Starting phenix.real_space_refine on Sat May 10 02:39:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3l_61118/05_2025/9j3l_61118.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3l_61118/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9j3l_61118/05_2025/9j3l_61118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3l_61118/05_2025/9j3l_61118.map" model { file = "/net/cci-nas-00/data/ceres_data/9j3l_61118/05_2025/9j3l_61118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3l_61118/05_2025/9j3l_61118.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.093 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.28, per 1000 atoms: 1.12 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: 1.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.53 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: 1.41 Time building geometry restraints manager: 1.48 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: 1.220 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (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 TRP 0.016 0.001 TRP A 333 HIS 0.001 0.001 HIS A 210 PHE 0.016 0.001 PHE A 452 TYR 0.027 0.002 TYR A 337 ARG 0.010 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.20363 ( 316) hydrogen bonds : angle 8.63110 ( 918) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.87709 ( 2) covalent geometry : bond 0.00386 ( 4857) covalent geometry : angle 0.78729 ( 6609) *********************** 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 : 0.552 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: 0.8491 time to fit residues: 96.9203 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 : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 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 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 = 0.3509 r_free = 0.3509 target = 0.138190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.102279 restraints weight = 8670.738| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.09 r_work: 0.2974 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4858 Z= 0.173 Angle : 0.665 9.360 6611 Z= 0.348 Chirality : 0.043 0.169 751 Planarity : 0.005 0.043 803 Dihedral : 7.803 63.957 684 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.19 % Allowed : 8.70 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.34), residues: 599 helix: -0.32 (0.25), residues: 407 sheet: -1.52 (0.63), residues: 48 loop : -0.46 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 563 HIS 0.002 0.001 HIS A 210 PHE 0.022 0.002 PHE A 257 TYR 0.014 0.002 TYR A 378 ARG 0.004 0.001 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.05142 ( 316) hydrogen bonds : angle 5.90695 ( 918) SS BOND : bond 0.00250 ( 1) SS BOND : angle 1.62275 ( 2) covalent geometry : bond 0.00375 ( 4857) covalent geometry : angle 0.66438 ( 6609) *********************** 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 104 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.496 Fit side-chains REVERT: A 158 TRP cc_start: 0.8715 (m100) cc_final: 0.8289 (m100) REVERT: A 169 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8590 (mt) REVERT: A 173 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7546 (tptm) REVERT: A 294 TYR cc_start: 0.9060 (t80) cc_final: 0.8523 (t80) REVERT: A 353 MET cc_start: 0.6908 (tpt) cc_final: 0.6646 (tpt) REVERT: A 356 MET cc_start: 0.3735 (mmt) cc_final: 0.3491 (mmt) REVERT: A 554 MET cc_start: 0.8331 (mtm) cc_final: 0.8026 (mtp) REVERT: C 46 GLU cc_start: 0.8589 (tt0) cc_final: 0.8328 (tt0) outliers start: 6 outliers final: 0 residues processed: 100 average time/residue: 0.8046 time to fit residues: 85.0195 Evaluate side-chains 92 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.0070 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.0040 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 overall best weight: 0.3210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN A 401 ASN C 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.141152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.104837 restraints weight = 11634.891| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.35 r_work: 0.2941 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1726 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= 0.130 Angle : 0.601 7.794 6611 Z= 0.311 Chirality : 0.040 0.147 751 Planarity : 0.005 0.038 803 Dihedral : 6.976 56.292 684 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.99 % Allowed : 11.66 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.35), residues: 599 helix: 0.47 (0.26), residues: 404 sheet: -1.54 (0.56), residues: 48 loop : -0.19 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 309 HIS 0.000 0.000 HIS A 210 PHE 0.019 0.002 PHE A 257 TYR 0.011 0.001 TYR A 378 ARG 0.005 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 