), residues: 42 loop : -1.08 (0.53), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 336 TYR 0.027 0.002 TYR A 337 PHE 0.016 0.001 PHE A 452 TRP 0.016 0.001 TRP A 333 HIS 0.001 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 4857) covalent geometry : angle 0.78729 ( 6609) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.87709 ( 2) hydrogen bonds : bond 0.20363 ( 316) hydrogen bonds : angle 8.63110 ( 918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.203 Fit side-chains REVERT: A 167 PHE cc_start: 0.8247 (t80) cc_final: 0.7990 (t80) REVERT: A 170 LEU cc_start: 0.8960 (tp) cc_final: 0.8754 (tp) REVERT: A 173 LYS cc_start: 0.8125 (tmtt) cc_final: 0.7561 (tptm) REVERT: A 294 TYR cc_start: 0.8984 (t80) cc_final: 0.8535 (t80) REVERT: A 329 LEU cc_start: 0.8496 (tp) cc_final: 0.8177 (mt) REVERT: A 353 MET cc_start: 0.6887 (tpt) cc_final: 0.6645 (tpt) REVERT: A 356 MET cc_start: 0.3912 (mmt) cc_final: 0.3627 (mmt) REVERT: C 43 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8156 (mtpt) REVERT: C 77 THR cc_start: 0.8639 (m) cc_final: 0.8431 (p) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.4391 time to fit residues: 49.8551 Evaluate side-chains 93 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN C 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.101343 restraints weight = 7925.491| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.01 r_work: 0.2970 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4858 Z= 0.193 Angle : 0.681 9.489 6611 Z= 0.356 Chirality : 0.044 0.172 751 Planarity : 0.005 0.046 803 Dihedral : 7.857 64.608 684 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.19 % Allowed : 9.09 % Favored : 89.72 % 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: -0.90 (0.34), residues: 599 helix: -0.34 (0.25), residues: 407 sheet: -1.52 (0.64), residues: 48 loop : -0.46 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 290 TYR 0.015 0.002 TYR A 378 PHE 0.024 0.002 PHE A 257 TRP 0.009 0.001 TRP A 563 HIS 0.001 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 4857) covalent geometry : angle 0.68037 ( 6609) SS BOND : bond 0.00333 ( 1) SS BOND : angle 1.80179 ( 2) hydrogen bonds : bond 0.05111 ( 316) hydrogen bonds : angle 5.92994 ( 918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.187 Fit side-chains REVERT: A 158 TRP cc_start: 0.8719 (m100) cc_final: 0.8297 (m100) REVERT: A 169 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8598 (mt) REVERT: A 173 LYS cc_start: 0.8097 (tmtt) cc_final: 0.7545 (tptm) REVERT: A 294 TYR cc_start: 0.9062 (t80) cc_final: 0.8560 (t80) REVERT: A 353 MET cc_start: 0.6921 (tpt) cc_final: 0.6655 (tpt) REVERT: A 356 MET cc_start: 0.3734 (mmt) cc_final: 0.3492 (mmt) REVERT: A 554 MET cc_start: 0.8331 (mtm) cc_final: 0.8022 (mtp) REVERT: C 46 GLU cc_start: 0.8583 (tt0) cc_final: 0.8317 (tt0) REVERT: C 58 ARG cc_start: 0.8930 (mtm180) cc_final: 0.8705 (mtm-85) outliers start: 6 outliers final: 0 residues processed: 99 average time/residue: 0.4373 time to fit residues: 45.5408 Evaluate side-chains 94 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.0070 chunk 39 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.139289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.103353 restraints weight = 9777.469| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.19 r_work: 0.2923 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4858 Z= 0.139 Angle : 0.610 7.982 6611 Z= 0.317 Chirality : 0.041 0.153 751 Planarity : 0.005 0.040 803 Dihedral : 7.209 58.448 684 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.58 % Allowed : 11.26 % Favored : 87.15 % 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: -0.13 (0.34), residues: 599 helix: 0.31 (0.26), residues: 403 sheet: -1.61 (0.56), residues: 48 loop : -0.24 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 290 TYR 0.012 0.001 TYR A 378 PHE 0.020 0.002 PHE A 257 TRP 0.009 0.001 TRP A 309 HIS 0.001 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4857) covalent geometry : angle 0.60971 ( 6609) SS BOND : bond 0.00059 ( 1) SS BOND : angle 1.10904 ( 2) hydrogen bonds : bond 0.04448 ( 316) hydrogen bonds : angle 5.39624 ( 918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.168 Fit side-chains REVERT: A 169 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8549 (mt) REVERT: A 173 LYS cc_start: 0.8073 (tmtt) cc_final: 0.7499 (tptm) REVERT: A 294 TYR cc_start: 0.9069 (t80) cc_final: 0.8484 (t80) REVERT: A 353 MET cc_start: 0.6971 (tpt) cc_final: 0.6656 (tpt) REVERT: A 356 MET cc_start: 0.3713 (mmt) cc_final: 0.3447 (mmt) outliers start: 8 outliers final: 2 