Starting phenix.real_space_refine on Fri Sep 11 17:37:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlf_27500/09_2026/8dlf_27500.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlf_27500/09_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_27500/09_2026/8dlf_27500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlf_27500/09_2026/8dlf_27500.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlf_27500/09_2026/8dlf_27500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlf_27500/09_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-2.2.1-6174/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: 1.71, per 1000 atoms: 0.24 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: 0.63 Conformation dependent library (CDL) restraints added in 316.0 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: 1.06 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: 1.11 Time building geometry restraints manager: 0.81 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=" O3' DA E 39 " pdb=" P DG E 40 " ideal model delta sigma weight residual 1.607 1.656 -0.049 1.20e-02 6.94e+03 1.67e+01 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 ... (remaining 7576 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 9584 1.62 - 3.25: 782 3.25 - 4.87: 169 4.87 - 6.49: 199 6.49 - 8.11: 33 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=" C3' DT E 30 " pdb=" O3' DT E 30 " pdb=" P DA E 31 " ideal model delta sigma weight residual 119.70 113.70 6.00 1.20e+00 6.94e-01 2.50e+01 angle pdb=" C3' DG E 36 " pdb=" O3' DG E 36 " pdb=" P DG E 37 " ideal model delta sigma weight residual 119.70 113.72 5.98 1.20e+00 6.94e-01 2.48e+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 ... (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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.470 Find NCS groups from input model: 0.100 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.880 ------------------------------------------------------------------------------- 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= 0.557 Angle : 1.263 8.114 10767 Z= 0.733 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 / 0.56 ( 7581) covalent geometry : angle 1.26347 / 0.73 (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 : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.3676 (OUTLIER) cc_final: 0.3182 (m170) REVERT: A 495 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6631 (tt0) REVERT: A 602 ASP cc_start: 0.2129 (t0) cc_final: 0.1883 (p0) REVERT: B 497 THR cc_start: 0.5978 (OUTLIER) cc_final: 0.5633 (t) REVERT: B 565 PHE cc_start: 0.4431 (m-80) cc_final: 0.3269 (m-80) REVERT: C 497 THR cc_start: 0.6432 (OUTLIER) cc_final: 0.5875 (t) REVERT: C 562 PHE cc_start: 0.5176 (p90) cc_final: 0.4970 (p90) REVERT: C 565 PHE cc_start: 0.4890 (m-10) cc_final: 0.3895 (m-80) REVERT: D 467 LYS cc_start: 0.4095 (OUTLIER) cc_final: 0.3833 (mmmt) outliers start: 44 outliers final: 18 residues processed: 178 average time/residue: 0.1012 time to fit residues: 23.2720 Evaluate side-chains 113 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG 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: 10.0000 chunk 53 optimal weight: 0.0470 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.5073 r_free = 0.5073 target = 0.226281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.206190 restraints weight = 12979.723| |-----------------------------------------------------------------------------| r_work (start): 0.4866 rms_B_bonded: 1.82 r_work: 0.4726 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7581 Z= 0.208 Angle : 0.871 12.149 10767 Z= 0.483 Chirality : 0.059 0.417 1177 Planarity : 0.008 0.059 999 Dihedral : 30.517 174.121 1979 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 25.88 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.63 % Favored : 89.41 % Rotamer: Outliers : 6.94 % Allowed : 15.61 % Favored : 77.46 % 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: -1.89 (0.34), residues: 623 helix: 0.81 (0.37), residues: 196 sheet: -2.16 (0.55), residues: 81 loop : -2.37 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 469 TYR 0.013 0.002 TYR B 518 PHE 0.028 0.003 PHE D 610 TRP 0.017 0.003 TRP A 464 HIS 0.004 0.001 HIS C 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.21 ( 7581) covalent geometry : angle 0.87079 / 0.48 (10767) hydrogen bonds : bond 0.09834 / 7.19 ( 289) hydrogen bonds : angle 5.60005 / 3.95 ( 