Starting phenix.real_space_refine on Thu Jul 2 22:33:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlf_27500/07_2026/8dlf_27500.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlf_27500/07_2026/8dlf_27500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dlf_27500/07_2026/8dlf_27500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlf_27500/07_2026/8dlf_27500.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlf_27500/07_2026/8dlf_27500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlf_27500/07_2026/8dlf_27500.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4437 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 112 5.49 5 S 32 5.16 5 C 4224 2.51 5 N 1278 2.21 5 O 1521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7167 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1234 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "B" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1214 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 15, 'TRANS': 141} Chain: "C" Number of atoms: 1216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1216 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 15, 'TRANS': 141} Chain: "D" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1203 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 15, 'TRANS': 141} Chain: "E" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1146 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "F" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1150 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.57, per 1000 atoms: 0.22 Number of scatterers: 7167 At special positions: 0 Unit cell: (80.205, 194.631, 72.7192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 112 15.00 O 1521 8.00 N 1278 7.00 C 4224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 387.8 milliseconds 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1122 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 5 sheets defined 35.0% alpha, 13.8% beta 43 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 475 through 490 Processing helix chain 'A' and resid 513 through 526 removed outlier: 3.500A pdb=" N LEU A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 585 removed outlier: 4.043A pdb=" N ALA A 572 " --> pdb=" O THR A 568 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU A 573 " --> pdb=" O HIS A 569 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 591 Processing helix chain 'A' and resid 612 through 616 removed outlier: 3.557A pdb=" N GLU A 615 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 490 Processing helix chain 'B' and resid 513 through 528 Processing helix chain 'B' and resid 569 through 585 Processing helix chain 'B' and resid 587 through 591 removed outlier: 3.690A pdb=" N CYS B 591 " --> pdb=" O ALA B 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'C' and resid 513 through 528 removed outlier: 3.636A pdb=" N ASN C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 585 Processing helix chain 'C' and resid 587 through 593 Processing helix chain 'D' and resid 475 through 490 Processing helix chain 'D' and resid 513 through 526 Processing helix chain 'D' and resid 568 through 586 removed outlier: 3.514A pdb=" N LEU D 575 " --> pdb=" O PHE D 571 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS D 576 " --> pdb=" O ALA D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 614 removed outlier: 3.766A pdb=" N VAL D 614 " --> pdb=" O PRO D 611 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 505 through 510 removed outlier: 3.542A pdb=" N VAL A 509 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL A 559 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 532 through 533 removed outlier: 4.579A pdb=" N LEU B 539 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 559 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER B 537 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 532 through 533 removed outlier: 5.492A pdb=" N CYS B 560 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY B 506 " --> pdb=" O CYS B 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 532 through 533 removed outlier: 3.876A pdb=" N GLY C 506 " --> pdb=" O CYS C 598 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 537 through 540 removed outlier: 5.354A pdb=" N VAL D 559 " --> pdb=" O LEU D 539 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N CYS D 