316) hydrogen bonds : angle 5.25007 ( 918) SS BOND : bond 0.00104 ( 1) SS BOND : angle 1.15386 ( 2) covalent geometry : bond 0.00277 ( 4857) covalent geometry : angle 0.60120 ( 6609) *********************** 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 104 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.565 Fit side-chains REVERT: A 169 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8512 (mt) REVERT: A 173 LYS cc_start: 0.7997 (tmtt) cc_final: 0.7413 (tptm) REVERT: A 294 TYR cc_start: 0.9062 (t80) cc_final: 0.8469 (t80) REVERT: A 353 MET cc_start: 0.6950 (tpt) cc_final: 0.6612 (tpt) REVERT: A 356 MET cc_start: 0.3608 (mmt) cc_final: 0.3333 (mmt) REVERT: A 554 MET cc_start: 0.8249 (mtm) cc_final: 0.8044 (mtp) outliers start: 5 outliers final: 1 residues processed: 102 average time/residue: 0.8587 time to fit residues: 92.1691 Evaluate side-chains 94 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 207 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.0370 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.0170 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.140136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.103743 restraints weight = 10573.399| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.27 r_work: 0.3012 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4858 Z= 0.137 Angle : 0.591 7.263 6611 Z= 0.304 Chirality : 0.040 0.155 751 Planarity : 0.004 0.036 803 Dihedral : 6.666 61.151 684 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.99 % Allowed : 14.43 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.35), residues: 599 helix: 0.71 (0.26), residues: 404 sheet: -1.29 (0.59), residues: 46 loop : -0.04 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 309 HIS 0.001 0.001 HIS A 210 PHE 0.017 0.002 PHE A 257 TYR 0.012 0.001 TYR A 378 ARG 0.003 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 316) hydrogen bonds : angle 5.06453 ( 918) SS BOND : bond 0.00101 ( 1) SS BOND : angle 1.23317 ( 2) covalent geometry : bond 0.00300 ( 4857) covalent geometry : angle 0.59034 ( 6609) *********************** 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: 5 poor density : 98 time to evaluate : 0.529 Fit side-chains REVERT: A 169 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8575 (mt) REVERT: A 173 LYS cc_start: 0.8014 (tmtt) cc_final: 0.7464 (tptm) REVERT: A 294 TYR cc_start: 0.9079 (t80) cc_final: 0.8504 (t80) REVERT: A 353 MET cc_start: 0.6926 (tpt) cc_final: 0.6629 (tpt) REVERT: A 356 MET cc_start: 0.3732 (mmt) cc_final: 0.3397 (mmt) outliers start: 5 outliers final: 0 residues processed: 100 average time/residue: 0.8489 time to fit residues: 89.5589 Evaluate side-chains 92 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3524 r_free = 0.3524 target = 0.139243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.102878 restraints weight = 10024.523| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.21 r_work: 0.2997 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4858 Z= 0.148 Angle : 0.590 6.750 6611 Z= 0.305 Chirality : 0.041 0.164 751 Planarity : 0.004 0.035 803 Dihedral : 6.638 61.976 684 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.58 % Allowed : 14.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.35), residues: 599 helix: 0.70 (0.26), residues: 404 sheet: -1.20 (0.60), residues: 46 loop : 0.08 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 563 HIS 0.001 0.001 HIS A 210 PHE 0.017 0.002 PHE A 257 TYR 0.013 0.001 TYR A 378 ARG 0.004 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 316) hydrogen bonds : angle 5.03815 ( 918) SS BOND : bond 0.00119 ( 1) SS BOND : angle 1.27746 ( 2) covalent geometry : bond 0.00331 ( 4857) covalent geometry : angle 0.58951 ( 6609) *********************** 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 98 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.531 Fit side-chains REVERT: A 169 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8544 (mt) REVERT: A 173 LYS cc_start: 0.7974 (tmtt) cc_final: 0.7414 (tptm) REVERT: A 294 TYR cc_start: 0.9068 (t80) cc_final: 0.8542 (t80) REVERT: A 353 MET cc_start: 0.6921 (tpt) cc_final: 0.6618 (tpt) REVERT: A 356 MET cc_start: 0.3831 (mmt) cc_final: 0.3511 (mmt) REVERT: A 512 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6140 (ttmt) outliers start: 8 outliers final: 3 residues processed: 93 average time/residue: 0.8776 time to fit residues: 85.8866 Evaluate side-chains 93 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 A residue 512 LYS Chi-restraints excluded: chain C residue 17 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3504 r_free = 0.3504 target = 0.137548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100430 restraints weight = 12973.156| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.44 r_work: 