Starting phenix.real_space_refine on Fri Jul 25 08:18:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wxi_37908/07_2025/8wxi_37908_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wxi_37908/07_2025/8wxi_37908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wxi_37908/07_2025/8wxi_37908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wxi_37908/07_2025/8wxi_37908.map" model { file = "/net/cci-nas-00/data/ceres_data/8wxi_37908/07_2025/8wxi_37908_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wxi_37908/07_2025/8wxi_37908_neut.cif" } resolution = 2.57 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 4796 2.51 5 N 1142 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7194 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3585 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain breaks: 1 Chain: "B" Number of atoms: 3585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3585 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain breaks: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Unusual residues: {'SCN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Unusual residues: {'SCN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 9.74, per 1000 atoms: 1.35 Number of scatterers: 7194 At special positions: 0 Unit cell: (72.45, 107.45, 70.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1190 8.00 N 1142 7.00 C 4796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 2 sheets defined 74.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 115 through 153 Processing helix chain 'A' and resid 156 through 182 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 234 through 251 removed outlier: 5.715A pdb=" N SER A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 280 removed outlier: 3.938A pdb=" N PHE A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 298 through 323 Processing helix chain 'A' and resid 347 through 379 removed outlier: 3.929A pdb=" N ARG A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 391 through 405 Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.823A pdb=" N VAL A 448 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 475 Processing helix chain 'A' and resid 483 through 506 Processing helix chain 'A' and resid 520 through 538 Processing helix chain 'A' and resid 541 through 551 Processing helix chain 'A' and resid 555 through 572 Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'B' and resid 116 through 153 Processing helix chain 'B' and resid 156 through 182 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 208 through 224 Processing helix chain 'B' and resid 234 through 251 removed outlier: 5.715A pdb=" N SER B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 280 removed outlier: 3.938A pdb=" N PHE B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 298 through 323 Processing helix chain 'B' and resid 347 through 379 removed outlier: 3.929A pdb=" N ARG B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 Processing helix chain 'B' and resid 391 through 405 Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 443 through 448 removed outlier: 3.823A pdb=" N VAL B 448 " --> pdb=" O GLN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 475 Processing helix chain 'B' and resid 483 through 506 Processing helix chain 'B' and resid 520 through 538 Processing helix chain 'B' and resid 541 through 551 Processing helix chain 'B' and resid 555 through 572 Processing helix chain 'B' and resid 576 through 585 Processing sheet with id=AA1, first strand: chain 'A' and resid 510 through 511 Processing sheet with id=AA2, first strand: chain 'B' and resid 510 through 511 531 hydrogen bonds defined for protein. 1575 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: 2.28 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1070 1.29 - 1.42: 1992 1.42 - 1.55: 4169 1.55 - 1.68: 49 1.68 - 1.81: 106 Bond restraints: 7386 Sorted by residual: bond pdb=" C SER B 183 " pdb=" N PRO B 184 " ideal model delta sigma weight residual 1.334 1.378 -0.044 8.40e-03 1.42e+04 2.74e+01 bond pdb=" C SER A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 1.334 1.378 -0.044 8.40e-03 1.42e+04 2.74e+01 bond pdb=" C PHE A 506 " pdb=" N PRO A 507 " ideal model delta sigma weight residual 1.335 1.379 -0.044 9.40e-03 1.13e+04 2.23e+01 bond pdb=" C PHE B 506 " pdb=" N PRO B 507 " ideal model delta sigma weight residual 1.335 1.379 -0.044 9.40e-03 1.13e+04 2.23e+01 bond pdb=" CA THR B 281 " pdb=" C THR B 281 " ideal model delta sigma weight residual 1.520 1.578 -0.058 1.25e-02 6.40e+03 2.16e+01 ... (remaining 7381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.27: 9864 