560 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 509 " --> pdb=" O PHE D 562 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1507 1.33 - 1.45: 2160 1.45 - 1.57: 3644 1.57 - 1.69: 222 1.69 - 1.81: 48 Bond restraints: 7581 Sorted by residual: bond pdb=" P DA F 39 " pdb=" O5' DA F 39 " ideal model delta sigma weight residual 1.593 1.632 -0.039 1.00e-02 1.00e+04 1.55e+01 bond pdb=" C2' DT E 34 " pdb=" C1' DT E 34 " ideal model delta sigma weight residual 1.518 1.556 -0.038 1.00e-02 1.00e+04 1.41e+01 bond pdb=" P DC F 41 " pdb=" O5' DC F 41 " ideal model delta sigma weight residual 1.593 1.629 -0.036 1.00e-02 1.00e+04 1.27e+01 bond pdb=" P DG F 40 " pdb=" O5' DG F 40 " ideal model delta sigma weight residual 1.593 1.628 -0.035 1.00e-02 1.00e+04 1.26e+01 bond pdb=" C2' DA F 25 " pdb=" C1' DA F 25 " ideal model delta sigma weight residual 1.518 1.483 0.035 1.00e-02 1.00e+04 1.21e+01 ... (remaining 7576 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 9580 1.62 - 3.25: 781 3.25 - 4.87: 166 4.87 - 6.49: 206 6.49 - 8.11: 34 Bond angle restraints: 10767 Sorted by residual: angle pdb=" C2' DT E 34 " pdb=" C1' DT E 34 " pdb=" N1 DT E 34 " ideal model delta sigma weight residual 114.30 121.78 -7.48 1.40e+00 5.10e-01 2.85e+01 angle pdb=" CA GLY A 463 " pdb=" C GLY A 463 " pdb=" O GLY A 463 " ideal model delta sigma weight residual 122.52 118.34 4.18 7.90e-01 1.60e+00 2.80e+01 angle pdb=" O3' DG E 16 " pdb=" P DC E 17 " pdb=" O5' DC E 17 " ideal model delta sigma weight residual 104.00 96.31 7.69 1.50e+00 4.44e-01 2.62e+01 angle pdb=" C4' DA E 39 " pdb=" C3' DA E 39 " pdb=" C2' DA E 39 " ideal model delta sigma weight residual 103.10 98.68 4.42 9.00e-01 1.23e+00 2.41e+01 angle pdb=" O3' DT F 33 " pdb=" P DA F 34 " pdb=" O5' DA F 34 " ideal model delta sigma weight residual 104.00 111.00 -7.00 1.50e+00 4.44e-01 2.18e+01 ... (remaining 10762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 3637 34.38 - 68.76: 581 68.76 - 103.15: 10 103.15 - 137.53: 3 137.53 - 171.91: 6 Dihedral angle restraints: 4237 sinusoidal: 2476 harmonic: 1761 Sorted by residual: dihedral pdb=" CA PHE C 610 " pdb=" C PHE C 610 " pdb=" N PRO C 611 " pdb=" CA PRO C 611 " ideal model delta harmonic sigma weight residual 180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" C4' DC F 50 " pdb=" C3' DC F 50 " pdb=" O3' DC F 50 " pdb=" P DC F 51 " ideal model delta sinusoidal sigma weight residual 220.00 48.09 171.91 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG F 1 " pdb=" C3' DG F 1 " pdb=" O3' DG F 1 " pdb=" P DA F 2 " ideal model delta sinusoidal sigma weight residual 220.00 57.93 162.07 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 4234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 1051 0.130 - 0.260: 18 0.260 - 0.390: 8 0.390 - 0.521: 60 0.521 - 0.651: 40 Chirality restraints: 1177 Sorted by residual: chirality pdb=" P DG F 40 " pdb=" OP1 DG F 40 " pdb=" OP2 DG F 40 " pdb=" O5' DG F 40 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DG F 1 " pdb=" OP1 DG F 1 " pdb=" OP2 DG F 1 " pdb=" O5' DG F 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DA E 1 " pdb=" OP1 DA E 1 " pdb=" OP2 DA E 1 " pdb=" O5' DA E 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 1.01e+01 ... (remaining 1174 not shown) Planarity restraints: 999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 586 " 0.013 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C LYS D 586 " -0.043 2.00e-02 2.50e+03 pdb=" O LYS D 586 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO D 587 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 611 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO B 612 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 612 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 612 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 611 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO A 612 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 612 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 612 " -0.029 5.00e-02 4.00e+02 ... (remaining 996 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 260 2.66 - 3.22: 6953 3.22 - 3.78: 14282 3.78 - 4.34: 17543 4.34 - 4.90: 25998 Nonbonded interactions: 65036 Sorted by model distance: nonbonded pdb=" ND2 ASN B 480 " pdb=" OP2 DT E 34 " model vdw 2.103 3.120 nonbonded pdb=" NH1 ARG C 538 " pdb=" O SER C 557 " model vdw 