0.2948 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4858 Z= 0.162 Angle : 0.596 6.967 6611 Z= 0.309 Chirality : 0.041 0.154 751 Planarity : 0.004 0.035 803 Dihedral : 6.641 64.011 684 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.58 % Allowed : 14.62 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.35), residues: 599 helix: 0.68 (0.26), residues: 402 sheet: -1.19 (0.61), residues: 46 loop : -0.00 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 563 HIS 0.002 0.001 HIS A 210 PHE 0.017 0.002 PHE A 257 TYR 0.014 0.001 TYR A 378 ARG 0.003 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 316) hydrogen bonds : angle 5.08155 ( 918) SS BOND : bond 0.00128 ( 1) SS BOND : angle 1.36185 ( 2) covalent geometry : bond 0.00370 ( 4857) covalent geometry : angle 0.59522 ( 6609) *********************** 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 95 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.570 Fit side-chains REVERT: A 169 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8530 (mt) REVERT: A 173 LYS cc_start: 0.7944 (tmtt) cc_final: 0.7402 (tptm) REVERT: A 294 TYR cc_start: 0.9020 (t80) cc_final: 0.8474 (t80) REVERT: A 353 MET cc_start: 0.6846 (tpt) cc_final: 0.6599 (tpt) REVERT: A 356 MET cc_start: 0.3872 (mmt) cc_final: 0.3577 (mmt) outliers start: 8 outliers final: 3 residues processed: 90 average time/residue: 0.8596 time to fit residues: 81.5360 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 : 0.520 ------------------------------------------------------------------------------- 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 A residue 557 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.138074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.101523 restraints weight = 10750.192| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.26 r_work: 0.2977 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4858 Z= 0.148 Angle : 0.584 6.803 6611 Z= 0.303 Chirality : 0.041 0.153 751 Planarity : 0.004 0.035 803 Dihedral : 6.560 63.850 684 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.78 % Allowed : 15.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.35), residues: 599 helix: 0.84 (0.26), residues: 399 sheet: -1.12 (0.61), residues: 46 loop : -0.15 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.001 0.001 HIS A 210 PHE 0.017 0.002 PHE A 257 TYR 0.013 0.001 TYR A 378 ARG 0.002 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 316) hydrogen bonds : angle 5.02491 ( 918) SS BOND : bond 0.00103 ( 1) SS BOND : angle 1.23351 ( 2) covalent geometry : bond 0.00332 ( 4857) covalent geometry : angle 0.58344 ( 6609) *********************** 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 94 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.523 Fit side-chains REVERT: A 169 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8550 (mt) REVERT: A 173 LYS cc_start: 0.8061 (tmtt) cc_final: 0.7428 (tptm) REVERT: A 294 TYR cc_start: 0.9063 (t80) cc_final: 0.8514 (t80) REVERT: A 353 MET cc_start: 0.6947 (tpt) cc_final: 0.6740 (tmt) REVERT: A 356 MET cc_start: 0.4048 (mmt) cc_final: 0.3722 (mmt) REVERT: A 429 PHE cc_start: 0.8453 (m-10) cc_final: 0.8228 (m-80) outliers start: 9 outliers final: 6 residues processed: 89 average time/residue: 0.7985 time to fit residues: 75.1142 Evaluate side-chains 91 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 342 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain C residue 84 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 12 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.104319 restraints weight = 7746.261| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.96 r_work: 0.2951 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4858 Z= 0.132 Angle : 0.575 6.882 6611 Z= 0.298 Chirality : 0.040 0.150 751 Planarity : 0.004 0.035 803 Dihedral : 6.439 63.075 684 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.37 % Allowed : 14.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.35), residues: 599 helix: 0.90 (0.26), residues: 402 sheet: -1.07 (0.62), residues: 46 loop : -0.11 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 309 HIS 0.001 0.001 HIS A 210 PHE 0.016 0.002 PHE A 257 TYR 0.012 0.001 TYR A 378 ARG 0.002 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 316) hydrogen bonds : angle 4.96024 ( 918) SS BOND : bond 0.00043 ( 1) SS BOND : angle 1.08449 ( 2) covalent geometry : bond 0.00290 ( 4857) covalent geometry : angle 0.57458 ( 6609) *********************** 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 100 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.508 Fit side-chains REVERT: A 169 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8491 (mt) REVERT: A 173 LYS cc_start: 0.7959 (tmtt) cc_final: 0.7365 (tptm) REVERT: A 294 TYR cc_start: 0.9040 (t80) cc_final: 