4.27 - 8.54: 144 8.54 - 12.81: 20 12.81 - 17.08: 4 17.08 - 21.35: 2 Bond angle restraints: 10034 Sorted by residual: angle pdb=" N SER A 442 " pdb=" CA SER A 442 " pdb=" C SER A 442 " ideal model delta sigma weight residual 114.12 99.92 14.20 1.39e+00 5.18e-01 1.04e+02 angle pdb=" N SER B 442 " pdb=" CA SER B 442 " pdb=" C SER B 442 " ideal model delta sigma weight residual 114.12 99.92 14.20 1.39e+00 5.18e-01 1.04e+02 angle pdb=" N HIS B 237 " pdb=" CA HIS B 237 " pdb=" C HIS B 237 " ideal model delta sigma weight residual 110.80 89.45 21.35 2.13e+00 2.20e-01 1.00e+02 angle pdb=" N HIS A 237 " pdb=" CA HIS A 237 " pdb=" C HIS A 237 " ideal model delta sigma weight residual 110.80 89.45 21.35 2.13e+00 2.20e-01 1.00e+02 angle pdb=" N VAL A 236 " pdb=" CA VAL A 236 " pdb=" CB VAL A 236 " ideal model delta sigma weight residual 111.23 127.11 -15.88 1.65e+00 3.67e-01 9.26e+01 ... (remaining 10029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 3328 15.62 - 31.24: 421 31.24 - 46.86: 293 46.86 - 62.49: 202 62.49 - 78.11: 8 Dihedral angle restraints: 4252 sinusoidal: 1586 harmonic: 2666 Sorted by residual: dihedral pdb=" N VAL A 236 " pdb=" C VAL A 236 " pdb=" CA VAL A 236 " pdb=" CB VAL A 236 " ideal model delta harmonic sigma weight residual 123.40 145.63 -22.23 0 2.50e+00 1.60e-01 7.91e+01 dihedral pdb=" N VAL B 236 " pdb=" C VAL B 236 " pdb=" CA VAL B 236 " pdb=" CB VAL B 236 " ideal model delta harmonic sigma weight residual 123.40 145.63 -22.23 0 2.50e+00 1.60e-01 7.91e+01 dihedral pdb=" C VAL A 236 " pdb=" N VAL A 236 " pdb=" CA VAL A 236 " pdb=" CB VAL A 236 " ideal model delta harmonic sigma weight residual -122.00 -138.83 16.83 0 2.50e+00 1.60e-01 4.53e+01 ... (remaining 4249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1025 0.133 - 0.266: 123 0.266 - 0.398: 12 0.398 - 0.531: 4 0.531 - 0.664: 6 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA VAL A 236 " pdb=" N VAL A 236 " pdb=" C VAL A 236 " pdb=" CB VAL A 236 " both_signs ideal model delta sigma weight residual False 2.44 1.78 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA VAL B 236 " pdb=" N VAL B 236 " pdb=" C VAL B 236 " pdb=" CB VAL B 236 " both_signs ideal model delta sigma weight residual False 2.44 1.78 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA ASP B 429 " pdb=" N ASP B 429 " pdb=" C ASP B 429 " pdb=" CB ASP B 429 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.34e+00 ... (remaining 1167 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 233 " -0.047 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO B 234 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 233 " -0.047 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO A 234 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 407 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO A 408 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 408 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 408 " 0.038 5.00e-02 4.00e+02 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.78: 15 1.78 - 2.56: 54 2.56 - 3.34: 9498 3.34 - 4.12: 20736 4.12 - 4.90: 36761 Nonbonded interactions: 67064 Sorted by model distance: nonbonded pdb=" CE1 PHE A 297 " pdb=" CE1 PHE B 297 " model vdw 1.006 3.640 nonbonded pdb=" CZ PHE A 297 " pdb=" CE1 PHE B 297 " model vdw 1.176 3.640 nonbonded pdb=" CE1 PHE A 297 " pdb=" CZ PHE B 297 " model vdw 1.176 3.640 nonbonded pdb=" CE1 PHE A 297 " pdb=" CD1 PHE B 297 " model vdw 1.298 3.640 nonbonded pdb=" CD1 PHE A 297 " pdb=" CE1 PHE B 297 " model vdw 1.298 3.640 ... (remaining 67059 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 33.340 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: 0.440 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 26.690 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:15.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3523 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 : 0.015 0.594 7394 Z= 1.368 Angle : 1.436 21.347 10034 Z= 0.946 Chirality : 0.101 0.664 1170 Planarity : 0.008 0.072 1226 Dihedral : 22.852 78.108 2544 Min Nonbonded Distance : 1.006 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 1.08 % Allowed : 7.56 % Favored : 91.36 % Rotamer: Outliers : 33.33 % Allowed : 10.37 % Favored : 56.30 % Cbeta Deviations : 0.