2.243 3.120 nonbonded pdb=" OG SER C 599 " pdb=" O SER D 599 " model vdw 2.255 3.040 nonbonded pdb=" O PRO C 476 " pdb=" ND2 ASN C 480 " model vdw 2.267 3.120 nonbonded pdb=" O LEU D 582 " pdb=" OG1 THR D 585 " model vdw 2.277 3.040 ... (remaining 65031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 461 through 614) selection = (chain 'B' and resid 461 through 614) selection = (chain 'C' and resid 461 through 614) selection = (chain 'D' and resid 461 through 614) } 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.150 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4773 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 : 0.009 0.061 7581 Z= 0.555 Angle : 1.274 8.114 10767 Z= 0.724 Chirality : 0.159 0.651 1177 Planarity : 0.006 0.059 999 Dihedral : 25.899 171.910 3115 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 35.48 Ramachandran Plot: Outliers : 1.44 % Allowed : 8.35 % Favored : 90.21 % Rotamer: Outliers : 8.48 % Allowed : 10.02 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.34), residues: 623 helix: 1.15 (0.37), residues: 195 sheet: -2.01 (0.52), residues: 76 loop : -2.44 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 469 TYR 0.008 0.002 TYR C 518 PHE 0.017 0.002 PHE D 562 TRP 0.013 0.002 TRP D 464 HIS 0.002 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00901 / 0.55 ( 7581) covalent geometry : angle 1.27408 / 0.72 (10767) hydrogen bonds : bond 0.20520 / 14.20 ( 289) hydrogen bonds : angle 11.08637 / 7.55 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.3676 (OUTLIER) cc_final: 0.3171 (m170) REVERT: A 495 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6630 (tt0) REVERT: A 602 ASP cc_start: 0.2129 (t0) cc_final: 0.1885 (p0) REVERT: B 497 THR cc_start: 0.5978 (OUTLIER) cc_final: 0.5635 (t) REVERT: B 565 PHE cc_start: 0.4431 (m-80) cc_final: 0.3271 (m-80) REVERT: C 497 THR cc_start: 0.6432 (OUTLIER) cc_final: 0.5873 (t) REVERT: C 562 PHE cc_start: 0.5176 (p90) cc_final: 0.4971 (p90) REVERT: C 565 PHE cc_start: 0.4890 (m-10) cc_final: 0.3896 (m-80) REVERT: D 467 LYS cc_start: 0.4095 (OUTLIER) cc_final: 0.3833 (mmmt) outliers start: 44 outliers final: 17 residues processed: 178 average time/residue: 0.0936 time to fit residues: 21.3805 Evaluate side-chains 113 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 592 ASN Chi-restraints excluded: chain D residue 467 LYS Chi-restraints excluded: chain D residue 468 HIS Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 606 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 ASN B 475 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.225700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.205666 restraints weight = 12939.242| |-----------------------------------------------------------------------------| r_work (start): 0.4860 rms_B_bonded: 1.80 r_work: 0.4718 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5635 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7581 Z= 0.219 Angle : 0.907 12.409 10767 Z= 0.493 Chirality : 0.061 0.416 1177 Planarity : 0.008 0.059 999 Dihedral : 30.508 173.861 1975 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 26.48 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.47 % Favored : 89.57 % Rotamer: Outliers : 7.71 % Allowed : 14.45 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.34), residues: 623 helix: 0.69 (0.37), residues: 196 sheet: -2.19 (0.54), residues: 81 loop : -2.39 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 594 TYR 0.013 0.002 TYR B 518 PHE 0.029 0.003 PHE D 610 TRP 0.014 0.003 TRP A 503 HIS 0.005 0.001 HIS C 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.22 ( 7581) covalent geometry : angle 0.90717 / 0.49 (10767) hydrogen bonds : bond 0.09994 / 7.32 ( 289) hydrogen bonds : angle 5.62396 / 3.96 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.4932 (OUTLIER) cc_final: 0.4230 (m170) REVERT: A 509 VAL cc_start: 0.4997 (OUTLIER) cc_final: 0.4632 (t) REVERT: A 543 MET cc_start: 0.4030 (mmp) cc_final: 0.3737 (mmp) REVERT: B 497 THR cc_start: 0.6233 (OUTLIER) cc_final: 0.5926 (t) REVERT: B 556 GLU cc_start: 0.3359 (OUTLIER) cc_final: 0.2715 (pm20) REVERT: B 558 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7023 (pp) REVERT: C 565 PHE cc_start: 0.5088 (m-10) cc_final: 0.4634 (m-80) REVERT: D 510 TYR cc_start: 0.6893 (p90) cc_final: 0.6657 (p90) REVERT: D 565 PHE cc_start: 0.2358 (OUTLIER) cc_final: 