residues processed: 102 average time/residue: 0.4555 time to fit residues: 48.7729 Evaluate side-chains 96 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain C residue 84 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.136523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.100264 restraints weight = 10757.214| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.27 r_work: 0.2962 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4858 Z= 0.178 Angle : 0.618 7.441 6611 Z= 0.321 Chirality : 0.042 0.165 751 Planarity : 0.005 0.039 803 Dihedral : 7.015 62.534 684 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.37 % Allowed : 11.66 % Favored : 85.97 % 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: 0.17 (0.35), residues: 599 helix: 0.49 (0.26), residues: 403 sheet: -1.50 (0.58), residues: 46 loop : -0.01 (0.56), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.014 0.002 TYR A 378 PHE 0.020 0.002 PHE A 257 TRP 0.008 0.001 TRP A 563 HIS 0.002 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 4857) covalent geometry : angle 0.61799 ( 6609) SS BOND : bond 0.00136 ( 1) SS BOND : angle 1.41715 ( 2) hydrogen bonds : bond 0.04497 ( 316) hydrogen bonds : angle 5.35559 ( 918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.119 Fit side-chains REVERT: A 169 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8561 (mt) REVERT: A 173 LYS cc_start: 0.8061 (tmtt) cc_final: 0.7514 (tptm) REVERT: A 294 TYR cc_start: 0.9109 (t80) cc_final: 0.8562 (t80) REVERT: A 353 MET cc_start: 0.6919 (tpt) cc_final: 0.6605 (tpt) REVERT: A 356 MET cc_start: 0.3854 (mmt) cc_final: 0.3590 (mmt) REVERT: A 554 MET cc_start: 0.8150 (mtp) cc_final: 0.7889 (mtp) outliers start: 12 outliers final: 4 residues processed: 98 average time/residue: 0.4557 time to fit residues: 47.0447 Evaluate side-chains 94 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 84 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.0970 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.138351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.101176 restraints weight = 12902.799| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.47 r_work: 0.2960 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4858 Z= 0.147 Angle : 0.588 6.778 6611 Z= 0.307 Chirality : 0.041 0.159 751 Planarity : 0.004 0.038 803 Dihedral : 6.808 62.923 684 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.78 % Allowed : 13.04 % Favored : 85.18 % 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: 0.16 (0.35), residues: 599 helix: 0.51 (0.26), residues: 405 sheet: -1.35 (0.59), residues: 46 loop : -0.14 (0.56), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.013 0.001 TYR A 378 PHE 0.018 0.002 PHE A 257 TRP 0.008 0.001 TRP A 309 HIS 0.001 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4857) covalent geometry : angle 0.58823 ( 6609) SS BOND : bond 0.00076 ( 1) SS BOND : angle 1.14379 ( 2) hydrogen bonds : bond 0.04227 ( 316) hydrogen bonds : angle 5.21284 ( 918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.189 Fit side-chains REVERT: A 169 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8527 (mt) REVERT: A 173 LYS cc_start: 0.7987 (tmtt) cc_final: 0.7447 (tptm) REVERT: A 294 TYR cc_start: 0.9028 (t80) cc_final: 0.8500 (t80) REVERT: A 336 ARG cc_start: 0.8036 (ttt-90) cc_final: 0.7706 (ttt-90) REVERT: A 353 MET cc_start: 0.6887 (tpt) cc_final: 0.6630 (tpt) REVERT: A 356 MET cc_start: 0.3845 (mmt) cc_final: 0.3534 (mmt) REVERT: A 554 MET cc_start: 0.7856 (mtp) cc_final: 0.7650 (mtt) outliers start: 9 outliers final: 3 residues processed: 91 average time/residue: 0.4298 time to fit residues: 41.1796 Evaluate side-chains 91 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain C residue 84 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 8.9990 chunk 43 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 33 optimal weight: 0.4980 chunk 54 optimal weight: 0.1980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.140061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.104707 restraints weight = 8999.414| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.10 r_work: 0.2946 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4858 Z= 0.128 Angle : 0.579 7.289 6611 Z= 0.299 Chirality : 0.040 0.152 751 Planarity : 0.004 0.037 803 Dihedral : 6.576 62.247 684 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.78 % Allowed : 14.23 % Favored : 83.99 % 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: 0.46 (0.35), residues: 599 helix: 0.70 (0.26), residues: 404 sheet: -1.25 (0.60), residues: 46 loop : 0.10 