0.8429 (t80) REVERT: A 353 MET cc_start: 0.6914 (tpt) cc_final: 0.6570 (tpt) REVERT: A 356 MET cc_start: 0.4090 (mmt) cc_final: 0.3729 (mmt) outliers start: 12 outliers final: 5 residues processed: 95 average time/residue: 0.8390 time to fit residues: 84.6433 Evaluate side-chains 93 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 557 LEU Chi-restraints excluded: chain C residue 84 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.138038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.101509 restraints weight = 10571.599| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.25 r_work: 0.2895 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4858 Z= 0.155 Angle : 0.589 6.941 6611 Z= 0.306 Chirality : 0.041 0.154 751 Planarity : 0.004 0.035 803 Dihedral : 6.505 63.805 684 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.78 % Allowed : 15.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.35), residues: 599 helix: 0.90 (0.26), residues: 398 sheet: -1.07 (0.62), residues: 46 loop : -0.28 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.002 0.001 HIS A 210 PHE 0.017 0.002 PHE A 257 TYR 0.014 0.002 TYR A 378 ARG 0.002 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 316) hydrogen bonds : angle 5.02038 ( 918) SS BOND : bond 0.00085 ( 1) SS BOND : angle 1.28082 ( 2) covalent geometry : bond 0.00352 ( 4857) covalent geometry : angle 0.58876 ( 6609) *********************** 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 97 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.491 Fit side-chains REVERT: A 169 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8544 (mt) REVERT: A 173 LYS cc_start: 0.7986 (tmtt) cc_final: 0.7420 (tptm) REVERT: A 294 TYR cc_start: 0.9083 (t80) cc_final: 0.8538 (t80) REVERT: A 353 MET cc_start: 0.6910 (tpt) cc_final: 0.6571 (tpt) REVERT: A 356 MET cc_start: 0.4079 (mmt) cc_final: 0.3724 (mmt) REVERT: A 429 PHE cc_start: 0.8576 (m-80) cc_final: 0.8374 (m-80) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.8718 time to fit residues: 84.6530 Evaluate side-chains 94 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 557 LEU Chi-restraints excluded: chain C residue 84 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.138410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.101764 restraints weight = 11455.812| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.34 r_work: 0.2960 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4858 Z= 0.146 Angle : 0.587 6.763 6611 Z= 0.305 Chirality : 0.041 0.152 751 Planarity : 0.004 0.035 803 Dihedral : 6.468 63.453 684 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.35), residues: 599 helix: 0.88 (0.26), residues: 402 sheet: -1.06 (0.62), residues: 46 loop : -0.33 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 47 HIS 0.001 0.001 HIS A 210 PHE 0.017 0.002 PHE A 257 TYR 0.013 0.001 TYR A 378 ARG 0.003 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 316) hydrogen bonds : angle 5.00434 ( 918) SS BOND : bond 0.00089 ( 1) SS BOND : angle 1.19966 ( 2) covalent geometry : bond 0.00331 ( 4857) covalent geometry : angle 0.58715 ( 6609) ********************** 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 94 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8558 (mt) REVERT: A 173 LYS cc_start: 0.7981 (tmtt) cc_final: 0.7414 (tptm) REVERT: A 294 TYR cc_start: 0.9062 (t80) cc_final: 0.8464 (t80) REVERT: A 356 MET cc_start: 0.4070 (mmt) cc_final: 0.3732 (mmt) REVERT: A 429 PHE cc_start: 0.8582 (m-80) cc_final: 0.8353 (m-80) outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 0.8610 time to fit residues: 81.8955 Evaluate side-chains 93 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 557 LEU Chi-restraints excluded: chain C residue 84 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 52 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.102627 restraints weight = 13592.224| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.56 r_work: 0.2981 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4858 Z= 0.132 Angle : 0.582 6.704 6611 Z= 0.301 Chirality : 0.041 0.148 751 Planarity : 0.004 0.035 803 Dihedral : 6.342 62.793 684 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.35), residues: 599 helix: 1.00 (0.26), residues: 401 sheet: -1.05 (0.62), residues: 46 loop : -0.04 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 309 HIS 0.001 0.000 HIS A 210 PHE 0.016 0.002 PHE A 257 TYR 0.013 0.001 TYR A 378 ARG 0.002 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 316) hydrogen bonds : angle 4.92975 ( 918) SS BOND : bond 0.00040 ( 1) SS BOND : angle 1.02811 ( 2) covalent geometry : bond 0.00292 ( 4857) covalent geometry : angle 0.58159 ( 6609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4124.27 seconds wall clock time: 71 minutes 53.72 seconds (4313.72 seconds total)