0.1658 (m-80) outliers start: 40 outliers final: 21 residues processed: 130 average time/residue: 0.0825 time to fit residues: 14.4607 Evaluate side-chains 114 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 468 HIS Chi-restraints excluded: chain D residue 503 TRP Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 606 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.225212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.204175 restraints weight = 13035.812| |-----------------------------------------------------------------------------| r_work (start): 0.4834 rms_B_bonded: 1.87 r_work: 0.4691 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5682 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7581 Z= 0.197 Angle : 0.805 12.123 10767 Z= 0.444 Chirality : 0.053 0.332 1177 Planarity : 0.007 0.059 999 Dihedral : 30.487 176.665 1963 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 25.66 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.83 % Favored : 90.21 % Rotamer: Outliers : 7.51 % Allowed : 16.76 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.34), residues: 623 helix: 0.61 (0.38), residues: 199 sheet: -2.50 (0.50), residues: 81 loop : -2.37 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 538 TYR 0.013 0.002 TYR B 518 PHE 0.028 0.002 PHE D 562 TRP 0.016 0.002 TRP D 464 HIS 0.002 0.001 HIS A 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.20 ( 7581) covalent geometry : angle 0.80475 / 0.44 (10767) hydrogen bonds : bond 0.08211 / 5.95 ( 289) hydrogen bonds : angle 5.46579 / 3.86 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5173 (OUTLIER) cc_final: 0.4489 (m170) REVERT: B 556 GLU cc_start: 0.3317 (OUTLIER) cc_final: 0.2647 (pm20) REVERT: B 558 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.7005 (pp) REVERT: B 596 THR cc_start: 0.5401 (t) cc_final: 0.5042 (p) REVERT: C 565 PHE cc_start: 0.5121 (m-10) cc_final: 0.4500 (m-80) outliers start: 39 outliers final: 24 residues processed: 128 average time/residue: 0.0782 time to fit residues: 13.8791 Evaluate side-chains 116 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 468 HIS Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 40 optimal weight: 0.0040 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.224325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.204271 restraints weight = 13207.426| |-----------------------------------------------------------------------------| r_work (start): 0.4832 rms_B_bonded: 1.78 r_work: 0.4695 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7581 Z= 0.192 Angle : 0.797 11.305 10767 Z= 0.436 Chirality : 0.054 0.340 1177 Planarity : 0.007 0.062 999 Dihedral : 30.475 178.484 1960 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 1.12 % Allowed : 9.47 % Favored : 89.41 % Rotamer: Outliers : 7.51 % Allowed : 17.34 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.34), residues: 623 helix: 0.58 (0.38), residues: 199 sheet: -2.47 (0.53), residues: 72 loop : -2.33 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 594 TYR 0.015 0.002 TYR C 510 PHE 0.019 0.002 PHE D 562 TRP 0.017 0.002 TRP A 503 HIS 0.002 0.001 HIS C 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 ( 7581) covalent geometry : angle 0.79667 / 0.44 (10767) hydrogen bonds : bond 0.07461 / 5.51 ( 289) hydrogen bonds : angle 5.32692 / 3.77 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5534 (OUTLIER) cc_final: 0.4838 (m170) REVERT: B 556 GLU cc_start: 0.3829 (OUTLIER) cc_final: 0.3179 (pm20) REVERT: B 558 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6995 (pp) REVERT: B 596 THR cc_start: 0.5144 (t) cc_final: 0.4873 (p) REVERT: B 610 PHE cc_start: 0.7056 (t80) cc_final: 0.6153 (p90) REVERT: C 565 PHE cc_start: 0.5205 (m-80) cc_final: 0.4552 (m-80) REVERT: C 591 CYS cc_start: 0.5872 (OUTLIER) cc_final: 0.4248 (p) outliers start: 39 outliers final: 26 residues processed: 125 average time/residue: 0.0770 time to fit residues: 13.3930 Evaluate side-chains 118 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain D residue 468 HIS Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.223750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.204847 restraints weight = 13426.929| |-----------------------------------------------------------------------------| r_work (start): 0.4842 rms_B_bonded: 1.76 r_work: 0.4699 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7581 