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.23), residues: 926 helix: -1.69 (0.16), residues: 684 sheet: None (None), residues: 0 loop : -3.62 (0.33), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 469 HIS 0.007 0.001 HIS B 436 PHE 0.021 0.003 PHE B 279 TYR 0.022 0.003 TYR A 206 ARG 0.003 0.000 ARG A 496 Details of bonding type rmsd hydrogen bonds : bond 0.14935 ( 531) hydrogen bonds : angle 6.73505 ( 1575) covalent geometry : bond 0.00931 ( 7386) covalent geometry : angle 1.43592 (10034) Misc. bond : bond 0.36096 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 197 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 ILE cc_start: 0.3790 (OUTLIER) cc_final: 0.3524 (mt) REVERT: A 250 MET cc_start: 0.5459 (OUTLIER) cc_final: 0.5003 (mtp) REVERT: A 329 ILE cc_start: 0.4151 (OUTLIER) cc_final: 0.3672 (mp) REVERT: A 332 LEU cc_start: 0.4039 (OUTLIER) cc_final: 0.3775 (pt) REVERT: A 339 MET cc_start: 0.4855 (tpp) cc_final: 0.4136 (tpt) REVERT: A 510 ILE cc_start: 0.4001 (OUTLIER) cc_final: 0.3756 (mt) REVERT: A 515 ILE cc_start: 0.3854 (OUTLIER) cc_final: 0.3580 (mt) REVERT: B 238 ILE cc_start: 0.3785 (OUTLIER) cc_final: 0.3521 (mt) REVERT: B 250 MET cc_start: 0.5457 (OUTLIER) cc_final: 0.4997 (mtp) REVERT: B 264 SER cc_start: 0.4752 (OUTLIER) cc_final: 0.4315 (p) REVERT: B 329 ILE cc_start: 0.4154 (OUTLIER) cc_final: 0.3674 (mp) REVERT: B 332 LEU cc_start: 0.4039 (OUTLIER) cc_final: 0.3776 (pt) REVERT: B 339 MET cc_start: 0.4859 (tpp) cc_final: 0.4141 (tpt) REVERT: B 510 ILE cc_start: 0.3999 (OUTLIER) cc_final: 0.3753 (mt) REVERT: B 515 ILE cc_start: 0.3854 (OUTLIER) cc_final: 0.3581 (mt) outliers start: 254 outliers final: 46 residues processed: 355 average time/residue: 0.9498 time to fit residues: 359.4432 Evaluate side-chains 192 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 133 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 513 ASP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 546 CYS Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 546 CYS Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 580 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 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 144 GLN A 160 GLN A 451 HIS A 455 ASN B 144 GLN B 160 GLN B 451 HIS B 455 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.148530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114786 restraints weight = 7562.814| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.98 r_work: 0.3256 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7394 Z= 0.176 Angle : 0.682 8.214 10034 Z= 0.367 Chirality : 0.045 0.204 1170 Planarity : 0.007 0.065 1226 Dihedral : 11.715 59.724 1107 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.67 % Favored : 95.90 % Rotamer: Outliers : 10.89 % Allowed : 20.34 % Favored : 68.77 % 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: -0.77 (0.26), residues: 926 helix: 0.34 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -3.05 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 469 HIS 0.003 0.001 HIS A 369 PHE 0.026 0.002 PHE B 341 TYR 0.009 0.001 TYR B 578 ARG 0.003 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04687 ( 531) hydrogen bonds : angle 4.75820 ( 1575) covalent geometry : bond 0.00408 ( 7386) covalent geometry : angle 0.68199 (10034) Misc. bond : bond 0.00237 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 131 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 THR cc_start: 0.8264 (m) cc_final: 0.8035 (p) REVERT: A 290 ILE cc_start: 0.8043 (mp) cc_final: 0.7719 (mt) REVERT: A 300 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6059 (ptt-90) REVERT: A 332 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5884 (pt) REVERT: A 338 ARG cc_start: 0.8335 (mtp180) cc_final: 0.8064 (mtt-85) REVERT: A 385 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6443 (t80) REVERT: A 421 ARG cc_start: 0.7959 (ptp-170) cc_final: 0.7409 (mtm110) REVERT: A 439 ASP cc_start: 0.6381 (t70) cc_final: 0.6161 (p0) REVERT: B 245 VAL cc_start: 0.7466 (t) cc_final: 0.7266 (m) REVERT: B 281 THR cc_start: 0.8257 (m) cc_final: 0.8025 (p) REVERT: B 290 ILE cc_start: 0.8037 (mp) cc_final: 0.7713 (mt) REVERT: B 300 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6065 (ptt-90) REVERT: B 332 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5864 (pt) REVERT: B 385 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6437 (t80) REVERT: B 421 ARG cc_start: 0.7978 (ptp-170) cc_final: 0.7432 (mtm110) REVERT: B 439 ASP cc_start: 0.6370 (t70) cc_final: 0.6162 (p0) outliers start: 83 outliers final: 21 residues processed: 192 average time/residue: 0.9491 time to fit residues: 194.9662 Evaluate side-chains 148 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 515 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112879 restraints weight = 7487.100| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.96 r_work: 0.3188 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7394 Z= 0.163 Angle : 0.652 