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.012 0.001 TYR A 378 PHE 0.017 0.002 PHE A 257 TRP 0.009 0.001 TRP A 309 HIS 0.000 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4857) covalent geometry : angle 0.57850 ( 6609) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.98124 ( 2) hydrogen bonds : bond 0.03989 ( 316) hydrogen bonds : angle 5.06074 ( 918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.158 Fit side-chains REVERT: A 169 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8523 (mt) REVERT: A 173 LYS cc_start: 0.8018 (tmtt) cc_final: 0.7429 (tptm) REVERT: A 294 TYR cc_start: 0.9058 (t80) cc_final: 0.8494 (t80) REVERT: A 336 ARG cc_start: 0.8146 (ttt-90) cc_final: 0.7848 (ttt-90) REVERT: A 353 MET cc_start: 0.6938 (tpt) cc_final: 0.6615 (tpt) REVERT: A 356 MET cc_start: 0.3844 (mmt) cc_final: 0.3539 (mmt) REVERT: A 551 TYR cc_start: 0.8416 (m-80) cc_final: 0.8077 (m-80) outliers start: 9 outliers final: 5 residues processed: 91 average time/residue: 0.4340 time to fit residues: 41.5107 Evaluate side-chains 89 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 84 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.137737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.101311 restraints weight = 8749.777| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.16 r_work: 0.2971 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4858 Z= 0.174 Angle : 0.599 6.883 6611 Z= 0.313 Chirality : 0.041 0.159 751 Planarity : 0.004 0.037 803 Dihedral : 6.733 64.558 684 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.98 % Allowed : 14.43 % Favored : 83.60 % 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: 0.33 (0.35), residues: 599 helix: 0.63 (0.26), residues: 401 sheet: -1.18 (0.62), residues: 46 loop : -0.07 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.014 0.001 TYR A 378 PHE 0.018 0.002 PHE A 257 TRP 0.007 0.001 TRP A 563 HIS 0.002 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 4857) covalent geometry : angle 0.59827 ( 6609) SS BOND : bond 0.00152 ( 1) SS BOND : angle 1.46066 ( 2) hydrogen bonds : bond 0.04316 ( 316) hydrogen bonds : angle 5.21284 ( 918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.134 Fit side-chains REVERT: A 158 TRP cc_start: 0.8776 (m100) cc_final: 0.8381 (m100) REVERT: A 169 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8431 (mt) REVERT: A 173 LYS cc_start: 0.7888 (tmtt) cc_final: 0.7266 (tptm) REVERT: A 294 TYR cc_start: 0.9054 (t80) cc_final: 0.8456 (t80) REVERT: A 353 MET cc_start: 0.7012 (tpt) cc_final: 0.6617 (tpt) REVERT: A 356 MET cc_start: 0.4064 (mmt) cc_final: 0.3700 (mmt) REVERT: A 512 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.5964 (ttmm) REVERT: A 551 TYR cc_start: 0.8377 (m-80) cc_final: 0.8135 (m-80) outliers start: 10 outliers final: 3 residues processed: 90 average time/residue: 0.4524 time to fit residues: 42.7847 Evaluate side-chains 89 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 512 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 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 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.100330 restraints weight = 12232.723| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.38 r_work: 0.2948 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4858 Z= 0.164 Angle : 0.594 6.885 6611 Z= 0.310 Chirality : 0.041 0.157 751 Planarity : 0.004 0.036 803 Dihedral : 6.685 64.483 684 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.38 % Allowed : 15.42 % Favored : 83.20 % 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: 0.38 (0.35), residues: 599 helix: 0.76 (0.26), residues: 395 sheet: -1.25 (0.62), residues: 46 loop : -0.29 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.014 0.001 TYR A 378 PHE 0.018 0.002 PHE A 257 TRP 0.005 0.001 TRP C 47 HIS 0.002 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4857) covalent geometry : angle 0.59406 ( 6609) SS BOND : bond 0.00120 ( 1) SS BOND : angle 1.30414 ( 2) hydrogen bonds : bond 0.04226 ( 316) hydrogen bonds : angle 5.18981 ( 918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.205 Fit side-chains REVERT: A 158 TRP cc_start: 0.8791 (m100) cc_final: 0.8385 (m100) REVERT: A 169 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8546 (mt) REVERT: A 173 LYS cc_start: 0.8007 (tmtt) cc_final: 0.7409 (tptm) REVERT: A 294 TYR cc_start: 0.9095 (t80) cc_final: 0.8550 (t80) REVERT: A 353 MET cc_start: 0.6951 (tpt) cc_final: 0.6584 (tpt) REVERT: A 356 MET cc_start: 0.4135 (mmt) cc_final: 0.3759 (mmt) REVERT: A 551 TYR cc_start: 0.8483 (m-80) cc_final: 0.8196 (m-80) outliers start: 7 