Z= 0.183 Angle : 0.782 12.400 10767 Z= 0.427 Chirality : 0.053 0.304 1177 Planarity : 0.007 0.064 999 Dihedral : 30.498 179.566 1960 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.99 % Favored : 90.05 % Rotamer: Outliers : 7.90 % Allowed : 17.73 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.34), residues: 623 helix: 0.70 (0.38), residues: 198 sheet: -2.35 (0.56), residues: 70 loop : -2.38 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 532 TYR 0.013 0.002 TYR B 518 PHE 0.039 0.002 PHE D 610 TRP 0.017 0.002 TRP A 503 HIS 0.002 0.001 HIS A 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 ( 7581) covalent geometry : angle 0.78186 / 0.43 (10767) hydrogen bonds : bond 0.07303 / 5.34 ( 289) hydrogen bonds : angle 5.24226 / 3.70 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 91 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5755 (OUTLIER) cc_final: 0.5003 (m170) REVERT: B 556 GLU cc_start: 0.3854 (OUTLIER) cc_final: 0.3242 (pm20) REVERT: B 558 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7009 (pp) REVERT: B 596 THR cc_start: 0.4905 (t) cc_final: 0.4525 (p) REVERT: B 610 PHE cc_start: 0.7052 (t80) cc_final: 0.6192 (p90) REVERT: C 565 PHE cc_start: 0.4924 (m-80) cc_final: 0.4278 (m-80) REVERT: D 584 MET cc_start: 0.6195 (tmt) cc_final: 0.5901 (tmt) outliers start: 41 outliers final: 26 residues processed: 121 average time/residue: 0.0758 time to fit residues: 12.8879 Evaluate side-chains 117 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 0.0970 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.225615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.207549 restraints weight = 13403.406| |-----------------------------------------------------------------------------| r_work (start): 0.4869 rms_B_bonded: 1.72 r_work: 0.4731 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5635 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7581 Z= 0.162 Angle : 0.745 11.255 10767 Z= 0.411 Chirality : 0.051 0.302 1177 Planarity : 0.007 0.067 999 Dihedral : 30.474 179.122 1956 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.35 % Favored : 90.85 % Rotamer: Outliers : 6.36 % Allowed : 19.85 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.34), residues: 623 helix: 0.96 (0.39), residues: 192 sheet: -2.39 (0.55), residues: 71 loop : -2.36 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 594 TYR 0.010 0.002 TYR C 518 PHE 0.016 0.002 PHE C 562 TRP 0.007 0.001 TRP D 609 HIS 0.003 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 7581) covalent geometry : angle 0.74491 / 0.41 (10767) hydrogen bonds : bond 0.06695 / 4.94 ( 289) hydrogen bonds : angle 5.04655 / 3.57 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5715 (OUTLIER) cc_final: 0.4991 (m170) REVERT: B 558 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.7021 (pp) REVERT: B 596 THR cc_start: 0.5188 (t) cc_final: 0.4714 (m) REVERT: B 610 PHE cc_start: 0.7012 (t80) cc_final: 0.6216 (p90) REVERT: C 543 MET cc_start: 0.2083 (ttm) cc_final: 0.1409 (tmm) REVERT: C 565 PHE cc_start: 0.4918 (m-80) cc_final: 0.4334 (m-80) REVERT: C 591 CYS cc_start: 0.5505 (OUTLIER) cc_final: 0.4009 (p) REVERT: D 550 GLN cc_start: 0.2398 (OUTLIER) cc_final: 0.1794 (mt0) REVERT: D 584 MET cc_start: 0.6303 (tmt) cc_final: 0.6039 (tmt) outliers start: 33 outliers final: 23 residues processed: 116 average time/residue: 0.0752 time to fit residues: 12.1543 Evaluate side-chains 115 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain D residue 468 HIS Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.223097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.205084 restraints weight = 13281.630| |-----------------------------------------------------------------------------| r_work (start): 0.4844 rms_B_bonded: 1.65 r_work: 0.4707 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5717 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7581 Z= 0.193 Angle : 0.774 11.751 10767 Z= 0.423 Chirality : 0.053 0.302 1177 Planarity : 0.008 0.079 999 Dihedral : 30.469 177.755 1953 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 25.51 Ramachandran Plot: Outliers : 0.80 % Allowed : 10.91 % Favored : 88.28 % Rotamer: Outliers : 7.32 % Allowed : 20.42 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.34), residues: 623 helix: 0.79 (0.38), residues: 191 sheet: -2.42 (0.55), residues: 71 loop : -2.47 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 555 TYR 0.012 0.002 TYR B 518 PHE 0.042 0.003 PHE D 610 TRP 0.011 0.002 TRP A 503 HIS 0.003 0.001 HIS C 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 ( 7581) covalent geometry : angle 0.77354 / 0.42 (10767) hydrogen bonds : bond 0.07132 / 5.24 ( 289) hydrogen bonds : angle 5.16967 / 3.65 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5552 (OUTLIER) cc_final: 0.4896 (m170) REVERT: B 556 GLU cc_start: 0.3877 (OUTLIER) cc_final: 0.3289 (pm20) REVERT: B 558 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6936 (pp) REVERT: B 596 THR cc_start: 0.5212 (t) cc_final: 0.4793 (m) REVERT: B 610 PHE cc_start: 0.6993 (t80) cc_final: 0.6201 (p90) REVERT: C 543 MET cc_start: 0.2201 (ttm) cc_final: 0.1423 (tmm) REVERT: C 565 PHE cc_start: 0.5103 (m-80) cc_final: 0.4346 (m-80) REVERT: C 591 CYS cc_start: 0.5665 (OUTLIER) cc_final: 0.4199 (p) REVERT: D 584 MET cc_start: 0.6338 (tmt) cc_final: 0.6096 (tmt) outliers start: 38 outliers final: 26 residues processed: 112 average time/residue: 0.0796 time to fit residues: 12.3340 Evaluate side-chains 115 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 TRP Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.223637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.205794 restraints weight = 13361.252| |-----------------------------------------------------------------------------| r_work (start): 0.4851 rms_B_bonded: 1.66 r_work: 0.4715 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7581 Z= 0.174 Angle : 0.748 12.039 10767 Z= 0.410 Chirality : 0.052 0.297 1177 Planarity : 0.008 0.072 999 Dihedral : 30.521 178.118 1953 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 23.63 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.95 % Favored : 89.25 % Rotamer: Outliers : 6.74 % Allowed : 21.19 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.34), residues: 623 helix: 0.78 (0.38), residues: 191 sheet: -2.24 (0.57), residues: 66 loop : -2.53 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 555 TYR 0.011 0.002 TYR B 518 PHE 0.042 0.002 PHE D 610 TRP 0.014 0.002 TRP D 609 HIS 0.003 0.001 HIS C 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 7581) covalent geometry : angle 0.74763 / 0.41 (10767) hydrogen bonds : bond 0.06640 / 4.88 ( 289) hydrogen bonds : angle 5.03166 / 3.56 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5441 (OUTLIER) cc_final: 0.4655 (m170) REVERT: B 558 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6952 (pp) REVERT: B 596 THR cc_start: 0.4996 (t) cc_final: 0.4475 (p) REVERT: B 610 PHE cc_start: 0.6967 (t80) cc_final: 0.6189 (p90) REVERT: C 543 MET cc_start: 0.2041 (ttm) cc_final: 0.1292 (tmm) REVERT: C 565 PHE cc_start: 0.4995 (m-80) cc_final: 0.4343 (m-80) REVERT: C 591 CYS cc_start: 0.5544 (OUTLIER) cc_final: 0.4192 (p) REVERT: D 485 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.6040 (tt) outliers start: 35 outliers final: 22 residues processed: 112 average time/residue: 0.0767 time to fit residues: 11.9403 Evaluate side-chains 112 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 53 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 56 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.224394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.206586 restraints weight = 13089.642| |-----------------------------------------------------------------------------| r_work (start): 0.4860 rms_B_bonded: 1.65 r_work: 0.4727 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5676 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7581 Z= 0.167 Angle : 0.742 11.459 10767 Z= 0.406 Chirality : 0.051 0.298 1177 Planarity : 0.008 0.074 999 Dihedral : 30.506 177.990 1953 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 22.88 Ramachandran Plot: Outliers : 0.80 % Allowed : 10.75 % Favored : 88.44 % Rotamer: Outliers : 5.78 % Allowed : 21.97 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.34), residues: 623 helix: 0.83 (0.39), residues: 192 sheet: -2.24 (0.57), residues: 66 loop : -2.53 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 555 TYR 0.012 0.002 TYR B 518 PHE 0.018 0.002 PHE D 562 TRP 0.011 0.001 TRP D 609 HIS 0.003 0.001 HIS A 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 ( 7581) covalent geometry : angle 0.74219 / 0.41 (10767) hydrogen bonds : bond 0.06606 / 4.84 ( 