Starting phenix.real_space_refine on Wed Mar 4 03:57:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlf_27500/03_2026/8dlf_27500.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlf_27500/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dlf_27500/03_2026/8dlf_27500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlf_27500/03_2026/8dlf_27500.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dlf_27500/03_2026/8dlf_27500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlf_27500/03_2026/8dlf_27500.map" } 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-5986/lib/python3.9/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: 1.53, per 1000 atoms: 0.21 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 193.1 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: 1.12 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: 1.15 Time building geometry restraints manager: 0.85 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 1.50e-02 4.44e+03 1.07e+01 bond pdb=" P DA E 54 " pdb=" OP1 DA E 54 " ideal model delta sigma weight residual 1.480 1.541 -0.061 2.00e-02 2.50e+03 9.31e+00 bond pdb=" N GLY A 463 " pdb=" CA GLY A 463 " ideal model delta sigma weight residual 1.447 1.474 -0.027 9.90e-03 1.02e+04 7.18e+00 bond pdb=" O3' DT F 3 " pdb=" P DA F 4 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.50e-02 4.44e+03 6.93e+00 bond pdb=" N TRP A 464 " pdb=" CA TRP A 464 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.22e-02 6.72e+03 6.08e+00 ... (remaining 7576 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 9608 1.66 - 3.31: 755 3.31 - 4.97: 178 4.97 - 6.62: 205 6.62 - 8.28: 21 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 113.50 121.78 -8.28 1.50e+00 4.44e-01 3.05e+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=" 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 angle pdb=" C3' DT E 30 " pdb=" O3' DT E 30 " pdb=" P DA E 31 " ideal model delta sigma weight residual 120.20 113.70 6.50 1.50e+00 4.44e-01 1.88e+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 - 0.128: 1054 0.128 - 0.256: 16 0.256 - 0.384: 7 0.384 - 0.512: 65 0.512 - 0.641: 35 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 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+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 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+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 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.74e+00 ... (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: 0.870 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.610 Find NCS groups from input model: 0.110 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4623 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= 0.413 Angle : 1.289 8.280 10767 Z= 0.656 Chirality : 0.156 0.641 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 covalent geometry : bond 0.00863 ( 7581) covalent geometry : angle 1.28878 (10767) hydrogen bonds : bond 0.20520 ( 289) hydrogen bonds : angle 11.08637 ( 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 : 0.207 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: 0.1067 time to fit residues: 24.2889 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 : 0.221 ------------------------------------------------------------------------------- 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: 0.1980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN D 480 ASN ** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.225792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.205205 restraints weight = 12885.528| |-----------------------------------------------------------------------------| r_work (start): 0.4842 rms_B_bonded: 1.88 r_work: 0.4698 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5584 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7581 Z= 0.206 Angle : 0.778 12.604 10767 Z= 0.424 Chirality : 0.047 0.216 1177 Planarity : 0.007 0.058 999 Dihedral : 30.326 176.637 1975 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 24.76 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.63 % Favored : 89.41 % Rotamer: Outliers : 7.13 % Allowed : 14.45 % Favored : 78.42 % 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: 197 sheet: -2.13 (0.53), residues: 82 loop : -2.39 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 491 TYR 0.011 0.002 TYR B 518 PHE 0.026 0.002 PHE D 610 TRP 0.011 0.002 TRP A 503 HIS 0.003 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 7581) covalent geometry : angle 0.77783 (10767) hydrogen bonds : bond 0.07616 ( 289) hydrogen bonds : angle 5.39808 ( 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 143 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5102 (OUTLIER) cc_final: 0.4352 (m170) REVERT: A 602 ASP cc_start: 0.3058 (t0) cc_final: 0.2801 (p0) REVERT: B 556 GLU cc_start: 0.3444 (OUTLIER) cc_final: 0.2707 (pm20) REVERT: B 558 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6949 (pp) REVERT: C 497 THR cc_start: 0.6407 (OUTLIER) cc_final: 0.5937 (t) REVERT: C 562 PHE cc_start: 0.5424 (p90) cc_final: 0.5201 (p90) REVERT: C 565 PHE cc_start: 0.5139 (m-10) cc_final: 0.4733 (m-80) REVERT: D 510 TYR cc_start: 0.7053 (p90) cc_final: 0.6776 (p90) REVERT: D 565 PHE cc_start: 0.1814 (OUTLIER) cc_final: 0.1311 (m-80) outliers start: 37 outliers final: 17 residues processed: 135 average time/residue: 0.0971 time to fit residues: 17.3290 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 : 0.192 ------------------------------------------------------------------------------- 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 586 LYS Chi-restraints excluded: chain B residue 468 HIS Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 ILE 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 583 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 534 THR 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 596 THR 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: 0.6980 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN ** D 567 GLN ** 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 = 0.5045 r_free = 0.5045 target = 0.223642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.204794 restraints weight = 13239.067| |-----------------------------------------------------------------------------| r_work (start): 0.4846 rms_B_bonded: 1.76 r_work: 0.4703 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5654 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7581 Z= 0.204 Angle : 0.762 12.845 10767 Z= 0.412 Chirality : 0.046 0.207 1177 Planarity : 0.007 0.060 999 Dihedral : 30.168 172.052 1957 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.79 % Favored : 89.25 % Rotamer: Outliers : 7.51 % Allowed : 15.41 % Favored : 77.07 % 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: -1.85 (0.34), residues: 623 helix: 0.44 (0.37), residues: 201 sheet: -1.81 (0.60), residues: 69 loop : -2.20 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 538 TYR 0.012 0.002 TYR B 518 PHE 0.034 0.002 PHE D 610 TRP 0.008 0.001 TRP C 464 HIS 0.003 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 7581) covalent geometry : angle 0.76230 (10767) hydrogen bonds : bond 0.06736 ( 289) hydrogen bonds : angle 5.27643 ( 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 146 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5649 (OUTLIER) cc_final: 0.5010 (m170) REVERT: A 543 MET cc_start: 0.3908 (mmp) cc_final: 0.3665 (mmp) REVERT: A 602 ASP cc_start: 0.3215 (t0) cc_final: 0.2718 (p0) REVERT: B 475 ASN cc_start: 0.3859 (OUTLIER) cc_final: 0.3533 (t0) REVERT: B 558 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.7002 (pp) REVERT: C 497 THR cc_start: 0.6423 (OUTLIER) cc_final: 0.5992 (t) REVERT: C 543 MET cc_start: 0.1985 (OUTLIER) cc_final: 0.1779 (tmm) REVERT: C 565 PHE cc_start: 0.4970 (m-10) cc_final: 0.4357 (m-80) outliers start: 39 outliers final: 21 residues processed: 136 average time/residue: 0.0909 time to fit residues: 16.2606 Evaluate side-chains 115 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 475 ASN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 543 MET 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 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 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: 0.0570 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** B 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.226418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.207985 restraints weight = 13481.534| |-----------------------------------------------------------------------------| r_work (start): 0.4874 rms_B_bonded: 1.78 r_work: 0.4732 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5552 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7581 Z= 0.169 Angle : 0.723 10.681 10767 Z= 0.390 Chirality : 0.043 0.198 1177 Planarity : 0.007 0.058 999 Dihedral : 30.100 174.222 1957 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.96 % Allowed : 7.54 % Favored : 91.49 % Rotamer: Outliers : 6.17 % Allowed : 18.30 % 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: -1.83 (0.34), residues: 623 helix: 0.78 (0.38), residues: 195 sheet: -2.26 (0.57), residues: 73 loop : -2.25 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 532 TYR 0.010 0.002 TYR A 510 PHE 0.018 0.002 PHE B 610 TRP 0.006 0.001 TRP D 609 HIS 0.003 0.000 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 7581) covalent geometry : angle 0.72321 (10767) hydrogen bonds : bond 0.05833 ( 289) hydrogen bonds : angle 4.92630 ( 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 129 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 LYS cc_start: 0.4853 (mttt) cc_final: 0.4597 (mtmt) REVERT: A 468 HIS cc_start: 0.5830 (OUTLIER) cc_final: 0.5007 (m170) REVERT: A 543 MET cc_start: 0.3847 (mmp) cc_final: 0.3544 (mmp) REVERT: A 602 ASP cc_start: 0.3242 (t0) cc_final: 0.2665 (p0) REVERT: B 556 GLU cc_start: 0.3761 (OUTLIER) cc_final: 0.3163 (pm20) REVERT: B 558 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7051 (pp) REVERT: C 565 PHE cc_start: 0.4853 (m-10) cc_final: 0.4503 (m-80) outliers start: 32 outliers final: 24 residues processed: 123 average time/residue: 0.0943 time to fit residues: 15.3683 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 : 0.214 ------------------------------------------------------------------------------- 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 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 586 LYS 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 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 D residue 477 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN ** D 567 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 = 0.5009 r_free = 0.5009 target = 0.219834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.201556 restraints weight = 13248.788| |-----------------------------------------------------------------------------| r_work (start): 0.4805 rms_B_bonded: 1.68 r_work: 0.4659 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5780 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7581 Z= 0.246 Angle : 0.801 13.537 10767 Z= 0.428 Chirality : 0.048 0.210 1177 Planarity : 0.008 0.062 999 Dihedral : 30.175 173.625 1955 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.75 % Favored : 88.28 % Rotamer: Outliers : 7.90 % Allowed : 18.11 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.33), residues: 623 helix: 0.26 (0.37), residues: 201 sheet: -2.16 (0.58), residues: 64 loop : -2.36 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 555 TYR 0.016 0.003 TYR C 510 PHE 0.028 0.002 PHE D 610 TRP 0.013 0.002 TRP A 609 HIS 0.005 0.001 HIS C 468 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 7581) covalent geometry : angle 0.80071 (10767) hydrogen bonds : bond 0.07234 ( 289) hydrogen bonds : angle 5.35754 ( 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 130 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.6341 (OUTLIER) cc_final: 0.5541 (m170) REVERT: A 602 ASP cc_start: 0.3157 (t0) cc_final: 0.2596 (p0) REVERT: B 556 GLU cc_start: 0.4203 (OUTLIER) cc_final: 0.3757 (pm20) REVERT: B 558 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6901 (pp) REVERT: C 565 PHE cc_start: 0.5164 (m-10) cc_final: 0.4594 (m-80) REVERT: C 591 CYS cc_start: 0.5596 (OUTLIER) cc_final: 0.4307 (p) outliers start: 41 outliers final: 24 residues processed: 120 average time/residue: 0.0924 time to fit residues: 14.7572 Evaluate side-chains 106 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 A residue 598 CYS 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 583 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 509 VAL 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 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: 1.9990 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.225166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.207690 restraints weight = 13268.163| |-----------------------------------------------------------------------------| r_work (start): 0.4867 rms_B_bonded: 1.66 r_work: 0.4734 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5599 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7581 Z= 0.171 Angle : 0.712 11.189 10767 Z= 0.384 Chirality : 0.044 0.230 1177 Planarity : 0.007 0.062 999 Dihedral : 30.136 176.514 1953 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.19 % Favored : 90.85 % Rotamer: Outliers : 5.39 % Allowed : 19.85 % Favored : 74.76 % 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: 0.53 (0.38), residues: 203 sheet: -2.51 (0.54), residues: 74 loop : -2.25 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 555 TYR 0.011 0.002 TYR B 510 PHE 0.019 0.002 PHE D 562 TRP 0.011 0.001 TRP D 609 HIS 0.002 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 7581) covalent geometry : angle 0.71183 (10767) hydrogen bonds : bond 0.05667 ( 289) hydrogen bonds : angle 4.87795 ( 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 119 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 HIS cc_start: 0.5921 (OUTLIER) cc_final: 0.5200 (m170) REVERT: A 602 ASP cc_start: 0.3297 (t0) cc_final: 0.2602 (p0) REVERT: B 556 GLU cc_start: 0.3508 (OUTLIER) cc_final: 0.3169 (pm20) REVERT: B 558 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6937 (pp) REVERT: C 565 PHE cc_start: 0.4915 (m-10) cc_final: 0.4629 (m-80) REVERT: C 591 CYS cc_start: 0.5229 (OUTLIER) cc_final: 0.3950 (p) outliers start: 28 outliers final: 21 residues processed: 110 average time/residue: 0.0923 time to fit residues: 13.5503 Evaluate side-chains 107 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 A residue 586 LYS Chi-restraints excluded: chain A residue 598 CYS Chi-restraints excluded: chain B residue 468 HIS 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 