outliers final: 3 residues processed: 91 average time/residue: 0.4528 time to fit residues: 43.2855 Evaluate side-chains 90 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.138103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.100888 restraints weight = 14322.581| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.55 r_work: 0.2947 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4858 Z= 0.147 Angle : 0.586 6.764 6611 Z= 0.305 Chirality : 0.041 0.154 751 Planarity : 0.004 0.036 803 Dihedral : 6.597 63.795 684 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.58 % Allowed : 15.42 % Favored : 83.00 % 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: 0.47 (0.35), residues: 599 helix: 0.83 (0.26), residues: 395 sheet: -1.21 (0.63), residues: 46 loop : -0.26 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.013 0.001 TYR A 378 PHE 0.018 0.002 PHE A 257 TRP 0.006 0.001 TRP A 309 HIS 0.001 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4857) covalent geometry : angle 0.58592 ( 6609) SS BOND : bond 0.00088 ( 1) SS BOND : angle 1.22271 ( 2) hydrogen bonds : bond 0.04121 ( 316) hydrogen bonds : angle 5.14095 ( 918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.183 Fit side-chains REVERT: A 158 TRP cc_start: 0.8714 (m100) cc_final: 0.8302 (m100) REVERT: A 169 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8529 (mt) REVERT: A 173 LYS cc_start: 0.8064 (tmtt) cc_final: 0.7441 (tptm) REVERT: A 294 TYR cc_start: 0.8993 (t80) cc_final: 0.8388 (t80) REVERT: A 356 MET cc_start: 0.4150 (mmt) cc_final: 0.3846 (mmt) REVERT: A 551 TYR cc_start: 0.8307 (m-80) cc_final: 0.7963 (m-80) outliers start: 8 outliers final: 4 residues processed: 91 average time/residue: 0.4630 time to fit residues: 44.2715 Evaluate side-chains 91 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.138426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.101768 restraints weight = 9836.055| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.28 r_work: 0.2982 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4858 Z= 0.155 Angle : 0.613 10.230 6611 Z= 0.314 Chirality : 0.041 0.156 751 Planarity : 0.004 0.036 803 Dihedral : 6.631 64.126 684 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.99 % Allowed : 16.21 % Favored : 82.81 % 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: 0.53 (0.35), residues: 599 helix: 0.87 (0.26), residues: 398 sheet: -1.21 (0.62), residues: 46 loop : -0.20 (0.55), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.013 0.001 TYR A 378 PHE 0.018 0.002 PHE A 257 TRP 0.006 0.001 TRP A 309 HIS 0.001 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4857) covalent geometry : angle 0.61319 ( 6609) SS BOND : bond 0.00098 ( 1) SS BOND : angle 1.24834 ( 2) hydrogen bonds : bond 0.04152 ( 316) hydrogen bonds : angle 5.15949 ( 918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.179 Fit side-chains REVERT: A 158 TRP cc_start: 0.8752 (m100) cc_final: 0.8414 (m100) REVERT: A 169 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8429 (mt) REVERT: A 173 LYS cc_start: 0.7946 (tmtt) cc_final: 0.7287 (tptm) REVERT: A 294 TYR cc_start: 0.9029 (t80) cc_final: 0.8377 (t80) REVERT: A 356 MET cc_start: 0.3975 (mmt) cc_final: 0.3583 (mmt) REVERT: A 551 TYR cc_start: 0.8348 (m-80) cc_final: 0.8050 (m-80) REVERT: A 557 LEU cc_start: 0.8568 (mm) cc_final: 0.8295 (tp) outliers start: 5 outliers final: 3 residues processed: 88 average time/residue: 0.4862 time to fit residues: 44.7994 Evaluate side-chains 89 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.103263 restraints weight = 11585.426| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.37 r_work: 0.2997 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4858 Z= 0.133 Angle : 0.613 14.060 6611 Z= 0.310 Chirality : 0.040 0.152 751 Planarity : 0.004 0.036 803 Dihedral : 6.502 62.877 684 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.38 % Allowed : 15.61 % Favored : 83.00 % 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: 0.69 (0.35), residues: 599 helix: 0.96 (0.26), residues: 401 sheet: -1.17 (0.63), residues: 46 loop : -0.08 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.012 0.001 TYR A 378 PHE 0.017 0.002 PHE A 257 TRP 0.008 0.001 TRP A 309 HIS 0.001 0.000 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4857) covalent geometry : angle 0.61326 ( 6609) SS BOND : bond 0.00040 ( 1) SS BOND : angle 1.00732 ( 2) hydrogen bonds : bond 0.03955 ( 316) hydrogen bonds : angle 5.05904 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2166.37 seconds wall clock time: 37 minutes 42.99 seconds (2262.99 seconds total)