7.283 10034 Z= 0.339 Chirality : 0.043 0.149 1170 Planarity : 0.006 0.061 1226 Dihedral : 6.751 47.682 1014 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.67 % Favored : 95.90 % Rotamer: Outliers : 7.09 % Allowed : 21.78 % Favored : 71.13 % 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: 0.37 (0.27), residues: 926 helix: 1.18 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.72 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 469 HIS 0.003 0.001 HIS B 451 PHE 0.016 0.002 PHE A 343 TYR 0.007 0.001 TYR B 206 ARG 0.003 0.001 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 531) hydrogen bonds : angle 4.42775 ( 1575) covalent geometry : bond 0.00375 ( 7386) covalent geometry : angle 0.65165 (10034) Misc. bond : bond 0.00341 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 126 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8392 (mm) REVERT: A 231 LYS cc_start: 0.6469 (OUTLIER) cc_final: 0.6021 (ptmt) REVERT: A 300 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6254 (ptt-90) REVERT: A 332 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6103 (pt) REVERT: A 338 ARG cc_start: 0.8359 (mtp180) cc_final: 0.8135 (mtt-85) REVERT: A 385 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6513 (t80) REVERT: A 421 ARG cc_start: 0.8042 (ptp-170) cc_final: 0.7507 (mtm110) REVERT: A 439 ASP cc_start: 0.6487 (t70) cc_final: 0.6286 (p0) REVERT: B 123 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8387 (mm) REVERT: B 231 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.6025 (ptmt) REVERT: B 300 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6231 (ptt-90) REVERT: B 306 PHE cc_start: 0.8434 (t80) cc_final: 0.8227 (t80) REVERT: B 332 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6101 (pt) REVERT: B 385 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6516 (t80) REVERT: B 421 ARG cc_start: 0.8034 (ptp-170) cc_final: 0.7501 (mtm110) outliers start: 54 outliers final: 20 residues processed: 166 average time/residue: 1.0657 time to fit residues: 187.8644 Evaluate side-chains 146 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 550 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS B 180 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.141994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107741 restraints weight = 7552.008| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.98 r_work: 0.3105 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7394 Z= 0.201 Angle : 0.655 7.243 10034 Z= 0.339 Chirality : 0.046 0.267 1170 Planarity : 0.006 0.063 1226 Dihedral : 6.404 47.846 1010 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.56 % Favored : 96.00 % Rotamer: Outliers : 7.87 % Allowed : 22.31 % Favored : 69.82 % 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: 0.68 (0.27), residues: 926 helix: 1.47 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -2.68 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 469 HIS 0.002 0.001 HIS A 451 PHE 0.015 0.002 PHE A 306 TYR 0.009 0.001 TYR A 206 ARG 0.003 0.001 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 531) hydrogen bonds : angle 4.39523 ( 1575) covalent geometry : bond 0.00488 ( 7386) covalent geometry : angle 0.65486 (10034) Misc. bond : bond 0.00216 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 124 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5330 (mt-10) REVERT: A 231 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.6169 (ptmt) REVERT: A 262 TYR cc_start: 0.5034 (OUTLIER) cc_final: 0.3333 (p90) REVERT: A 300 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6302 (ptt-90) REVERT: A 332 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6105 (pt) REVERT: A 338 ARG cc_start: 0.8373 (mtp180) cc_final: 0.8141 (mtt-85) REVERT: A 346 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8147 (mtmm) REVERT: A 385 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6102 (t80) REVERT: A 421 ARG cc_start: 0.8031 (ptp-170) cc_final: 0.7537 (mtm110) REVERT: A 439 ASP cc_start: 0.6519 (t70) cc_final: 0.6282 (p0) REVERT: B 116 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5419 (mt-10) REVERT: B 231 LYS cc_start: 0.6390 (OUTLIER) cc_final: 0.6146 (ptmt) REVERT: B 300 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6275 (ptt-90) REVERT: B 317 ARG cc_start: 0.6988 (mpt180) cc_final: 0.5785 (tmt-80) REVERT: B 332 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6089 (pt) REVERT: B 345 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8487 (tt) REVERT: B 346 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8136 (mtmm) REVERT: B 385 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6105 (t80) REVERT: B 421 ARG cc_start: 0.8026 (ptp-170) cc_final: 0.7530 (mtm110) outliers start: 60 outliers final: 22 residues processed: 166 average time/residue: 1.2907 time to fit residues: 226.6786 Evaluate side-chains 155 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 550 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110610 restraints weight = 7527.575| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.00 r_work: 0.3146 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7394 Z= 0.150 Angle : 0.604 6.683 10034 Z= 0.309 Chirality : 0.044 0.205 1170 Planarity : 0.006 0.061 1226 Dihedral : 6.026 47.611 1006 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.00 % Favored : 95.57 % Rotamer: Outliers : 6.69 % Allowed : 22.70 % Favored : 70.60 % 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: 1.04 (0.27), residues: 926 helix: 1.85 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -2.74 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 469 HIS 0.002 0.001 HIS B 451 PHE 0.016 0.001 PHE A 306 TYR 0.007 0.001 TYR A 206 ARG 0.002 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 531) hydrogen bonds : angle 4.17212 ( 1575) covalent geometry : bond 0.00348 ( 7386) covalent geometry : angle 0.60408 (10034) Misc. bond : bond 0.00204 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5475 (mt-10) REVERT: A 204 LYS cc_start: 0.3799 (OUTLIER) cc_final: 0.3568 (ptmt) REVERT: A 262 TYR cc_start: 0.5074 (OUTLIER) cc_final: 0.3424 (p90) REVERT: A 281 THR cc_start: 0.8353 (m) cc_final: 0.8027 (p) REVERT: A 300 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6269 (ptt-90) REVERT: A 332 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6393 (pp) REVERT: A 338 ARG cc_start: 0.8358 (mtp180) cc_final: 0.8139 (mtt-85) REVERT: A 346 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8134 (mtmm) REVERT: A 385 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6037 (t80) REVERT: A 421 ARG cc_start: 0.7989 (ptp-170) cc_final: 0.7499 (mtm110) REVERT: A 439 ASP cc_start: 0.6602 (t70) cc_final: 0.6315 (p0) REVERT: B 116 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5498 (mt-10) REVERT: B 204 LYS cc_start: 0.3812 (OUTLIER) cc_final: 0.3581 (ptmt) REVERT: B 281 THR cc_start: 0.8346 (m) cc_final: 0.8018 (p) REVERT: B 300 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6236 (ptt-90) REVERT: B 317 ARG cc_start: 0.6892 (mpt180) cc_final: 0.5707 (tmt-80) REVERT: B 332 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6378 (pp) REVERT: B 345 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8415 (tt) REVERT: B 346 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8103 (mtmm) REVERT: B 385 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6052 (t80) REVERT: B 421 ARG cc_start: 0.7981 (ptp-170) cc_final: 0.7492 (mtm110) outliers start: 51 outliers final: 16 residues processed: 167 average time/residue: 1.1144 time to fit residues: 196.8791 Evaluate side-chains 152 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 443 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.143946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110194 restraints weight = 7458.215| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.98 r_work: 0.3099 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7394 Z= 0.158 Angle : 0.609 6.894 10034 Z= 0.311 Chirality : 0.043 0.207 1170 Planarity : 0.006 0.062 1226 Dihedral : 5.753 47.382 1004 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.67 % Favored : 95.90 % Rotamer: Outliers : 7.22 % Allowed : 21.39 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.27), residues: 926 helix: 1.93 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -2.63 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 469 HIS 0.002 0.001 HIS B 180 PHE 0.019 0.002 PHE A 306 TYR 0.010 0.001 TYR A 263 ARG 0.003 0.001 ARG B 390 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 531) hydrogen bonds : angle 4.16212 ( 1575) covalent geometry : bond 0.00371 ( 7386) covalent geometry : angle 0.60879 (10034) Misc. bond : bond 0.00202 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5916 (tt0) REVERT: A 204 LYS cc_start: 0.3760 (OUTLIER) cc_final: 0.3529 (ptmt) REVERT: A 231 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.6107 (ptmt) REVERT: A 262 TYR cc_start: 0.4970 (OUTLIER) cc_final: 0.3450 (p90) REVERT: A 281 THR cc_start: 0.8404 (m) cc_final: 0.8031 (p) REVERT: A 300 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6313 (ptt-90) REVERT: A 338 ARG cc_start: 0.8341 (mtp180) cc_final: 0.8108 (mtt-85) REVERT: A 346 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8080 (mtmm) REVERT: A 385 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6075 (t80) REVERT: A 421 ARG cc_start: 0.8010 (ptp-170) cc_final: 0.7523 (mtm110) REVERT: A 439 ASP cc_start: 0.6657 (t70) cc_final: 0.6313 (p0) REVERT: B 116 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5613 (mt-10) REVERT: B 204 LYS cc_start: 0.3795 (OUTLIER) cc_final: 0.3570 (ptmt) REVERT: B 231 LYS cc_start: 0.6347 (OUTLIER) cc_final: 0.6115 (ptmt) REVERT: B 281 THR cc_start: 0.8411 (m) cc_final: 0.8031 (p) REVERT: B 300 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6281 (ptt-90) REVERT: B 345 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8415 (tt) REVERT: B 346 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8084 (mtmm) REVERT: B 385 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6077 (t80) REVERT: B 421 ARG cc_start: 0.7999 (ptp-170) cc_final: 0.7513 (mtm110) outliers start: 55 outliers final: 22 residues processed: 173 average time/residue: 1.1293 time to fit residues: 206.2612 Evaluate side-chains 156 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 443 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 86 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.146384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112775 restraints weight = 7389.855| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.99 r_work: 0.3175 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7394 Z= 0.135 Angle : 0.605 6.933 10034 Z= 0.304 Chirality : 0.042 0.145 1170 Planarity : 0.006 0.062 1226 Dihedral : 5.376 46.937 1000 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.56 % Favored : 96.00 % Rotamer: Outliers : 5.25 % Allowed : 23.49 % Favored : 71.26 % 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: 1.37 (0.27), residues: 926 helix: 2.08 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -2.58 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 469 HIS 0.002 0.000 HIS A 180 PHE 0.019 0.001 PHE A 306 TYR 0.008 0.001 TYR A 206 ARG 0.002 0.000 ARG B 317 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 531) hydrogen bonds : angle 4.09159 ( 1575) covalent geometry : bond 0.00306 ( 7386) covalent geometry : angle 0.60474 (10034) Misc. bond : bond 0.00211 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5958 (tt0) REVERT: A 204 LYS cc_start: 0.3710 (OUTLIER) cc_final: 0.3505 (ptmt) REVERT: A 281 THR cc_start: 0.8411 (m) cc_final: 0.8027 (p) REVERT: A 300 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6265 (ptt-90) REVERT: A 346 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8061 (mtmm) REVERT: A 385 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6067 (t80) REVERT: A 421 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7478 (mtm110) REVERT: A 439 ASP cc_start: 0.6688 (t70) cc_final: 0.6312 (p0) REVERT: B 116 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5644 (mt-10) REVERT: B 204 LYS cc_start: 0.3718 (OUTLIER) cc_final: 0.3480 (ptmm) REVERT: B 262 TYR cc_start: 0.5251 (OUTLIER) cc_final: 0.3647 (p90) REVERT: B 281 THR cc_start: 0.8385 (m) cc_final: 0.8014 (p) REVERT: B 283 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7829 (tp) REVERT: B 300 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6244 (ptt-90) REVERT: B 317 ARG cc_start: 0.6980 (mpt180) cc_final: 0.5782 (tmt-80) REVERT: B 338 ARG cc_start: 0.8331 (mtp180) cc_final: 0.7334 (mmt-90) REVERT: B 346 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8075 (mtmm) REVERT: B 385 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6073 (t80) REVERT: B 421 ARG cc_start: 0.7957 (ptp-170) cc_final: 0.7469 (mtm110) outliers start: 40 outliers final: 18 residues processed: 162 average time/residue: 1.1356 time to fit residues: 194.4440 Evaluate side-chains 157 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 443 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.0060 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.148548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115582 restraints weight = 7628.391| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.04 r_work: 0.3267 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7394 Z= 0.130 Angle : 0.597 6.736 10034 Z= 0.301 Chirality : 0.042 0.145 1170 Planarity : 0.006 0.066 1226 Dihedral : 5.074 41.130 998 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.78 % Favored : 95.79 % Rotamer: Outliers : 5.25 % Allowed : 23.62 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.27), residues: 926 helix: 2.25 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -2.58 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 469 HIS 0.002 0.000 HIS B 555 PHE 