289) hydrogen bonds : angle 4.94152 / 3.46 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5747 (OUTLIER) cc_final: 0.4959 (m170) REVERT: B 556 GLU cc_start: 0.3836 (OUTLIER) cc_final: 0.3320 (pm20) REVERT: B 558 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6989 (pp) REVERT: B 596 THR cc_start: 0.4973 (t) cc_final: 0.4407 (p) REVERT: B 610 PHE cc_start: 0.6868 (t80) cc_final: 0.6117 (p90) REVERT: C 543 MET cc_start: 0.2039 (ttm) cc_final: 0.1799 (tmm) REVERT: C 565 PHE cc_start: 0.4971 (m-80) cc_final: 0.4387 (m-80) REVERT: C 591 CYS cc_start: 0.5464 (OUTLIER) cc_final: 0.4144 (p) outliers start: 30 outliers final: 22 residues processed: 113 average time/residue: 0.0662 time to fit residues: 10.3711 Evaluate side-chains 113 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 66 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 40 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5022 r_free = 0.5022 target = 0.221255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.203124 restraints weight = 13118.093| |-----------------------------------------------------------------------------| r_work (start): 0.4823 rms_B_bonded: 1.65 r_work: 0.4679 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7581 Z= 0.199 Angle : 0.792 11.747 10767 Z= 0.428 Chirality : 0.054 0.313 1177 Planarity : 0.008 0.073 999 Dihedral : 30.521 175.818 1953 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 25.81 Ramachandran Plot: Outliers : 0.80 % Allowed : 11.24 % Favored : 87.96 % Rotamer: Outliers : 5.20 % Allowed : 22.74 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.33), residues: 623 helix: 0.43 (0.38), residues: 193 sheet: -2.29 (0.56), residues: 64 loop : -2.61 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 555 TYR 0.016 0.003 TYR C 510 PHE 0.024 0.002 PHE D 562 TRP 0.015 0.002 TRP D 609 HIS 0.003 0.001 HIS C 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 ( 7581) covalent geometry : angle 0.79237 / 0.43 (10767) hydrogen bonds : bond 0.07237 / 5.24 ( 289) hydrogen bonds : angle 5.14104 / 3.60 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5857 (OUTLIER) cc_final: 0.5194 (m170) REVERT: A 584 MET cc_start: 0.4009 (mmm) cc_final: 0.3683 (tpt) REVERT: B 556 GLU cc_start: 0.4025 (OUTLIER) cc_final: 0.3558 (pm20) REVERT: B 558 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6945 (pp) REVERT: B 596 THR cc_start: 0.5074 (t) cc_final: 0.4539 (p) REVERT: B 610 PHE cc_start: 0.6969 (t80) cc_final: 0.6220 (p90) REVERT: C 543 MET cc_start: 0.2159 (ttm) cc_final: 0.1334 (tmm) REVERT: C 565 PHE cc_start: 0.5192 (m-80) cc_final: 0.4361 (m-80) REVERT: C 591 CYS cc_start: 0.5569 (OUTLIER) cc_final: 0.4266 (p) outliers start: 27 outliers final: 21 residues processed: 103 average time/residue: 0.0740 time to fit residues: 10.6304 Evaluate side-chains 106 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 614 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 54 optimal weight: 0.0070 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.0060 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 0.0770 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.2572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.225973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.208741 restraints weight = 13254.505| |-----------------------------------------------------------------------------| r_work (start): 0.4882 rms_B_bonded: 1.65 r_work: 0.4750 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7581 Z= 0.155 Angle : 0.732 10.924 10767 Z= 0.400 Chirality : 0.050 0.300 1177 Planarity : 0.007 0.074 999 Dihedral : 30.432 178.766 1953 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.19 % Favored : 91.01 % Rotamer: Outliers : 4.05 % Allowed : 23.51 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.34), residues: 623 helix: 0.92 (0.38), residues: 193 sheet: -2.31 (0.55), residues: 66 loop : -2.60 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 555 TYR 0.009 0.001 TYR B 518 PHE 0.018 0.002 PHE C 562 TRP 0.015 0.001 TRP D 609 HIS 0.002 0.000 HIS A 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 ( 7581) covalent geometry : angle 0.73191 / 0.40 (10767) hydrogen bonds : bond 0.06160 / 4.48 ( 289) hydrogen bonds : angle 4.82877 / 3.37 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1630.69 seconds wall clock time: 28 minutes 42.92 seconds (1722.92 seconds total)