591 CYS Chi-restraints excluded: chain D residue 509 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 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: 10.0000 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 0.0370 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5053 r_free = 0.5053 target = 0.224655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.207473 restraints weight = 13290.869| |-----------------------------------------------------------------------------| r_work (start): 0.4863 rms_B_bonded: 1.59 r_work: 0.4732 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7581 Z= 0.175 Angle : 0.709 10.803 10767 Z= 0.383 Chirality : 0.044 0.245 1177 Planarity : 0.007 0.064 999 Dihedral : 29.967 176.841 1953 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.47 % Favored : 89.57 % Rotamer: Outliers : 5.78 % Allowed : 20.04 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.34), residues: 623 helix: 0.59 (0.38), residues: 204 sheet: -2.38 (0.55), residues: 72 loop : -2.32 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 555 TYR 0.021 0.003 TYR D 510 PHE 0.018 0.002 PHE D 562 TRP 0.009 0.001 TRP D 609 HIS 0.004 0.001 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 7581) covalent geometry : angle 0.70950 (10767) hydrogen bonds : bond 0.05654 ( 289) hydrogen bonds : angle 4.84211 ( 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 114 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 LEU cc_start: 0.4512 (OUTLIER) cc_final: 0.4236 (mt) REVERT: A 602 ASP cc_start: 0.3514 (t0) cc_final: 0.2693 (p0) REVERT: A 613 MET cc_start: 0.5540 (pmm) cc_final: 0.5294 (ttp) REVERT: B 556 GLU cc_start: 0.3609 (OUTLIER) cc_final: 0.3174 (pm20) REVERT: B 558 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.7023 (pp) REVERT: C 565 PHE cc_start: 0.4880 (m-10) cc_final: 0.4520 (m-80) REVERT: C 591 CYS cc_start: 0.5321 (OUTLIER) cc_final: 0.4017 (p) outliers start: 30 outliers final: 23 residues processed: 106 average time/residue: 0.0908 time to fit residues: 12.9349 Evaluate side-chains 110 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 586 LYS Chi-restraints excluded: chain A residue 598 CYS 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 502 THR Chi-restraints excluded: chain D residue 509 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 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: 2.9990 chunk 28 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 19 optimal weight: 0.0060 chunk 34 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS ** 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 = 0.5069 r_free = 0.5069 target = 0.226244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.208798 restraints weight = 13361.778| |-----------------------------------------------------------------------------| r_work (start): 0.4879 rms_B_bonded: 1.63 r_work: 0.4747 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5567 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7581 Z= 0.167 Angle : 0.698 9.771 10767 Z= 0.378 Chirality : 0.043 0.246 1177 Planarity : 0.007 0.063 999 Dihedral : 29.831 178.297 1951 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.35 % Favored : 90.69 % Rotamer: Outliers : 4.62 % Allowed : 21.00 % 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: -1.89 (0.34), residues: 623 helix: 0.80 (0.38), residues: 199 sheet: -2.49 (0.54), residues: 73 loop : -2.31 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 555 TYR 0.020 0.002 TYR D 510 PHE 0.017 0.002 PHE B 610 TRP 0.013 0.001 TRP D 609 HIS 0.002 0.000 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 7581) covalent geometry : angle 0.69798 (10767) hydrogen bonds : bond 0.05342 ( 289) hydrogen bonds : angle 4.67373 ( 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 : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 LEU cc_start: 0.4154 (OUTLIER) cc_final: 0.3880 (mt) REVERT: A 602 ASP cc_start: 0.3485 (t0) cc_final: 0.2693 (p0) REVERT: B 556 GLU cc_start: 0.3490 (OUTLIER) cc_final: 0.3154 (pm20) REVERT: C 565 PHE cc_start: 0.4717 (m-10) cc_final: 0.3600 (m-80) REVERT: C 591 CYS cc_start: 0.5335 (OUTLIER) cc_final: 0.4059 (p) outliers start: 24 outliers final: 18 residues processed: 109 average time/residue: 0.0964 time to fit residues: 13.9284 Evaluate side-chains 105 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ILE 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 A residue 598 CYS 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 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 509 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 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: 0.7980 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.224785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.207590 restraints weight = 13201.564| |-----------------------------------------------------------------------------| r_work (start): 0.4865 rms_B_bonded: 