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 137 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.4934 (OUTLIER) cc_final: 0.4228 (m170) REVERT: B 497 THR cc_start: 0.6219 (OUTLIER) cc_final: 0.5908 (t) REVERT: B 556 GLU cc_start: 0.3315 (OUTLIER) cc_final: 0.2644 (pm20) REVERT: B 558 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.7024 (pp) REVERT: C 562 PHE cc_start: 0.5435 (p90) cc_final: 0.5224 (p90) REVERT: C 565 PHE cc_start: 0.5201 (m-10) cc_final: 0.4738 (m-80) REVERT: D 477 LYS cc_start: 0.4671 (mtmt) cc_final: 0.4269 (mtmt) REVERT: D 510 TYR cc_start: 0.6933 (p90) cc_final: 0.6710 (p90) REVERT: D 565 PHE cc_start: 0.2286 (OUTLIER) cc_final: 0.1684 (m-80) outliers start: 36 outliers final: 19 residues processed: 128 average time/residue: 0.0842 time to fit residues: 14.7241 Evaluate side-chains 113 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 488 LEU 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 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 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: 0.9980 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 7 optimal weight: 0.0980 chunk 13 optimal weight: 0.0770 chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 475 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.227777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.208586 restraints weight = 13115.628| |-----------------------------------------------------------------------------| r_work (start): 0.4882 rms_B_bonded: 1.72 r_work: 0.4750 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5557 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7581 Z= 0.177 Angle : 0.798 11.705 10767 Z= 0.436 Chirality : 0.054 0.352 1177 Planarity : 0.007 0.059 999 Dihedral : 30.515 176.481 1967 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.35 % Favored : 90.69 % Rotamer: Outliers : 6.94 % Allowed : 17.15 % Favored : 75.92 % 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: 0.90 (0.38), residues: 199 sheet: -2.61 (0.49), residues: 82 loop : -2.29 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 521 TYR 0.011 0.001 TYR B 518 PHE 0.026 0.002 PHE D 562 TRP 0.009 0.001 TRP C 503 HIS 0.003 0.001 HIS C 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.18 ( 7581) covalent geometry : angle 0.79800 / 0.44 (10767) hydrogen bonds : bond 0.07613 / 5.53 ( 289) hydrogen bonds : angle 5.23767 / 3.70 ( 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 139 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.4788 (OUTLIER) cc_final: 0.4173 (m170) REVERT: B 558 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6953 (pp) REVERT: B 596 THR cc_start: 0.5130 (t) cc_final: 0.4718 (p) REVERT: C 565 PHE cc_start: 0.5065 (m-10) cc_final: 0.4557 (m-80) REVERT: D 510 TYR cc_start: 0.6842 (p90) cc_final: 0.6609 (p90) outliers start: 36 outliers final: 23 residues processed: 128 average time/residue: 0.0850 time to fit residues: 14.7256 Evaluate side-chains 117 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 468 HIS 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 492 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 558 ILE 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 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 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: 0.0000 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 = 0.5068 r_free = 0.5068 target = 0.225632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.204916 restraints weight = 13391.772| |-----------------------------------------------------------------------------| r_work (start): 0.4844 rms_B_bonded: 1.89 r_work: 0.4699 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5681 moved from start: 0.3175 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= 0.189 Angle : 0.785 11.031 10767 Z= 0.430 Chirality : 0.053 0.345 1177 Planarity : 0.007 0.063 999 Dihedral : 30.426 178.423 1964 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.83 % Favored : 90.21 % Rotamer: Outliers : 7.32 % Allowed : 16.96 % 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: -1.81 (0.34), residues: 623 helix: 0.85 (0.38), residues: 196 sheet: -2.26 (0.55), residues: 70 loop : -2.28 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 594 TYR 0.013 0.002 TYR B 518 PHE 0.019 0.002 PHE A 562 TRP 0.010 0.001 TRP A 503 HIS 0.002 0.001 HIS C 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 ( 7581) covalent geometry : angle 0.78494 / 0.43 (10767) hydrogen bonds : bond 0.07441 / 5.47 ( 289) hydrogen bonds : angle 5.29958 / 3.73 ( 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 133 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5392 (OUTLIER) cc_final: 0.4712 (m170) REVERT: B 556 GLU cc_start: 0.3761 (OUTLIER) cc_final: 0.3080 (pm20) REVERT: B 558 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.7056 (pp) REVERT: B 596 THR cc_start: 0.5351 (t) cc_final: 0.5051 (p) REVERT: B 610 PHE cc_start: 0.6957 (t80) cc_final: 0.6048 (p90) REVERT: C 565 PHE cc_start: 0.5140 (m-10) cc_final: 0.4478 (m-80) outliers start: 38 outliers final: 24 residues processed: 125 average time/residue: 0.0811 time to fit residues: 13.9766 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 : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG 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 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 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 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: 0.8980 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.224847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.206382 restraints weight = 13490.921| |-----------------------------------------------------------------------------| r_work (start): 0.4855 rms_B_bonded: 1.74 r_work: 0.4715 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5658 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7581 Z= 0.178 Angle : 0.778 11.162 10767 Z= 0.425 Chirality : 0.053 0.326 1177 Planarity : 0.007 0.058 999 Dihedral : 30.389 178.922 1960 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.96 % Allowed : 7.87 % Favored : 91.17 % Rotamer: Outliers : 7.51 % Allowed : 16.96 % Favored : 75.53 % 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: -1.90 (0.34), residues: 623 helix: 0.88 (0.38), residues: 192 sheet: -2.42 (0.54), residues: 71 loop : -2.35 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 469 TYR 0.012 0.002 TYR B 518 PHE 0.018 0.002 PHE D 562 TRP 0.015 0.002 TRP A 503 HIS 0.002 0.001 HIS A 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 ( 7581) covalent geometry : angle 0.77844 / 0.42 (10767) hydrogen bonds : bond 0.07067 / 5.19 ( 289) hydrogen bonds : angle 5.23993 / 3.71 ( 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 139 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5710 (OUTLIER) cc_final: 0.4977 (m170) REVERT: B 543 MET cc_start: 0.1450 (OUTLIER) cc_final: 0.0973 (ttm) REVERT: B 556 GLU cc_start: 0.3753 (OUTLIER) cc_final: 0.3126 (pm20) REVERT: B 558 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7053 (pp) REVERT: B 596 THR cc_start: 0.5021 (t) cc_final: 0.4663 (p) REVERT: B 610 PHE cc_start: 0.7069 (t80) cc_final: 0.6188 (p90) REVERT: C 543 MET cc_start: 0.2061 (ttm) cc_final: 0.1436 (tmm) REVERT: C 565 PHE cc_start: 0.5138 (m-10) cc_final: 0.4580 (m-80) outliers start: 39 outliers final: 27 residues processed: 128 average time/residue: 0.0757 time to fit residues: 13.5533 Evaluate side-chains 123 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 468 HIS 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 475 ASN 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 C residue 591 CYS Chi-restraints excluded: chain D residue 468 HIS 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 590 THR Chi-restraints excluded: chain D residue 593 ILE 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: 3.9990 chunk 47 optimal weight: 0.1980 chunk 65 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.0570 chunk 38 optimal weight: 0.6980 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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** ** D 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 = 0.5072 r_free = 0.5072 target = 0.226718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.208697 restraints weight = 13476.429| |-----------------------------------------------------------------------------| r_work (start): 0.4879 rms_B_bonded: 1.74 r_work: 0.4743 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5586 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7581 Z= 0.160 Angle : 0.742 11.113 10767 Z= 0.407 Chirality : 0.053 0.328 1177 Planarity : 0.007 0.066 999 Dihedral : 30.386 179.962 1960 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.15 % Favored : 90.05 % Rotamer: Outliers : 6.36 % Allowed : 18.50 % 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: -1.79 (0.34), residues: 623 helix: 1.13 (0.38), residues: 193 sheet: -2.53 (0.52), residues: 74 loop : -2.34 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.012 0.002 TYR C 518 PHE 0.036 0.002 PHE D 610 TRP 0.009 0.001 TRP A 503 HIS 0.008 0.001 HIS C 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 ( 7581) covalent geometry : angle 0.74237 / 0.41 (10767) hydrogen bonds : bond 0.06550 / 4.82 ( 289) hydrogen bonds : angle 4.98306 / 3.50 ( 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 129 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5610 (OUTLIER) cc_final: 0.4925 (m170) REVERT: B 543 MET cc_start: 0.1404 (OUTLIER) cc_final: 0.0905 (ttm) REVERT: B 556 GLU cc_start: 0.3725 (OUTLIER) cc_final: 0.3102 (pm20) REVERT: B 558 ILE cc_start: 0.7349 (OUTLIER) cc_final: 0.7063 (pp) REVERT: B 596 THR cc_start: 0.5164 (t) cc_final: 0.4677 (p) REVERT: B 610 PHE cc_start: 0.7017 (t80) cc_final: 0.6173 (p90) REVERT: C 543 MET cc_start: 0.2188 (ttm) cc_final: 0.1509 (tmm) REVERT: C 565 PHE cc_start: 0.5057 (m-10) cc_final: 0.4605 (m-80) REVERT: C 591 CYS cc_start: 0.5672 (OUTLIER) cc_final: 0.4124 (p) REVERT: D 538 ARG cc_start: 0.6819 (mtt180) cc_final: 0.6537 (mtp180) REVERT: D 555 ARG cc_start: 0.3801 (mmt180) cc_final: 0.3101 (mmt-90) outliers start: 33 outliers final: 21 residues processed: 120 average time/residue: 0.0806 time to fit residues: 13.2350 Evaluate side-chains 117 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG 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 A residue 602 ASP 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 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 583 VAL Chi-restraints excluded: chain C residue 591 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.5038 r_free = 0.5038 target = 0.222960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.205163 restraints weight = 13395.456| |-----------------------------------------------------------------------------| r_work (start): 0.4842 rms_B_bonded: 1.62 r_work: 0.4705 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7581 Z= 0.191 Angle : 0.780 11.628 10767 Z= 0.425 Chirality : 0.054 0.325 1177 Planarity : 0.008 0.062 999 Dihedral : 30.353 174.769 1957 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.79 % Favored : 89.41 % Rotamer: Outliers : 6.74 % Allowed : 19.46 % 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: -1.88 (0.34), residues: 623 helix: 0.84 (0.38), residues: 191 sheet: -2.21 (0.56), residues: 68 loop : -2.33 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 555 TYR 0.021 0.003 TYR A 518 PHE 0.022 0.003 PHE A 562 TRP 0.016 0.002 TRP A 503 HIS 0.005 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 ( 7581) covalent geometry : angle 0.77961 / 0.42 (10767) hydrogen bonds : bond 0.07274 / 5.35 ( 289) hydrogen bonds : angle 5.13525 / 3.62 ( 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 129 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5694 (OUTLIER) cc_final: 0.4922 (m170) REVERT: B 543 MET cc_start: 0.1550 (OUTLIER) cc_final: 0.1211 (ttm) REVERT: B 556 GLU cc_start: 0.3920 (OUTLIER) cc_final: 0.3362 (pm20) REVERT: B 558 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6950 (pp) REVERT: B 596 THR cc_start: 0.5052 (t) cc_final: 0.4721 (p) REVERT: B 610 PHE cc_start: 0.6976 (t80) cc_final: 0.6175 (p90) REVERT: C 543 MET cc_start: 0.2039 (ttm) cc_final: 0.1310 (tmm) REVERT: C 565 PHE cc_start: 0.5135 (m-80) cc_final: 0.4328 (m-80) REVERT: C 591 CYS cc_start: 0.5690 (OUTLIER) cc_final: 0.4226 (p) REVERT: D 550 GLN cc_start: 0.2699 (OUTLIER) cc_final: 0.1990 (mt0) REVERT: D 584 MET cc_start: 0.6311 (tmt) cc_final: 0.6032 (tmt) outliers start: 35 outliers final: 22 residues processed: 119 average time/residue: 0.0889 time to fit residues: 14.2837 Evaluate side-chains 119 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG 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 475 ASN 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 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 550 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 43 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** D 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 = 0.5058 r_free = 0.5058 target = 0.224910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.207413 restraints weight = 13417.257| |-----------------------------------------------------------------------------| r_work (start): 0.4865 rms_B_bonded: 1.63 r_work: 0.4731 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5641 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7581 Z= 0.162 Angle : 0.741 11.173 10767 Z= 0.405 Chirality : 0.051 0.316 1177 Planarity : 0.008 0.071 999 Dihedral : 30.423 177.984 1957 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.51 % Favored : 90.69 % Rotamer: Outliers : 4.62 % Allowed : 22.35 % Favored : 73.03 % 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: -1.91 (0.34), residues: 623 helix: 0.97 (0.38), residues: 194 sheet: -2.30 (0.55), residues: 72 loop : -2.47 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 469 TYR 0.014 0.002 TYR A 518 PHE 0.016 0.002 PHE C 562 TRP 0.012 0.001 TRP A 503 HIS 0.004 0.001 HIS C 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 7581) covalent geometry : angle 0.74124 / 0.40 (10767) hydrogen bonds : bond 0.06429 / 4.73 ( 289) hydrogen bonds : angle 4.97392 / 3.50 ( 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 115 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5405 (OUTLIER) cc_final: 0.4658 (m170) REVERT: B 543 MET cc_start: 0.1360 (OUTLIER) cc_final: 0.1069 (ttm) REVERT: B 556 GLU cc_start: 0.3825 (OUTLIER) cc_final: 0.3296 (pm20) REVERT: B 558 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6977 (pp) REVERT: B 596 THR cc_start: 0.5178 (t) cc_final: 0.4689 (m) REVERT: B 610 PHE cc_start: 0.6912 (t80) cc_final: 0.6139 (p90) REVERT: C 543 MET cc_start: 0.2056 (ttm) cc_final: 0.1840 (tmm) REVERT: C 565 PHE cc_start: 0.5153 (m-80) cc_final: 0.4611 (m-80) REVERT: C 591 CYS cc_start: 0.5462 (OUTLIER) cc_final: 0.4096 (p) REVERT: D 538 ARG cc_start: 0.6779 (mtt180) cc_final: 0.6519 (mtp180) REVERT: D 584 MET cc_start: 0.6203 (tmt) cc_final: 0.5943 (tmt) outliers start: 24 outliers final: 17 residues processed: 110 average time/residue: 0.0911 time to fit residues: 13.5371 Evaluate side-chains 108 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 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 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 528 ILE Chi-restraints excluded: chain D residue 533 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 53 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 14 optimal weight: 0.0020 chunk 56 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 overall best weight: 0.4388 ------------------------------------------------------------------------------- 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 = 0.5071 r_free = 0.5071 target = 0.226303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.209096 restraints weight = 13257.180| |-----------------------------------------------------------------------------| r_work (start): 0.4882 rms_B_bonded: 1.61 r_work: 0.4750 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5597 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7581 Z= 0.156 Angle : 0.730 10.943 10767 Z= 0.398 Chirality : 0.051 0.315 1177 Planarity : 0.007 0.068 999 Dihedral : 30.329 177.558 1953 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.31 % Favored : 89.89 % Rotamer: Outliers : 4.43 % Allowed : 22.54 % Favored : 73.03 % 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: -1.82 (0.34), residues: 623 helix: 1.11 (0.38), residues: 194 sheet: -2.26 (0.55), residues: 73 loop : -2.44 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 469 TYR 0.018 0.002 TYR A 518 PHE 0.017 0.002 PHE C 562 TRP 0.013 0.001 TRP D 609 HIS 0.003 0.001 HIS A 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 ( 7581) covalent geometry : angle 0.73025 / 0.40 (10767) hydrogen bonds : bond 0.06351 / 4.66 ( 289) hydrogen bonds : angle 4.83672 / 3.40 ( 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 113 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5302 (OUTLIER) cc_final: 0.4559 (m170) REVERT: B 543 MET cc_start: 0.1176 (OUTLIER) cc_final: 0.0958 (ttm) REVERT: B 556 GLU cc_start: 0.3826 (OUTLIER) cc_final: 0.3404 (pm20) REVERT: B 558 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.7010 (pp) REVERT: B 596 THR cc_start: 0.4851 (t) cc_final: 0.4372 (p) REVERT: B 610 PHE cc_start: 0.6873 (t80) cc_final: 0.6101 (p90) REVERT: C 565 PHE cc_start: 0.4965 (m-80) cc_final: 0.4504 (m-80) REVERT: C 591 CYS cc_start: 0.5511 (OUTLIER) cc_final: 0.4115 (p) REVERT: D 538 ARG cc_start: 0.6712 (mtt180) cc_final: 0.6477 (mtp180) REVERT: D 584 MET cc_start: 0.6308 (tmt) cc_final: 0.6090 (tmt) outliers