0.019 0.001 PHE A 306 TYR 0.007 0.001 TYR A 206 ARG 0.004 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 531) hydrogen bonds : angle 4.03659 ( 1575) covalent geometry : bond 0.00290 ( 7386) covalent geometry : angle 0.59705 (10034) Misc. bond : bond 0.00211 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5880 (tt0) REVERT: A 204 LYS cc_start: 0.3594 (OUTLIER) cc_final: 0.3358 (ptmm) REVERT: A 281 THR cc_start: 0.8365 (m) cc_final: 0.7965 (p) REVERT: A 300 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6175 (ptt-90) REVERT: A 304 ARG cc_start: 0.8012 (mtm110) cc_final: 0.7773 (mtm110) REVERT: A 332 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6304 (pp) REVERT: A 338 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.6966 (mmt-90) REVERT: A 346 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8175 (mtmm) REVERT: A 385 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.5980 (t80) REVERT: A 421 ARG cc_start: 0.7842 (ptp-170) cc_final: 0.7329 (mtm110) REVERT: A 439 ASP cc_start: 0.6678 (t70) cc_final: 0.6279 (p0) REVERT: B 204 LYS cc_start: 0.3609 (OUTLIER) cc_final: 0.3382 (ptmm) REVERT: B 281 THR cc_start: 0.8284 (m) cc_final: 0.8016 (p) REVERT: B 300 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6146 (ptt-90) REVERT: B 304 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7758 (mtm110) REVERT: B 317 ARG cc_start: 0.6739 (mpt180) cc_final: 0.5614 (tmt-80) REVERT: B 332 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6291 (pp) REVERT: B 338 ARG cc_start: 0.8124 (mtp180) cc_final: 0.7267 (mmt-90) REVERT: B 345 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8271 (tp) REVERT: B 346 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7978 (mtmm) REVERT: B 385 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.5983 (t80) REVERT: B 421 ARG cc_start: 0.7851 (ptp-170) cc_final: 0.7336 (mtm110) outliers start: 40 outliers final: 14 residues processed: 156 average time/residue: 1.2123 time to fit residues: 199.2653 Evaluate side-chains 145 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 443 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.145573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112868 restraints weight = 7701.505| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.00 r_work: 0.3231 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7394 Z= 0.156 Angle : 0.617 6.888 10034 Z= 0.313 Chirality : 0.043 0.150 1170 Planarity : 0.006 0.061 1226 Dihedral : 5.118 39.526 998 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.67 % Favored : 96.00 % Rotamer: Outliers : 4.99 % Allowed : 24.28 % Favored : 70.73 % 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: 1.53 (0.27), residues: 926 helix: 2.19 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -2.48 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 469 HIS 0.002 0.000 HIS B 555 PHE 0.022 0.002 PHE A 306 TYR 0.009 0.001 TYR B 206 ARG 0.003 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 531) hydrogen bonds : angle 4.12597 ( 1575) covalent geometry : bond 0.00369 ( 7386) covalent geometry : angle 0.61663 (10034) Misc. bond : bond 0.00194 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5878 (tt0) REVERT: A 157 LEU cc_start: 0.8620 (tp) cc_final: 0.8397 (mt) REVERT: A 204 LYS cc_start: 0.3620 (OUTLIER) cc_final: 0.3384 (ptmm) REVERT: A 281 THR cc_start: 0.8389 (m) cc_final: 0.7992 (p) REVERT: A 300 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6237 (ptt-90) REVERT: A 332 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6304 (pp) REVERT: A 338 ARG cc_start: 0.8104 (mtt-85) cc_final: 0.7000 (mmt-90) REVERT: A 346 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.7960 (mtmm) REVERT: A 385 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6035 (t80) REVERT: A 421 ARG cc_start: 0.7879 (ptp-170) cc_final: 0.7369 (mtm110) REVERT: A 439 ASP cc_start: 0.6683 (t70) cc_final: 0.6237 (p0) REVERT: B 157 LEU cc_start: 0.8616 (tp) cc_final: 0.8398 (mt) REVERT: B 204 LYS cc_start: 0.3607 (OUTLIER) cc_final: 0.3356 (ptmm) REVERT: B 281 THR cc_start: 0.8359 (m) cc_final: 0.8012 (p) REVERT: B 300 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6220 (ptt-90) REVERT: B 332 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6303 (pp) REVERT: B 338 ARG cc_start: 0.8162 (mtp180) cc_final: 0.7287 (mmt-90) REVERT: B 346 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7957 (mtmm) REVERT: B 385 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6020 (t80) REVERT: B 421 ARG cc_start: 0.7875 (ptp-170) cc_final: 0.7368 (mtm110) REVERT: B 441 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7248 (pm20) outliers start: 38 outliers final: 17 residues processed: 149 average time/residue: 1.2585 time to fit residues: 197.3276 Evaluate side-chains 148 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 443 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.146532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.113803 restraints weight = 7791.561| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.02 r_work: 0.3244 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7394 Z= 0.143 Angle : 0.609 6.797 10034 Z= 0.307 Chirality : 0.042 0.149 1170 Planarity : 0.006 0.062 1226 Dihedral : 5.092 40.929 998 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.21 % Favored : 95.57 % Rotamer: Outliers : 4.99 % Allowed : 24.15 % Favored : 70.87 % 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: 1.60 (0.27), residues: 926 helix: 2.23 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -2.43 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 469 HIS 0.002 0.000 HIS A 555 PHE 0.023 0.002 PHE A 306 TYR 0.009 0.001 TYR B 263 ARG 0.003 0.000 ARG B 390 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 531) hydrogen bonds : angle 4.09107 ( 1575) covalent geometry : bond 0.00333 ( 7386) covalent geometry : angle 0.60891 (10034) Misc. bond : bond 0.00197 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5892 (tt0) REVERT: A 157 LEU cc_start: 0.8603 (tp) cc_final: 0.8382 (mt) REVERT: A 204 LYS cc_start: 0.3588 (OUTLIER) cc_final: 0.3366 (ptmm) REVERT: A 281 THR cc_start: 0.8383 (m) cc_final: 0.7992 (p) REVERT: A 300 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6236 (ptt-90) REVERT: A 304 ARG cc_start: 0.8022 (mtm110) cc_final: 0.7796 (mtm110) REVERT: A 332 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6295 (pp) REVERT: A 338 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.6987 (mmt-90) REVERT: A 346 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7962 (mtmm) REVERT: A 385 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.5991 (t80) REVERT: A 421 ARG cc_start: 0.7860 (ptp-170) cc_final: 0.7349 (mtm110) REVERT: A 439 ASP cc_start: 0.6700 (t70) cc_final: 0.6192 (p0) REVERT: A 441 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7206 (pm20) REVERT: B 157 LEU cc_start: 0.8613 (tp) cc_final: 0.8396 (mt) REVERT: B 199 ARG cc_start: 0.7525 (mmp80) cc_final: 0.7014 (mpt180) REVERT: B 204 LYS cc_start: 0.3564 (OUTLIER) cc_final: 0.3339 (ptmm) REVERT: B 281 THR cc_start: 0.8337 (m) cc_final: 0.7996 (p) REVERT: B 300 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6212 (ptt-90) REVERT: B 304 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7788 (mtm110) REVERT: B 317 ARG cc_start: 0.6872 (mpt180) cc_final: 0.5700 (tmt-80) REVERT: B 332 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6293 (pp) REVERT: B 338 ARG cc_start: 0.8172 (mtp180) cc_final: 0.7287 (mmt-90) REVERT: B 346 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7952 (mtmm) REVERT: B 385 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.5961 (t80) REVERT: B 421 ARG cc_start: 0.7870 (ptp-170) cc_final: 0.7357 (mtm110) REVERT: B 441 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7318 (pm20) outliers start: 38 outliers final: 17 residues processed: 153 average time/residue: 1.2448 time to fit residues: 200.5740 Evaluate side-chains 147 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 443 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 85 optimal weight: 0.0670 chunk 84 optimal weight: 0.9980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116970 restraints weight = 7618.014| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.00 r_work: 0.3288 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7394 Z= 0.127 Angle : 0.593 6.605 10034 Z= 0.298 Chirality : 0.042 0.175 1170 Planarity : 0.006 0.064 1226 Dihedral : 5.027 41.156 998 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.78 % Favored : 95.90 % Rotamer: Outliers : 3.81 % Allowed : 25.33 % Favored : 70.87 % 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: 1.82 (0.27), residues: 926 helix: 2.40 (0.19), residues: 678 sheet: None (None), residues: 0 loop : -2.40 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 469 HIS 0.002 0.000 HIS A 555 PHE 0.023 0.001 PHE A 306 TYR 0.009 0.001 TYR B 263 ARG 0.002 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 531) hydrogen bonds : angle 4.03103 ( 1575) covalent geometry : bond 0.00283 ( 7386) covalent geometry : angle 0.59294 (10034) Misc. bond : bond 0.00211 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9989.46 seconds wall clock time: 174 minutes 26.73 seconds (10466.73 seconds total)