1.58 r_work: 0.4735 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5606 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7581 Z= 0.177 Angle : 0.717 10.881 10767 Z= 0.387 Chirality : 0.044 0.244 1177 Planarity : 0.007 0.063 999 Dihedral : 29.839 178.201 1951 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.15 % Favored : 89.89 % Rotamer: Outliers : 5.01 % Allowed : 20.23 % Favored : 74.76 % 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: 0.64 (0.38), residues: 205 sheet: -2.43 (0.53), residues: 72 loop : -2.25 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 532 TYR 0.019 0.003 TYR D 510 PHE 0.038 0.002 PHE D 610 TRP 0.014 0.001 TRP D 609 HIS 0.001 0.001 HIS C 569 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 7581) covalent geometry : angle 0.71663 (10767) hydrogen bonds : bond 0.05487 ( 289) hydrogen bonds : angle 4.75559 ( 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 111 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 ASP cc_start: 0.3523 (t0) cc_final: 0.2716 (p0) REVERT: B 556 GLU cc_start: 0.3536 (OUTLIER) cc_final: 0.3242 (pm20) REVERT: C 565 PHE cc_start: 0.4908 (m-10) cc_final: 0.3716 (m-80) outliers start: 26 outliers final: 21 residues processed: 103 average time/residue: 0.0915 time to fit residues: 12.6033 Evaluate side-chains 107 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain A residue 598 CYS 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 C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 509 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 66 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 GLN ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 ASN ** D 567 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 = 0.5048 r_free = 0.5048 target = 0.223657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.206297 restraints weight = 13243.472| |-----------------------------------------------------------------------------| r_work (start): 0.4852 rms_B_bonded: 1.59 r_work: 0.4716 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 moved from start: 0.5678 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= 0.190 Angle : 0.736 10.738 10767 Z= 0.397 Chirality : 0.045 0.262 1177 Planarity : 0.007 0.065 999 Dihedral : 29.848 178.232 1949 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.47 % Favored : 89.73 % Rotamer: Outliers : 4.62 % Allowed : 20.62 % Favored : 74.76 % 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: -1.96 (0.34), residues: 623 helix: 0.67 (0.38), residues: 197 sheet: -2.41 (0.53), residues: 72 loop : -2.32 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 532 TYR 0.018 0.003 TYR D 510 PHE 0.021 0.002 PHE B 610 TRP 0.015 0.001 TRP D 609 HIS 0.002 0.001 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 7581) covalent geometry : angle 0.73608 (10767) hydrogen bonds : bond 0.05672 ( 289) hydrogen bonds : angle 4.84163 ( 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 107 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 ASP cc_start: 0.3403 (t0) cc_final: 0.2634 (p0) REVERT: B 556 GLU cc_start: 0.3505 (OUTLIER) cc_final: 0.3209 (pm20) REVERT: C 565 PHE cc_start: 0.5011 (m-10) cc_final: 0.4458 (m-80) outliers start: 24 outliers final: 23 residues processed: 101 average time/residue: 0.0926 time to fit residues: 12.4661 Evaluate side-chains 107 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 516 SER 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 567 GLN Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 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 54 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5056 r_free = 0.5056 target = 0.224494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.207197 restraints weight = 13315.460| |-----------------------------------------------------------------------------| r_work (start): 0.4858 rms_B_bonded: 1.59 r_work: 0.4719 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5640 moved from start: 0.5776 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= 0.180 Angle : 0.726 10.703 10767 Z= 0.393 Chirality : 0.044 0.249 1177 Planarity : 0.007 0.065 999 Dihedral : 29.840 178.731 1949 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.47 % Favored : 89.73 % Rotamer: Outliers : 4.24 % Allowed : 21.19 % Favored : 74.57 % 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: -1.96 (0.34), residues: 623 helix: 0.68 (0.38), residues: 198 sheet: -2.36 (0.54), residues: 72 loop : -2.35 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 532 TYR 0.019 0.002 TYR D 510 PHE 0.021 0.002 PHE B 565 TRP 0.014 0.001 TRP D 609 HIS 0.003 0.001 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7581) covalent geometry : angle 0.72620 (10767) hydrogen bonds : bond 0.05503 ( 289) hydrogen bonds : angle 4.82144 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1764.27 seconds wall clock time: 30 minutes 54.83 seconds (1854.83 seconds total)