start: 23 outliers final: 16 residues processed: 108 average time/residue: 0.0830 time to fit residues: 12.3653 Evaluate side-chains 109 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 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 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 591 CYS Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU 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: 10.0000 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 567 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.224823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.207186 restraints weight = 13273.201| |-----------------------------------------------------------------------------| r_work (start): 0.4861 rms_B_bonded: 1.62 r_work: 0.4727 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5661 moved from start: 0.4585 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= 0.170 Angle : 0.743 10.908 10767 Z= 0.403 Chirality : 0.051 0.314 1177 Planarity : 0.007 0.067 999 Dihedral : 30.379 175.882 1953 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.31 % Favored : 89.89 % Rotamer: Outliers : 4.82 % Allowed : 21.97 % Favored : 73.22 % 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: -1.93 (0.34), residues: 623 helix: 0.94 (0.38), residues: 195 sheet: -2.41 (0.54), residues: 75 loop : -2.45 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 469 TYR 0.013 0.002 TYR A 518 PHE 0.018 0.002 PHE D 562 TRP 0.012 0.002 TRP D 609 HIS 0.003 0.001 HIS A 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 7581) covalent geometry : angle 0.74275 / 0.40 (10767) hydrogen bonds : bond 0.06387 / 4.67 ( 289) hydrogen bonds : angle 4.93228 / 3.46 ( 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 108 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5706 (OUTLIER) cc_final: 0.4835 (m170) REVERT: B 543 MET cc_start: 0.1207 (OUTLIER) cc_final: 0.0963 (ttm) REVERT: B 556 GLU cc_start: 0.3931 (OUTLIER) cc_final: 0.3501 (pm20) REVERT: B 558 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.7006 (pp) REVERT: B 596 THR cc_start: 0.5061 (t) cc_final: 0.4539 (p) REVERT: B 610 PHE cc_start: 0.6889 (t80) cc_final: 0.6127 (p90) REVERT: C 565 PHE cc_start: 0.5152 (m-80) cc_final: 0.4585 (m-80) REVERT: C 591 CYS cc_start: 0.5464 (OUTLIER) cc_final: 0.4041 (p) REVERT: D 538 ARG cc_start: 0.6713 (mtt180) cc_final: 0.6487 (mmm-85) outliers start: 25 outliers final: 20 residues processed: 101 average time/residue: 0.0802 time to fit residues: 11.1799 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 : 0.250 ------------------------------------------------------------------------------- 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 526 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 598 CYS 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 543 MET Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 567 GLN 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 502 THR Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 533 LEU 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 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.5058 r_free = 0.5058 target = 0.224739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.207062 restraints weight = 13317.881| |-----------------------------------------------------------------------------| r_work (start): 0.4861 rms_B_bonded: 1.62 r_work: 0.4727 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5661 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 7581 Z= 0.211 Angle : 1.046 59.199 10767 Z= 0.598 Chirality : 0.051 0.316 1177 Planarity : 0.007 0.076 999 Dihedral : 30.380 175.956 1953 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.63 % Favored : 89.57 % Rotamer: Outliers : 5.01 % Allowed : 21.97 % Favored : 73.03 % 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: -1.93 (0.34), residues: 623 helix: 0.94 (0.38), residues: 195 sheet: -2.42 (0.54), residues: 75 loop : -2.45 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 469 TYR 0.012 0.002 TYR A 518 PHE 0.018 0.002 PHE D 562 TRP 0.012 0.001 TRP D 609 HIS 0.003 0.001 HIS A 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.21 ( 7581) covalent geometry : angle 1.04627 / 0.60 (10767) hydrogen bonds : bond 0.06376 / 4.67 ( 289) hydrogen bonds : angle 4.93013 / 3.46 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1733.34 seconds wall clock time: 30 minutes 26.43 seconds (1826.43 seconds total)